diff --git a/DESCRIPTION b/DESCRIPTION
index 8408ef1..b7f573a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: scPred
 Type: Package
 Title: scPred - accurate supervised method for cell-type classification from single-cell RNA-seq data
-Version: 1.9.1
+Version: 1.9.2
 Author: c(person("Jose", "Alquicira-Hernandez", email = "j.alquicira@garvan.au", rol = "aut, cre", comment = c(ORCID = "0000-0002-9049-7780")))
 Maintainer: Jose Alquicira-Hernandez <j.alquicira@garvan.org.au>
 Description: Provides a series of functions to train a prediction model based on gene expression data to classify single cells.
@@ -24,6 +24,8 @@ Imports:
     pbapply,
     cli,
     crayon
+Suggests:
+    magrittr, mda
 Remotes:
     immunogenomics/harmony
 RoxygenNote: 7.1.1
diff --git a/docs/404.html b/docs/404.html
index 4189371..12a72fe 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -89,7 +89,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -112,7 +112,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -152,7 +152,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index e4bfe3b..799882f 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -89,7 +89,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
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 </li>
@@ -112,7 +112,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -173,7 +173,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 3cf39ff..d453f70 100644
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+++ b/docs/articles/index.html
@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -89,7 +89,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
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 </li>
@@ -112,7 +112,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -151,7 +151,7 @@ <h3>All vignettes</h3>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html
index 9c2a9b5..6244c5c 100644
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+++ b/docs/articles/introduction.html
@@ -37,7 +37,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
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       <ul class="nav navbar-nav">
 <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
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@@ -68,7 +68,7 @@
 <ul class="nav navbar-nav navbar-right">
 <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
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@@ -82,13 +82,13 @@
 
       
 
-      </header><script src="introduction_files/header-attrs-2.3/header-attrs.js"></script><script src="introduction_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
+      </header><script src="introduction_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Introduction to scPred</h1>
                         <h4 class="author">Jose Alquicira Hernandez</h4>
             
-            <h4 class="date">2020-09-14</h4>
+            <h4 class="date">2021-07-12</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/powellgenomicslab/scPred/blob/master/vignettes/introduction.Rmd"><code>vignettes/introduction.Rmd</code></a></small>
       <div class="hidden name"><code>introduction.Rmd</code></div>
@@ -109,13 +109,15 @@ <h1 class="hasAnchor">
 <a href="#application-of-scpred" class="anchor"></a>Application of <code>scPred</code>
 </h1>
 <p>First, we’ll load the <code>scPred</code> package and <code>Seurat</code>.</p>
-<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="st">"scPred"</span>)
-<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="st">"Seurat"</span>)
-<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="st">"magrittr"</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="st"><a href="https://github.com/powellgenomicslab/scPred">"scPred"</a></span><span class="op">)</span>
+<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="st"><a href="https://satijalab.org/seurat">"Seurat"</a></span><span class="op">)</span>
+<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="st"><a href="https://magrittr.tidyverse.org">"magrittr"</a></span><span class="op">)</span></code></pre></div>
 <p>We will work with Peripheral Mononuclear Blood Cells (PBMCs) from two different individuals. The libraries were processed using the Chromium system -10× Genomics- and sequenced with an Illumina NovaSeq 6000 platform. See <a href="https://academic.oup.com/nargab/article/2/2/lqaa034/5836690">Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing</a> for more details on the samples.</p>
 <p>For this tutorial, we’ll use the PBMCs from one individual to build cell classifiers for the populations of interest. Then, we’ll apply these models to an indepent dataset of PBMCs from another independent individual.</p>
-<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">reference</span> <span class="kw">&lt;-</span> <span class="kw pkg">scPred</span><span class="kw ns">::</span><span class="no"><a href="../reference/pbmc_1.html">pbmc_1</a></span>
-<span class="no">query</span> <span class="kw">&lt;-</span> <span class="kw pkg">scPred</span><span class="kw ns">::</span><span class="no"><a href="../reference/pbmc_2.html">pbmc_2</a></span></pre></body></html></div>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">reference</span> <span class="op">&lt;-</span> <span class="fu">scPred</span><span class="fu">::</span><span class="va"><a href="../reference/pbmc_1.html">pbmc_1</a></span>
+<span class="va">query</span> <span class="op">&lt;-</span> <span class="fu">scPred</span><span class="fu">::</span><span class="va"><a href="../reference/pbmc_2.html">pbmc_2</a></span></code></pre></div>
 <p><code>scPred</code> is now built to be incorporated withing the Seurat framework. Similar to clustering in <code>Seurat</code>, <code>scPred</code> uses the cell embeddings from a principal component analysis to make inferences about cell-type identity. However —unlike clustering—, <code>scPred</code> trains classifiers for each cell type of interest in a supervised manner by using the known cell identity from a reference dataset to guide the classification of cells in a different data set.</p>
 <p>The following code:</p>
 <ol style="list-style-type: decimal">
@@ -125,12 +127,13 @@ <h1 class="hasAnchor">
 <li>Runs a PCA</li>
 <li>Runs a UMAP using the top 30 most variable PCs</li>
 </ol>
-<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">reference</span> <span class="kw">&lt;-</span> <span class="no">reference</span> <span class="kw">%&gt;%</span>
-  <span class="fu"><a href="https://rdrr.io/pkg/Seurat/man/NormalizeData.html">NormalizeData</a></span>() <span class="kw">%&gt;%</span>
-  <span class="fu"><a href="https://rdrr.io/pkg/Seurat/man/FindVariableFeatures.html">FindVariableFeatures</a></span>() <span class="kw">%&gt;%</span>
-  <span class="fu"><a href="https://rdrr.io/pkg/Seurat/man/ScaleData.html">ScaleData</a></span>() <span class="kw">%&gt;%</span>
-  <span class="fu"><a href="https://rdrr.io/pkg/Seurat/man/RunPCA.html">RunPCA</a></span>() <span class="kw">%&gt;%</span>
-  <span class="fu"><a href="https://rdrr.io/pkg/Seurat/man/RunUMAP.html">RunUMAP</a></span>(<span class="kw">dims</span> <span class="kw">=</span> <span class="fl">1</span>:<span class="fl">30</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">reference</span> <span class="op">&lt;-</span> <span class="va">reference</span> <span class="op">%&gt;%</span> 
+  <span class="fu"><a href="https://satijalab.org/seurat/reference/NormalizeData.html">NormalizeData</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%&gt;%</span> 
+  <span class="fu"><a href="https://satijalab.org/seurat/reference/FindVariableFeatures.html">FindVariableFeatures</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%&gt;%</span> 
+  <span class="fu"><a href="https://satijalab.org/seurat/reference/ScaleData.html">ScaleData</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%&gt;%</span> 
+  <span class="fu"><a href="https://satijalab.org/seurat/reference/RunPCA.html">RunPCA</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%&gt;%</span> 
+  <span class="fu"><a href="https://satijalab.org/seurat/reference/RunUMAP.html">RunUMAP</a></span><span class="op">(</span>dims <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">30</span><span class="op">)</span></code></pre></div>
 <pre><code>## Centering and scaling data matrix</code></pre>
 <pre><code>## PC_ 1 
 ## Positive:  MALAT1, RPS12, RPL13, RPS18, RPS4X, LTB, IL32, IL7R, EEF1A1, RPL10 
@@ -170,25 +173,23 @@ <h1 class="hasAnchor">
 <pre><code>## Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
 ## To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
 ## This message will be shown once per session</code></pre>
-<pre><code>## 02:31:57 UMAP embedding parameters a = 0.9922 b = 1.112</code></pre>
-<pre><code>## 02:31:57 Read 3500 rows and found 30 numeric columns</code></pre>
-<pre><code>## 02:31:57 Using Annoy for neighbor search, n_neighbors = 30</code></pre>
-<pre><code>## 02:31:57 Building Annoy index with metric = cosine, n_trees = 50</code></pre>
+<pre><code>## 01:05:04 UMAP embedding parameters a = 0.9922 b = 1.112</code></pre>
+<pre><code>## 01:05:04 Read 3500 rows and found 30 numeric columns</code></pre>
+<pre><code>## 01:05:04 Using Annoy for neighbor search, n_neighbors = 30</code></pre>
+<pre><code>## 01:05:04 Building Annoy index with metric = cosine, n_trees = 50</code></pre>
 <pre><code>## 0%   10   20   30   40   50   60   70   80   90   100%</code></pre>
 <pre><code>## [----|----|----|----|----|----|----|----|----|----|</code></pre>
 <pre><code>## **************************************************|
-## 02:31:58 Writing NN index file to temp file /var/folders/6y/nzcvsw7j5dn1g0k8b13x086w0000gp/T//RtmpvL3gNk/fileb92e12fbc97c
-## 02:31:58 Searching Annoy index using 1 thread, search_k = 3000
-## 02:31:58 Annoy recall = 100%
-## 02:31:58 Commencing smooth kNN distance calibration using 1 thread
-## 02:31:59 Initializing from normalized Laplacian + noise
-## 02:31:59 Commencing optimization for 500 epochs, with 157998 positive edges
-## 02:32:04 Optimization finished</code></pre>
+## 01:05:05 Writing NN index file to temp file /var/folders/yj/yd72sc650wq90dvmfl2869jm0000gq/T//RtmpkVwOki/file2c637a4757d1
+## 01:05:05 Searching Annoy index using 1 thread, search_k = 3000
+## 01:05:06 Annoy recall = 100%
+## 01:05:06 Commencing smooth kNN distance calibration using 1 thread
+## 01:05:06 Initializing from normalized Laplacian + noise
+## 01:05:07 Commencing optimization for 500 epochs, with 158046 positive edges
+## 01:05:12 Optimization finished</code></pre>
 <p>The column <code>cell_type</code> contains the identity of each cell in the meta data slot. Let’s plot the UMAP and grouping the cells by cell type.</p>
-<div class="sourceCode" id="cb14"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/pkg/Seurat/man/DimPlot.html">DimPlot</a></span>(<span class="no">reference</span>, <span class="kw">group.by</span> <span class="kw">=</span> <span class="st">"cell_type"</span>, <span class="kw">label</span> <span class="kw">=</span> <span class="fl">TRUE</span>, <span class="kw">repel</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
-<pre><code>## Warning: Using `as.character()` on a quosure is deprecated as of rlang 0.3.0.
-## Please use `as_label()` or `as_name()` instead.
-## This warning is displayed once per session.</code></pre>
+<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://satijalab.org/seurat/reference/DimPlot.html">DimPlot</a></span><span class="op">(</span><span class="va">reference</span>, group.by <span class="op">=</span> <span class="st">"cell_type"</span>, label <span class="op">=</span> <span class="cn">TRUE</span>, repel <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <p><img src="introduction_files/figure-html/plot_umap-1.png" width="576"></p>
 </div>
 <div id="training-classifiers-with-scpred" class="section level1">
@@ -197,20 +198,21 @@ <h1 class="hasAnchor">
 </h1>
 <p>Firstly, let’s get the feature space to train the classifiers. By default, <code>scPred</code> will use all principal components. The reference labels of each cells are specified as the second parameter value of the function (in this case the <code>cell_type</code> column.</p>
 <p><code>getFeatureSpace</code> will create a <code>scPred</code> object stored in the <code>@misc</code> slot. This object will contained all required information to classify cells. See <code><a href="../reference/getFeatureSpace.html">?getFeatureSpace</a></code> help documentation.</p>
-<div class="sourceCode" id="cb16"><html><body><pre class="r"><span class="no">reference</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/getFeatureSpace.html">getFeatureSpace</a></span>(<span class="no">reference</span>, <span class="st">"cell_type"</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">reference</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/getFeatureSpace.html">getFeatureSpace</a></span><span class="op">(</span><span class="va">reference</span>, <span class="st">"cell_type"</span><span class="op">)</span></code></pre></div>
 <pre><code>## Registered S3 method overwritten by 'cli':
-##   method     from    
-##   print.boxx spatstat</code></pre>
+##   method     from         
+##   print.boxx spatstat.geom</code></pre>
 <pre><code>## ●  Extracting feature space for each cell type...
 ## DONE!</code></pre>
 <p>Secondly, we train the classifiers for each cell using the <code>trainModel</code> function. By default, <code>scPred</code> will use a support vector machine with a radial kernel.</p>
-<div class="sourceCode" id="cb19"><html><body><pre class="r"><span class="no">reference</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/trainModel.html">trainModel</a></span>(<span class="no">reference</span>)</pre></body></html></div>
-<pre><code>## ●  Training models for each cell type...</code></pre>
-<pre><code>## Loading required package: lattice</code></pre>
-<pre><code>## Loading required package: ggplot2</code></pre>
-<pre><code>## maximum number of iterations reached 0.0001163544 -0.0001154305DONE!</code></pre>
+<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">reference</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/trainModel.html">trainModel</a></span><span class="op">(</span><span class="va">reference</span><span class="op">)</span></code></pre></div>
+<pre><code>## ●  Training models for each cell type...
+## maximum number of iterations reached 0.0001163544 -0.0001154305DONE!</code></pre>
 <p>Training probabilities for each cell in the reference data can be accessed using the <code>get_probabilities</code> method:</p>
-<div class="sourceCode" id="cb24"><html><body><pre class="r"><span class="fu"><a href="../reference/get_probabilities.html">get_probabilities</a></span>(<span class="no">reference</span>) <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>()</pre></body></html></div>
+<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/get_probabilities.html">get_probabilities</a></span><span class="op">(</span><span class="va">reference</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
 <pre><code>##                    CD8 T cell   CD4 T cell        cMono       B cell
 ## CCACGGACATGCTGGC-1 0.99997400 3.986948e-06 3.429930e-05 1.895677e-04
 ## GATTCAGGTCTCCACT-1 0.04042862 9.889574e-01 1.067423e-06 4.731890e-05
@@ -239,7 +241,8 @@ <h1 class="hasAnchor">
 <li>Prediction model (method)</li>
 <li>Performance metrics</li>
 </ul>
-<div class="sourceCode" id="cb26"><html><body><pre class="r"><span class="fu"><a href="../reference/get_scpred.html">get_scpred</a></span>(<span class="no">reference</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/get_scpred.html">get_scpred</a></span><span class="op">(</span><span class="va">reference</span><span class="op">)</span></code></pre></div>
 <pre><code>## 'scPred' object
 ## ✓  Prediction variable = cell_type 
 ## ✓  Discriminant features per cell type
@@ -258,17 +261,23 @@ <h1 class="hasAnchor">
 ## |pDC         |   20|       50|svmRadial | 1.000| 0.700| 1.000|
 ## |Plasma cell |    6|       50|svmRadial | 1.000| 0.800| 1.000|</code></pre>
 <p>To visualize the performance for each cell type we can use the <code>plot_probabilities</code> function:</p>
-<div class="sourceCode" id="cb28"><html><body><pre class="r"><span class="fu"><a href="../reference/plot_probabilities.html">plot_probabilities</a></span>(<span class="no">reference</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/plot_probabilities.html">plot_probabilities</a></span><span class="op">(</span><span class="va">reference</span><span class="op">)</span></code></pre></div>
 <p><img src="introduction_files/figure-html/unnamed-chunk-3-1.png" width="576"></p>
 <p>From the previous plot we can observe an overall lower performance for classical monocytes (cMono) and non-classical monocytes (ncMono).</p>
 <p>Depending on the data, other models may show an better performance. <code>scPred</code> is built on top of the <code>caret</code> package and allows using a large set of prediction models (e.g. logistic regression, decision trees, bagging, neural networks, etc). To see the list of available models see <a href="https://topepo.github.io/caret/available-models.html">available models in caret</a>.</p>
 <p>A different model can be specified using the <code>model</code> parameter and providing the <em>method value</em> from <code>caret</code> (e.g. <code>mda</code> for a mixture discriminant analysis using the <code>mda</code> package). Additionally, if only an <code>mda</code> model wants to be applied to a subset of cells, we can specify this using the <code>reclassify</code> parameter. In this case, we want to train different models for “cMono” and “ncMono” to improve their classification performance:</p>
-<div class="sourceCode" id="cb29"><html><body><pre class="r"><span class="no">reference</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/trainModel.html">trainModel</a></span>(<span class="no">reference</span>, <span class="kw">model</span> <span class="kw">=</span> <span class="st">"mda"</span>, <span class="kw">reclassify</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"cMono"</span>, <span class="st">"ncMono"</span>))</pre></body></html></div>
+<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">reference</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/trainModel.html">trainModel</a></span><span class="op">(</span><span class="va">reference</span>, model <span class="op">=</span> <span class="st">"mda"</span>, reclassify <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"cMono"</span>, <span class="st">"ncMono"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<pre><code>## Registered S3 method overwritten by 'cli':
+##   method     from         
+##   print.boxx spatstat.geom</code></pre>
 <pre><code>## ●  Training models for each cell type...
 ## DONE!</code></pre>
 <p>The code above trains a mixture discriminant analysis for two cell types and preserves the previous support vector machines for the remaing cell types.</p>
 <p>We can observe a change in the sensitivity for “cMono” and “ncMono”:</p>
-<div class="sourceCode" id="cb31"><html><body><pre class="r"><span class="fu"><a href="../reference/get_scpred.html">get_scpred</a></span>(<span class="no">reference</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/get_scpred.html">get_scpred</a></span><span class="op">(</span><span class="va">reference</span><span class="op">)</span></code></pre></div>
 <pre><code>## 'scPred' object
 ## ✓  Prediction variable = cell_type 
 ## ✓  Discriminant features per cell type
@@ -287,7 +296,8 @@ <h1 class="hasAnchor">
 ## |pDC         |   20|       50|svmRadial | 1.000| 0.700| 1.000|
 ## |Plasma cell |    6|       50|svmRadial | 1.000| 0.800| 1.000|</code></pre>
 <p>and also verify that higher probabilities for these cell types were obtained by plotting the training probabilities again:</p>
-<div class="sourceCode" id="cb33"><html><body><pre class="r"><span class="fu"><a href="../reference/plot_probabilities.html">plot_probabilities</a></span>(<span class="no">reference</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/plot_probabilities.html">plot_probabilities</a></span><span class="op">(</span><span class="va">reference</span><span class="op">)</span></code></pre></div>
 <p><img src="introduction_files/figure-html/unnamed-chunk-6-1.png" width="576"></p>
 </div>
 <div id="cell-classification" class="section level1">
@@ -295,13 +305,15 @@ <h1 class="hasAnchor">
 <a href="#cell-classification" class="anchor"></a>Cell classification</h1>
 <p>An important requirement for classifying cells is using the <strong>same normalization method</strong> for both the <code>reference</code> and the <code>query</code> datasets.</p>
 <p>First, let’s normalize the <strong>query</strong> dataset (cells to be classfied).</p>
-<div class="sourceCode" id="cb34"><html><body><pre class="r"><span class="no">query</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/Seurat/man/NormalizeData.html">NormalizeData</a></span>(<span class="no">query</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">query</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://satijalab.org/seurat/reference/NormalizeData.html">NormalizeData</a></span><span class="op">(</span><span class="va">query</span><span class="op">)</span></code></pre></div>
 <p>Finally, we ca classify the cells from the <code>query</code> data using the <code>scPredict</code> function. The first argument corresponds to the <code>query</code> object and the second to the <code>reference</code> object (with a scPred model trained already).</p>
 <p><code>scPred</code> now uses <code>Harmony</code> to align the query data onto the training low-dimensional space used as reference. Once the data is aligned, cells are classified using the pre-trained models.</p>
 <blockquote>
-<p><code>scPredict</code> will return the query dataset. Make sure the left-side value of the <code>&lt;-</code> operator corresponds to the query data.</p>
+<p><code>scPredict</code> will return the query dataset. Make sure the left-side value of the <code><a href="https://rdrr.io/r/base/assignOps.html">&lt;-</a></code> operator corresponds to the query data.</p>
 </blockquote>
-<div class="sourceCode" id="cb35"><html><body><pre class="r"><span class="no">query</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/scPredict.html">scPredict</a></span>(<span class="no">query</span>, <span class="no">reference</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">query</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/scPredict.html">scPredict</a></span><span class="op">(</span><span class="va">query</span>, <span class="va">reference</span><span class="op">)</span></code></pre></div>
 <pre><code>## ●  Matching reference with new dataset...
 ##   ─ 2000 features present in reference loadings
 ##   ─ 2000 features shared between reference and new dataset
@@ -322,37 +334,46 @@ <h1 class="hasAnchor">
 ## DONE!</code></pre>
 <p><code>scPred</code> will store the final classifications in the <code>scpred_prediction</code> column of the Seurat meta data. Likewise, it will store a the <em>aligned</em> data and store it as a <code>scpred</code> reduction.</p>
 <p>Let’s plot the classifications over the aligned data.</p>
-<div class="sourceCode" id="cb49"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/pkg/Seurat/man/DimPlot.html">DimPlot</a></span>(<span class="no">query</span>, <span class="kw">group.by</span> <span class="kw">=</span> <span class="st">"scpred_prediction"</span>, <span class="kw">reduction</span> <span class="kw">=</span> <span class="st">"scpred"</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://satijalab.org/seurat/reference/DimPlot.html">DimPlot</a></span><span class="op">(</span><span class="va">query</span>, group.by <span class="op">=</span> <span class="st">"scpred_prediction"</span>, reduction <span class="op">=</span> <span class="st">"scpred"</span><span class="op">)</span></code></pre></div>
 <p><img src="introduction_files/figure-html/unnamed-chunk-8-1.png" width="576"></p>
 <p>We can also run UMAP using the aligned data as an input</p>
-<div class="sourceCode" id="cb50"><html><body><pre class="r"><span class="no">query</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/Seurat/man/RunUMAP.html">RunUMAP</a></span>(<span class="no">query</span>, <span class="kw">reduction</span> <span class="kw">=</span> <span class="st">"scpred"</span>, <span class="kw">dims</span> <span class="kw">=</span> <span class="fl">1</span>:<span class="fl">30</span>)</pre></body></html></div>
-<pre><code>## 02:35:07 UMAP embedding parameters a = 0.9922 b = 1.112</code></pre>
-<pre><code>## 02:35:07 Read 3000 rows and found 30 numeric columns</code></pre>
-<pre><code>## 02:35:07 Using Annoy for neighbor search, n_neighbors = 30</code></pre>
-<pre><code>## 02:35:07 Building Annoy index with metric = cosine, n_trees = 50</code></pre>
+<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">query</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://satijalab.org/seurat/reference/RunUMAP.html">RunUMAP</a></span><span class="op">(</span><span class="va">query</span>, reduction <span class="op">=</span> <span class="st">"scpred"</span>, dims <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">30</span><span class="op">)</span></code></pre></div>
+<pre><code>## Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
+## To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
+## This message will be shown once per session</code></pre>
+<pre><code>## 01:17:09 UMAP embedding parameters a = 0.9922 b = 1.112</code></pre>
+<pre><code>## 01:17:09 Read 3000 rows and found 30 numeric columns</code></pre>
+<pre><code>## 01:17:09 Using Annoy for neighbor search, n_neighbors = 30</code></pre>
+<pre><code>## 01:17:09 Building Annoy index with metric = cosine, n_trees = 50</code></pre>
 <pre><code>## 0%   10   20   30   40   50   60   70   80   90   100%</code></pre>
 <pre><code>## [----|----|----|----|----|----|----|----|----|----|</code></pre>
 <pre><code>## **************************************************|
-## 02:35:07 Writing NN index file to temp file /var/folders/6y/nzcvsw7j5dn1g0k8b13x086w0000gp/T//RtmpvL3gNk/fileb92e189cf6d2
-## 02:35:07 Searching Annoy index using 1 thread, search_k = 3000
-## 02:35:08 Annoy recall = 100%
-## 02:35:08 Commencing smooth kNN distance calibration using 1 thread
-## 02:35:09 Initializing from normalized Laplacian + noise
-## 02:35:09 Commencing optimization for 500 epochs, with 134492 positive edges
-## 02:35:13 Optimization finished</code></pre>
+## 01:17:10 Writing NN index file to temp file /var/folders/yj/yd72sc650wq90dvmfl2869jm0000gq/T//Rtmp98X9YM/file2f24610613be
+## 01:17:10 Searching Annoy index using 1 thread, search_k = 3000
+## 01:17:10 Annoy recall = 100%
+## 01:17:11 Commencing smooth kNN distance calibration using 1 thread
+## 01:17:11 Initializing from normalized Laplacian + noise
+## 01:17:11 Commencing optimization for 500 epochs, with 134488 positive edges
+## 01:17:16 Optimization finished</code></pre>
 <p>and plot the predicted labels for each cell type over the UMAP:</p>
-<div class="sourceCode" id="cb58"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/pkg/Seurat/man/DimPlot.html">DimPlot</a></span>(<span class="no">query</span>, <span class="kw">group.by</span> <span class="kw">=</span> <span class="st">"scpred_prediction"</span>, <span class="kw">label</span> <span class="kw">=</span> <span class="fl">TRUE</span>, <span class="kw">repel</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://satijalab.org/seurat/reference/DimPlot.html">DimPlot</a></span><span class="op">(</span><span class="va">query</span>, group.by <span class="op">=</span> <span class="st">"scpred_prediction"</span>, label <span class="op">=</span> <span class="cn">TRUE</span>, repel <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <p><img src="introduction_files/figure-html/unnamed-chunk-10-1.png" width="576"></p>
 <p>We can compare the results with the original labels:</p>
-<div class="sourceCode" id="cb59"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/pkg/Seurat/man/DimPlot.html">DimPlot</a></span>(<span class="no">query</span>, <span class="kw">group.by</span> <span class="kw">=</span> <span class="st">"cell_type"</span>, <span class="kw">label</span> <span class="kw">=</span> <span class="fl">TRUE</span>, <span class="kw">repel</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb57"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://satijalab.org/seurat/reference/DimPlot.html">DimPlot</a></span><span class="op">(</span><span class="va">query</span>, group.by <span class="op">=</span> <span class="st">"cell_type"</span>, label <span class="op">=</span> <span class="cn">TRUE</span>, repel <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <p><img src="introduction_files/figure-html/unnamed-chunk-11-1.png" width="576"></p>
 <p>Additionally, <code>scPred</code> stores the probabilities of each cell in the <code>@meta.data</code> slot of the query Seurat object. We can visualize the probabilities over the UMAP plot:</p>
-<div class="sourceCode" id="cb60"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/pkg/Seurat/man/FeaturePlot.html">FeaturePlot</a></span>(<span class="no">query</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"scpred_B.cell"</span>, <span class="st">"scpred_CD4.T.cell"</span>, <span class="st">"scpred_CD8.T.cell"</span>,
-                     <span class="st">"scpred_cMono"</span>, <span class="st">"scpred_ncMono"</span>, <span class="st">"scpred_Plasma.cell"</span>,
-                     <span class="st">"scpred_cDC"</span>, <span class="st">"scpred_pDC"</span>))</pre></body></html></div>
+<div class="sourceCode" id="cb58"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://satijalab.org/seurat/reference/FeaturePlot.html">FeaturePlot</a></span><span class="op">(</span><span class="va">query</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"scpred_B.cell"</span>, <span class="st">"scpred_CD4.T.cell"</span>, <span class="st">"scpred_CD8.T.cell"</span>, 
+                     <span class="st">"scpred_cMono"</span>, <span class="st">"scpred_ncMono"</span>, <span class="st">"scpred_Plasma.cell"</span>, 
+                     <span class="st">"scpred_cDC"</span>, <span class="st">"scpred_pDC"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
 <p><img src="introduction_files/figure-html/unnamed-chunk-12-1.png" width="864"></p>
 <p>To verify the performance of the models in the <code>query</code> dataset, we can use the <code>crossTab</code> to create a contingency table using two colums from the metadata. In this example, the cell type info is sotred in the <code>cell_type</code> columns and the predicted labels for each cell in the <code>scpred_prediction</code> column.</p>
-<div class="sourceCode" id="cb61"><html><body><pre class="r"><span class="fu"><a href="../reference/crossTab.html">crossTab</a></span>(<span class="no">query</span>, <span class="st">"cell_type"</span>, <span class="st">"scpred_prediction"</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/crossTab.html">crossTab</a></span><span class="op">(</span><span class="va">query</span>, <span class="st">"cell_type"</span>, <span class="st">"scpred_prediction"</span><span class="op">)</span></code></pre></div>
 <pre><code>##             B cell CD4 T cell CD8 T cell cDC cMono ncMono NK cell pDC
 ## B cell         250          0          0   0     0      0       0   0
 ## CD4 T cell       0       1179         25   0     1      0       0   0
@@ -376,7 +397,8 @@ <h1 class="hasAnchor">
 ## Plasma cell           6
 ## unassigned            0</code></pre>
 <p>The proportion of cells can be obtained using <code>output = "prop</code></p>
-<div class="sourceCode" id="cb63"><html><body><pre class="r"><span class="fu"><a href="../reference/crossTab.html">crossTab</a></span>(<span class="no">query</span>, <span class="st">"cell_type"</span>, <span class="st">"scpred_prediction"</span>, <span class="kw">output</span> <span class="kw">=</span> <span class="st">"prop"</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb61"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/crossTab.html">crossTab</a></span><span class="op">(</span><span class="va">query</span>, <span class="st">"cell_type"</span>, <span class="st">"scpred_prediction"</span>, output <span class="op">=</span> <span class="st">"prop"</span><span class="op">)</span></code></pre></div>
 <pre><code>##             B cell CD4 T cell CD8 T cell  cDC cMono ncMono NK cell  pDC
 ## B cell           1       0.00       0.00 0.00  0.00   0.00    0.00 0.00
 ## CD4 T cell       0       0.95       0.04 0.00  0.00   0.00    0.00 0.00
@@ -407,7 +429,8 @@ <h1 class="hasAnchor">
 <h2 class="hasAnchor">
 <a href="#accessing-classifiers" class="anchor"></a>Accessing classifiers</h2>
 <p>The raw models for each cell type can be retrieved using the <code><a href="../reference/get_classifiers.html">get_classifiers()</a></code> function. This will return a list of <code>train</code> objects.</p>
-<div class="sourceCode" id="cb65"><html><body><pre class="r"><span class="fu"><a href="../reference/get_classifiers.html">get_classifiers</a></span>(<span class="no">reference</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/get_classifiers.html">get_classifiers</a></span><span class="op">(</span><span class="va">reference</span><span class="op">)</span></code></pre></div>
 <pre><code>## $`CD8 T cell`
 ## Support Vector Machines with Radial Basis Function Kernel 
 ## 
@@ -559,7 +582,8 @@ <h2 class="hasAnchor">
 ## ROC was used to select the optimal model using the largest value.
 ## The final values used for the model were sigma = 0.02458556 and C = 0.25.</code></pre>
 <p>Each model can be normally treated using the <code>caret</code> enviroment. For example, we can plot the performance resamples using the <code>plot.train</code>:</p>
-<div class="sourceCode" id="cb67"><html><body><pre class="r"><span class="kw pkg">caret</span><span class="kw ns">::</span><span class="fu"><a href="https://rdrr.io/pkg/caret/man/plot.train.html">plot.train</a></span>(<span class="fu"><a href="../reference/get_classifiers.html">get_classifiers</a></span>(<span class="no">reference</span>)<span class="kw">[[</span><span class="st">"NK cell"</span>]])</pre></body></html></div>
+<div class="sourceCode" id="cb65"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu">caret</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/caret/man/plot.train.html">plot.train</a></span><span class="op">(</span><span class="fu"><a href="../reference/get_classifiers.html">get_classifiers</a></span><span class="op">(</span><span class="va">reference</span><span class="op">)</span><span class="op">[[</span><span class="st">"NK cell"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
 <p><img src="introduction_files/figure-html/unnamed-chunk-16-1.png" width="576"></p>
 </div>
 <div id="using-a-different-prediction-model-approach" class="section level2">
@@ -567,10 +591,12 @@ <h2 class="hasAnchor">
 <a href="#using-a-different-prediction-model-approach" class="anchor"></a>Using a different prediction model approach</h2>
 <p>As shown before, a different classification method can be used using the <code>model</code> parameter by providing a distinct <em>method value</em> of type <strong>classification</strong> as handled by caret (see <a href="https://topepo.github.io/caret/available-models.html">available models in caret</a>). Most available models will require the user to install new packages.</p>
 <p>The following code trains a logistic regression via <code><a href="https://rdrr.io/r/stats/glm.html">glm()</a></code> for each cell type:</p>
-<div class="sourceCode" id="cb68"><html><body><pre class="r"><span class="no">reference</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/trainModel.html">trainModel</a></span>(<span class="no">reference</span>, <span class="kw">model</span> <span class="kw">=</span> <span class="st">"glm"</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb66"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">reference</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/trainModel.html">trainModel</a></span><span class="op">(</span><span class="va">reference</span>, model <span class="op">=</span> <span class="st">"glm"</span><span class="op">)</span></code></pre></div>
 <pre><code>## ●  Training models for each cell type...
 ## DONE!</code></pre>
-<div class="sourceCode" id="cb70"><html><body><pre class="r"><span class="fu"><a href="../reference/get_scpred.html">get_scpred</a></span>(<span class="no">reference</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb68"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="../reference/get_scpred.html">get_scpred</a></span><span class="op">(</span><span class="va">reference</span><span class="op">)</span></code></pre></div>
 <pre><code>## 'scPred' object
 ## ✓  Prediction variable = cell_type 
 ## ✓  Discriminant features per cell type
@@ -593,7 +619,8 @@ <h2 class="hasAnchor">
 <h2 class="hasAnchor">
 <a href="#avoid-aligning-the-data-multiple-times" class="anchor"></a>Avoid aligning the data multiple times</h2>
 <p>Training and alignning the data are separate processes. Therefore, if a <code>query</code> dataset has already being aligned to a <code>reference</code> data via scPred/harmony and the prediction models have changed, then we can use <code>recompute_alignment = FALSE</code> to avoid aligning step (as the alignment is already stored in the <code>query</code> object)</p>
-<div class="sourceCode" id="cb72"><html><body><pre class="r"><span class="no">query</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/scPredict.html">scPredict</a></span>(<span class="no">query</span>, <span class="no">reference</span>, <span class="kw">recompute_alignment</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb70"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">query</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/scPredict.html">scPredict</a></span><span class="op">(</span><span class="va">query</span>, <span class="va">reference</span>, recompute_alignment <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
 <pre><code>## ●  Classifying cells...
 ## DONE!</code></pre>
 <p>The code above will only apply the classificatio models.</p>
@@ -602,7 +629,8 @@ <h2 class="hasAnchor">
 <h2 class="hasAnchor">
 <a href="#using-a-different-probability-threshold" class="anchor"></a>Using a different probability threshold</h2>
 <p>By default, <code>scPred</code> now uses a relaxed probability theshold of <code>0.55</code> to label cells. If none of the classifiers provide a probability higher than the threshold for a given cell, then it is labelled as “unassigned”. This value can be changed using the <code>threshold</code> parameter:</p>
-<div class="sourceCode" id="cb74"><html><body><pre class="r"><span class="no">query</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/scPredict.html">scPredict</a></span>(<span class="no">query</span>, <span class="no">reference</span>, <span class="kw">recompute_alignment</span> <span class="kw">=</span> <span class="fl">FALSE</span>, <span class="kw">threshold</span> <span class="kw">=</span> <span class="fl">0.9</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb72"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">query</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/scPredict.html">scPredict</a></span><span class="op">(</span><span class="va">query</span>, <span class="va">reference</span>, recompute_alignment <span class="op">=</span> <span class="cn">FALSE</span>, threshold <span class="op">=</span> <span class="fl">0.9</span><span class="op">)</span></code></pre></div>
 <pre><code>## ●  Classifying cells...
 ## DONE!</code></pre>
 <p>In the case of a binary classification (only two cell types), a threshold equals <code>0.5</code> implies no “unassigned labeling”.</p>
@@ -611,16 +639,15 @@ <h2 class="hasAnchor">
 <h2 class="hasAnchor">
 <a href="#parallel-training" class="anchor"></a>Parallel training</h2>
 <p>Depending on the sample size of the reference dataset and the number of cell types, training models can be computatinally expensive. The resampling performed for each model can be parallelized via <code>doParallel</code> to speed-up the training step as follows:</p>
-<div class="sourceCode" id="cb76"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">doParallel</span>)</pre></body></html></div>
-<pre><code>## Loading required package: foreach</code></pre>
-<pre><code>## Loading required package: iterators</code></pre>
-<pre><code>## Loading required package: parallel</code></pre>
-<div class="sourceCode" id="cb80"><html><body><pre class="r"><span class="no">cl</span> <span class="kw">&lt;-</span> <span class="fu">makePSOCKcluster</span>(<span class="fl">2</span>)
-<span class="fu"><a href="https://rdrr.io/pkg/doParallel/man/registerDoParallel.html">registerDoParallel</a></span>(<span class="no">cl</span>)
-<span class="no">reference</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/trainModel.html">trainModel</a></span>(<span class="no">reference</span>, <span class="kw">model</span> <span class="kw">=</span> <span class="st">"mda"</span>, <span class="kw">allowParallel</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb74"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va">doParallel</span><span class="op">)</span>
+<span class="va">cl</span> <span class="op">&lt;-</span> <span class="fu">makePSOCKcluster</span><span class="op">(</span><span class="fl">2</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/pkg/doParallel/man/registerDoParallel.html">registerDoParallel</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span>
+<span class="va">reference</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/trainModel.html">trainModel</a></span><span class="op">(</span><span class="va">reference</span>, model <span class="op">=</span> <span class="st">"mda"</span>, allowParallel <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <pre><code>## ●  Training models for each cell type...
 ## DONE!</code></pre>
-<div class="sourceCode" id="cb82"><html><body><pre class="r"><span class="fu">stopCluster</span>(<span class="no">cl</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb76"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu">stopCluster</span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></code></pre></div>
 <blockquote>
 <p><code>allowParallel = TRUE</code> has to be set in order for <code>trainModel</code> to be able to run the resamplings in parallel</p>
 </blockquote>
@@ -633,9 +660,10 @@ <h2 class="hasAnchor">
 <h2 class="hasAnchor">
 <a href="#applying-scpred-classifiers-without-seurat-object" class="anchor"></a>Applying <code>scPred</code> classifiers without <code>Seurat</code> object</h2>
 <p>Once final <code>scPred</code> models have been obtained, we can extract the <code>scPred</code> object from the <code>Seurat</code> object and apply the classifiers in other datasets.</p>
-<div class="sourceCode" id="cb83"><html><body><pre class="r"><span class="no">scpred</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/get_scpred.html">get_scpred</a></span>(<span class="no">reference</span>)
-<span class="no">query</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/scPredict.html">scPredict</a></span>(<span class="no">query</span>, <span class="no">scpred</span>)</pre></body></html></div>
-<pre><code>## ‒ Data has already being aligned to a reference.
+<div class="sourceCode" id="cb77"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">scpred</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/get_scpred.html">get_scpred</a></span><span class="op">(</span><span class="va">reference</span><span class="op">)</span>
+<span class="va">query</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/scPredict.html">scPredict</a></span><span class="op">(</span><span class="va">query</span>, <span class="va">scpred</span><span class="op">)</span></code></pre></div>
+<pre><code>## ‒ Data has already been aligned to a reference.
 ## ⁺ Skip data alignment using `recompute.alignment = FALSE`.
 ## ●  Matching reference with new dataset...
 ##   ─ 2000 features present in reference loadings
@@ -661,165 +689,181 @@ <h2 class="hasAnchor">
 <div id="session-information" class="section level1">
 <h1 class="hasAnchor">
 <a href="#session-information" class="anchor"></a>Session information</h1>
-<div class="sourceCode" id="cb97"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/options.html">options</a></span>(<span class="kw">width</span> <span class="kw">=</span> <span class="fl">120</span>)
-<span class="kw pkg">devtools</span><span class="kw ns">::</span><span class="fu"><a href="https://devtools.r-lib.org//reference/reexports.html">session_info</a></span>()</pre></body></html></div>
-<pre><code>## Registered S3 method overwritten by 'cli':
-##   method     from    
-##   print.boxx spatstat</code></pre>
+<div class="sourceCode" id="cb91"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html">options</a></span><span class="op">(</span>width <span class="op">=</span> <span class="fl">120</span><span class="op">)</span>
+<span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/sessioninfo/man/session_info.html">session_info</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
 <pre><code>## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 ##  setting  value                       
-##  version  R version 4.0.2 (2020-06-22)
-##  os       macOS Catalina 10.15.6      
+##  version  R version 4.1.0 (2021-05-18)
+##  os       macOS Big Sur 10.16         
 ##  system   x86_64, darwin17.0          
 ##  ui       X11                         
 ##  language (EN)                        
 ##  collate  en_AU.UTF-8                 
 ##  ctype    en_AU.UTF-8                 
 ##  tz       Australia/Sydney            
-##  date     2020-09-14                  
+##  date     2021-07-12                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
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-##  ape              5.4-1      2020-08-13 [2] CRAN (R 4.0.2)                         
-##  assertthat       0.2.1      2019-03-21 [2] CRAN (R 4.0.0)                         
-##  backports        1.1.9      2020-08-24 [2] CRAN (R 4.0.2)                         
-##  beeswarm         0.2.3      2016-04-25 [2] CRAN (R 4.0.0)                         
-##  callr            3.4.3      2020-03-28 [2] CRAN (R 4.0.0)                         
-##  caret          * 6.0-86     2020-03-20 [2] CRAN (R 4.0.0)                         
-##  class            7.3-17     2020-04-26 [2] CRAN (R 4.0.2)                         
-##  cli              2.0.2      2020-02-28 [2] CRAN (R 4.0.0)                         
-##  cluster          2.1.0      2019-06-19 [2] CRAN (R 4.0.2)                         
-##  codetools        0.2-16     2018-12-24 [2] CRAN (R 4.0.2)                         
-##  colorspace       1.4-1      2019-03-18 [2] CRAN (R 4.0.0)                         
-##  cowplot          1.0.0      2019-07-11 [2] CRAN (R 4.0.0)                         
-##  crayon           1.3.4      2017-09-16 [2] CRAN (R 4.0.0)                         
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-##  deldir           0.1-28     2020-07-15 [2] CRAN (R 4.0.1)                         
-##  desc             1.2.0      2018-05-01 [2] CRAN (R 4.0.0)                         
-##  devtools         2.3.1      2020-07-21 [2] CRAN (R 4.0.2)                         
-##  digest           0.6.25     2020-02-23 [2] CRAN (R 4.0.0)                         
-##  doParallel     * 1.0.15     2019-08-02 [2] CRAN (R 4.0.0)                         
-##  dplyr            1.0.2      2020-08-18 [2] CRAN (R 4.0.2)                         
-##  ellipsis         0.3.1      2020-05-15 [2] CRAN (R 4.0.0)                         
-##  evaluate         0.14       2019-05-28 [2] CRAN (R 4.0.0)                         
-##  fansi            0.4.1      2020-01-08 [2] CRAN (R 4.0.0)                         
-##  fastmap          1.0.1      2019-10-08 [2] CRAN (R 4.0.0)                         
-##  fitdistrplus     1.1-1      2020-05-19 [2] CRAN (R 4.0.0)                         
-##  foreach        * 1.5.0      2020-03-30 [2] CRAN (R 4.0.0)                         
-##  fs               1.5.0      2020-07-31 [2] CRAN (R 4.0.2)                         
-##  future           1.18.0     2020-07-09 [2] CRAN (R 4.0.1)                         
-##  future.apply     1.6.0      2020-07-01 [2] CRAN (R 4.0.1)                         
-##  generics         0.0.2      2018-11-29 [2] CRAN (R 4.0.0)                         
-##  ggbeeswarm       0.6.0      2017-08-07 [2] CRAN (R 4.0.2)                         
-##  ggplot2        * 3.3.2      2020-06-19 [2] CRAN (R 4.0.1)                         
-##  ggrepel          0.8.2      2020-03-08 [2] CRAN (R 4.0.0)                         
-##  ggridges         0.5.2      2020-01-12 [2] CRAN (R 4.0.0)                         
-##  globals          0.12.5     2019-12-07 [2] CRAN (R 4.0.0)                         
-##  glue             1.4.2      2020-08-27 [2] CRAN (R 4.0.2)                         
-##  goftest          1.2-2      2019-12-02 [2] CRAN (R 4.0.0)                         
-##  gower            0.2.2      2020-06-23 [2] CRAN (R 4.0.1)                         
-##  gridExtra        2.3        2017-09-09 [2] CRAN (R 4.0.0)                         
-##  gtable           0.3.0      2019-03-25 [2] CRAN (R 4.0.0)                         
-##  harmony          1.0        2020-06-25 [2] Github (immunogenomics/harmony@88b1e2a)
-##  htmltools        0.5.0      2020-06-16 [2] CRAN (R 4.0.1)                         
-##  htmlwidgets      1.5.1      2019-10-08 [2] CRAN (R 4.0.0)                         
-##  httpuv           1.5.4      2020-06-06 [2] CRAN (R 4.0.0)                         
-##  httr             1.4.2      2020-07-20 [2] CRAN (R 4.0.2)                         
-##  ica              1.0-2      2018-05-24 [2] CRAN (R 4.0.0)                         
-##  igraph           1.2.5      2020-03-19 [2] CRAN (R 4.0.0)                         
-##  ipred            0.9-9      2019-04-28 [2] CRAN (R 4.0.0)                         
-##  irlba            2.3.3      2019-02-05 [2] CRAN (R 4.0.0)                         
-##  iterators      * 1.0.12     2019-07-26 [2] CRAN (R 4.0.0)                         
-##  jsonlite         1.7.0      2020-06-25 [2] CRAN (R 4.0.0)                         
-##  KernSmooth       2.23-17    2020-04-26 [2] CRAN (R 4.0.2)                         
-##  knitr            1.29       2020-06-23 [2] CRAN (R 4.0.1)                         
-##  later            1.1.0.1    2020-06-05 [2] CRAN (R 4.0.0)                         
-##  lattice        * 0.20-41    2020-04-02 [2] CRAN (R 4.0.2)                         
-##  lava             1.6.7      2020-03-05 [2] CRAN (R 4.0.0)                         
-##  lazyeval         0.2.2      2019-03-15 [2] CRAN (R 4.0.0)                         
-##  leiden           0.3.3      2020-02-04 [2] CRAN (R 4.0.0)                         
-##  lifecycle        0.2.0      2020-03-06 [2] CRAN (R 4.0.0)                         
-##  listenv          0.8.0      2019-12-05 [2] CRAN (R 4.0.0)                         
-##  lmtest           0.9-37     2019-04-30 [2] CRAN (R 4.0.0)                         
-##  lubridate        1.7.9      2020-06-08 [2] CRAN (R 4.0.0)                         
-##  magrittr       * 1.5        2014-11-22 [2] CRAN (R 4.0.0)                         
-##  MASS             7.3-52     2020-08-18 [2] CRAN (R 4.0.2)                         
-##  Matrix           1.2-18     2019-11-27 [2] CRAN (R 4.0.2)                         
-##  memoise          1.1.0      2017-04-21 [2] CRAN (R 4.0.0)                         
-##  mgcv             1.8-33     2020-08-27 [2] CRAN (R 4.0.2)                         
-##  mime             0.9        2020-02-04 [2] CRAN (R 4.0.0)                         
-##  miniUI           0.1.1.1    2018-05-18 [2] CRAN (R 4.0.0)                         
-##  ModelMetrics     1.2.2.2    2020-03-17 [2] CRAN (R 4.0.0)                         
-##  munsell          0.5.0      2018-06-12 [2] CRAN (R 4.0.0)                         
-##  nlme             3.1-149    2020-08-23 [2] CRAN (R 4.0.2)                         
-##  nnet             7.3-14     2020-04-26 [2] CRAN (R 4.0.2)                         
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-##  pbapply          1.4-3      2020-08-18 [2] CRAN (R 4.0.2)                         
-##  pillar           1.4.6      2020-07-10 [2] CRAN (R 4.0.1)                         
-##  pkgbuild         1.1.0      2020-07-13 [2] CRAN (R 4.0.1)                         
-##  pkgconfig        2.0.3      2019-09-22 [2] CRAN (R 4.0.0)                         
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-##  pkgload          1.1.0      2020-05-29 [2] CRAN (R 4.0.0)                         
-##  plotly           4.9.2.1    2020-04-04 [2] CRAN (R 4.0.0)                         
-##  plyr             1.8.6      2020-03-03 [2] CRAN (R 4.0.0)                         
-##  png              0.1-7      2013-12-03 [2] CRAN (R 4.0.0)                         
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-##  processx         3.4.4      2020-09-03 [2] CRAN (R 4.0.2)                         
-##  prodlim          2019.11.13 2019-11-17 [2] CRAN (R 4.0.0)                         
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-##  ps               1.3.4      2020-08-11 [2] CRAN (R 4.0.2)                         
-##  purrr            0.3.4      2020-04-17 [2] CRAN (R 4.0.0)                         
-##  R6               2.4.1      2019-11-12 [2] CRAN (R 4.0.0)                         
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-##  recipes          0.1.13     2020-06-23 [2] CRAN (R 4.0.1)                         
-##  remotes          2.2.0      2020-07-21 [2] CRAN (R 4.0.2)                         
-##  reshape2         1.4.4      2020-04-09 [2] CRAN (R 4.0.0)                         
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-##  ROCR             1.0-11     2020-05-02 [2] CRAN (R 4.0.0)                         
-##  rpart            4.1-15     2019-04-12 [2] CRAN (R 4.0.2)                         
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-##  rsvd             1.0.3      2020-02-17 [2] CRAN (R 4.0.0)                         
-##  Rtsne            0.15       2018-11-10 [2] CRAN (R 4.0.0)                         
-##  scales           1.1.1      2020-05-11 [2] CRAN (R 4.0.0)                         
-##  scPred         * 1.9.0      2020-09-13 [1] Bioconductor                           
-##  sctransform      0.2.1      2019-12-17 [2] CRAN (R 4.0.0)                         
-##  sessioninfo      1.1.1      2018-11-05 [2] CRAN (R 4.0.0)                         
-##  Seurat         * 3.2.0      2020-07-16 [2] CRAN (R 4.0.1)                         
-##  shiny            1.5.0      2020-06-23 [2] CRAN (R 4.0.1)                         
-##  spatstat         1.64-1     2020-05-12 [2] CRAN (R 4.0.0)                         
-##  spatstat.data    1.4-3      2020-01-26 [2] CRAN (R 4.0.0)                         
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-##  stringr          1.4.0      2019-02-10 [2] CRAN (R 4.0.0)                         
-##  survival         3.2-3      2020-06-13 [2] CRAN (R 4.0.2)                         
-##  tensor           1.5        2012-05-05 [2] CRAN (R 4.0.0)                         
-##  testthat         2.3.2      2020-03-02 [2] CRAN (R 4.0.0)                         
-##  tibble           3.0.3      2020-07-10 [2] CRAN (R 4.0.1)                         
-##  tidyr            1.1.2      2020-08-27 [2] CRAN (R 4.0.2)                         
-##  tidyselect       1.1.0      2020-05-11 [2] CRAN (R 4.0.0)                         
-##  timeDate         3043.102   2018-02-21 [2] CRAN (R 4.0.0)                         
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-##  vctrs            0.3.4      2020-08-29 [2] CRAN (R 4.0.2)                         
-##  vipor            0.4.5      2017-03-22 [2] CRAN (R 4.0.0)                         
-##  viridisLite      0.3.0      2018-02-01 [2] CRAN (R 4.0.0)                         
-##  withr            2.2.0      2020-04-20 [2] CRAN (R 4.0.0)                         
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-##  xtable           1.8-4      2019-04-21 [2] CRAN (R 4.0.0)                         
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-##  zoo              1.8-8      2020-05-02 [2] CRAN (R 4.0.0)                         
-## 
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-## [2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library</code></pre>
+##  package         * version    date       lib source                                 
+##  abind             1.4-5      2016-07-21 [2] CRAN (R 4.1.0)                         
+##  assertthat        0.2.1      2019-03-21 [2] CRAN (R 4.1.0)                         
+##  beeswarm          0.4.0      2021-06-01 [2] CRAN (R 4.1.0)                         
+##  bslib             0.2.5.1    2021-05-18 [2] CRAN (R 4.1.0)                         
+##  cachem            1.0.5      2021-05-15 [2] CRAN (R 4.1.0)                         
+##  callr             3.7.0      2021-04-20 [2] CRAN (R 4.1.0)                         
+##  caret           * 6.0-88     2021-05-15 [2] CRAN (R 4.1.0)                         
+##  class             7.3-19     2021-05-03 [2] CRAN (R 4.1.0)                         
+##  cli               3.0.0      2021-06-30 [2] CRAN (R 4.1.0)                         
+##  cluster           2.1.2      2021-04-17 [2] CRAN (R 4.1.0)                         
+##  codetools         0.2-18     2020-11-04 [2] CRAN (R 4.1.0)                         
+##  colorspace        2.0-2      2021-06-24 [2] CRAN (R 4.1.0)                         
+##  cowplot           1.1.1      2020-12-30 [2] CRAN (R 4.1.0)                         
+##  crayon            1.4.1      2021-02-08 [2] CRAN (R 4.1.0)                         
+##  data.table        1.14.1     2021-06-08 [2] local                                  
+##  DBI               1.1.1      2021-01-15 [2] CRAN (R 4.1.0)                         
+##  deldir            0.2-10     2021-02-16 [2] CRAN (R 4.1.0)                         
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+##  ps                1.6.0      2021-02-28 [2] CRAN (R 4.1.0)                         
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+##  R6                2.5.0      2020-10-28 [2] CRAN (R 4.1.0)                         
+##  ragg              1.1.3      2021-06-09 [2] CRAN (R 4.1.0)                         
+##  RANN              2.6.1      2019-01-08 [2] CRAN (R 4.1.0)                         
+##  RColorBrewer      1.1-2      2014-12-07 [2] CRAN (R 4.1.0)                         
+##  Rcpp              1.0.6      2021-01-15 [2] CRAN (R 4.1.0)                         
+##  RcppAnnoy         0.0.18     2020-12-15 [2] CRAN (R 4.1.0)                         
+##  recipes           0.1.16     2021-04-16 [2] CRAN (R 4.1.0)                         
+##  remotes           2.4.0      2021-06-02 [2] CRAN (R 4.1.0)                         
+##  reshape2          1.4.4      2020-04-09 [2] CRAN (R 4.1.0)                         
+##  reticulate        1.20       2021-05-03 [2] CRAN (R 4.1.0)                         
+##  rlang             0.4.11     2021-04-30 [2] CRAN (R 4.1.0)                         
+##  rmarkdown         2.9        2021-06-15 [2] CRAN (R 4.1.0)                         
+##  ROCR              1.0-11     2020-05-02 [2] CRAN (R 4.1.0)                         
+##  rpart             4.1-15     2019-04-12 [2] CRAN (R 4.1.0)                         
+##  rprojroot         2.0.2      2020-11-15 [2] CRAN (R 4.1.0)                         
+##  RSpectra          0.16-0     2019-12-01 [2] CRAN (R 4.1.0)                         
+##  rstudioapi        0.13       2020-11-12 [2] CRAN (R 4.1.0)                         
+##  Rtsne             0.15       2018-11-10 [2] CRAN (R 4.1.0)                         
+##  sass              0.4.0      2021-05-12 [2] CRAN (R 4.1.0)                         
+##  scales            1.1.1      2020-05-11 [2] CRAN (R 4.1.0)                         
+##  scattermore       0.7        2020-11-24 [2] CRAN (R 4.1.0)                         
+##  scPred          * 1.9.2      2021-07-11 [1] local                                  
+##  sctransform       0.3.2      2020-12-16 [2] CRAN (R 4.1.0)                         
+##  sessioninfo       1.1.1      2018-11-05 [2] CRAN (R 4.1.0)                         
+##  Seurat          * 4.0.3      2021-06-10 [2] CRAN (R 4.1.0)                         
+##  SeuratObject    * 4.0.2      2021-06-09 [2] CRAN (R 4.1.0)                         
+##  shiny             1.6.0      2021-01-25 [2] CRAN (R 4.1.0)                         
+##  spatstat.core     2.2-0      2021-06-17 [2] CRAN (R 4.1.0)                         
+##  spatstat.data     2.1-0      2021-03-21 [2] CRAN (R 4.1.0)                         
+##  spatstat.geom     2.2-0      2021-06-15 [2] CRAN (R 4.1.0)                         
+##  spatstat.sparse   2.0-0      2021-03-16 [2] CRAN (R 4.1.0)                         
+##  spatstat.utils    2.2-0      2021-06-14 [2] CRAN (R 4.1.0)                         
+##  stringi           1.6.2      2021-05-17 [2] CRAN (R 4.1.0)                         
+##  stringr           1.4.0      2019-02-10 [2] CRAN (R 4.1.0)                         
+##  survival          3.2-11     2021-04-26 [2] CRAN (R 4.1.0)                         
+##  systemfonts       1.0.2      2021-05-11 [2] CRAN (R 4.1.0)                         
+##  tensor            1.5        2012-05-05 [2] CRAN (R 4.1.0)                         
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+##  uwot              0.1.10     2020-12-15 [2] CRAN (R 4.1.0)                         
+##  vctrs             0.3.8      2021-04-29 [2] CRAN (R 4.1.0)                         
+##  vipor             0.4.5      2017-03-22 [2] CRAN (R 4.1.0)                         
+##  viridisLite       0.4.0      2021-04-13 [2] CRAN (R 4.1.0)                         
+##  withr             2.4.2      2021-04-18 [2] CRAN (R 4.1.0)                         
+##  xfun              0.24       2021-06-15 [2] CRAN (R 4.1.0)                         
+##  xtable            1.8-4      2019-04-21 [2] CRAN (R 4.1.0)                         
+##  yaml              2.2.1      2020-02-01 [2] CRAN (R 4.1.0)                         
+##  zoo               1.8-9      2021-03-09 [2] CRAN (R 4.1.0)                         
+## 
+## [1] /private/var/folders/yj/yd72sc650wq90dvmfl2869jm0000gq/T/RtmpbVhim7/temp_libpath2e33576e5670
+## [2] /Library/Frameworks/R.framework/Versions/4.1/Resources/library</code></pre>
 </div>
   </div>
 
@@ -838,7 +882,7 @@ <h1 class="hasAnchor">
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/articles/introduction_files/figure-html/plot_umap-1.png b/docs/articles/introduction_files/figure-html/plot_umap-1.png
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diff --git a/docs/articles/introduction_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/introduction_files/figure-html/unnamed-chunk-8-1.png
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diff --git a/docs/articles/introduction_files/header-attrs-2.9/header-attrs.js b/docs/articles/introduction_files/header-attrs-2.9/header-attrs.js
new file mode 100644
index 0000000..dd57d92
--- /dev/null
+++ b/docs/articles/introduction_files/header-attrs-2.9/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/authors.html b/docs/authors.html
index fc3d48e..c90bc07 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -89,7 +89,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -112,7 +112,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -151,7 +151,7 @@ <h1>Authors</h1>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/index.html b/docs/index.html
index 8b3cbb2..245c624 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -37,7 +37,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -45,7 +45,7 @@
       <ul class="nav navbar-nav">
 <li>
   <a href="index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -68,7 +68,7 @@
 <ul class="nav navbar-nav navbar-right">
 <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -97,9 +97,11 @@
 <h1 class="hasAnchor">
 <a href="#installation" class="anchor"></a>Installation</h1>
 <p>Before installing <code>scPred</code>, please install harmony as follows:</p>
-<div class="sourceCode" id="cb1"><pre class="r"><span class="kw pkg">devtools</span><span class="kw ns">::</span><span class="fu"><a href="https://devtools.r-lib.org//reference/remote-reexports.html">install_github</a></span>(<span class="st">"immunogenomics/harmony"</span>)</pre></div>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org//reference/remote-reexports.html">install_github</a></span><span class="op">(</span><span class="st">"immunogenomics/harmony"</span><span class="op">)</span></code></pre></div>
 <p>You can install <code>scPred</code> via devtools as follows:</p>
-<div class="sourceCode" id="cb2"><pre class="r"><span class="kw pkg">devtools</span><span class="kw ns">::</span><span class="fu"><a href="https://devtools.r-lib.org//reference/remote-reexports.html">install_github</a></span>(<span class="st">"powellgenomicslab/scPred"</span>)</pre></div>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org//reference/remote-reexports.html">install_github</a></span><span class="op">(</span><span class="st">"powellgenomicslab/scPred"</span><span class="op">)</span></code></pre></div>
 </div>
 <div id="how-to-use-scpred" class="section level1">
 <h1 class="hasAnchor">
@@ -147,7 +149,7 @@ <h2>Dev status</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index c01e592..1273238 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -244,14 +244,14 @@ nav[data-toggle='toc'] .nav .nav > .active:focus > a {
 
 .ref-index th {font-weight: normal;}
 
-.ref-index td {vertical-align: top;}
+.ref-index td {vertical-align: top; min-width: 100px}
 .ref-index .icon {width: 40px;}
 .ref-index .alias {width: 40%;}
 .ref-index-icons .alias {width: calc(40% - 40px);}
 .ref-index .title {width: 60%;}
 
 .ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
+.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px}
 .ref-arguments .name {width: 20%;}
 .ref-arguments .desc {width: 80%;}
 
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 2c3237f..b55521c 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,7 +1,7 @@
-pandoc: 2.9.2.1
-pkgdown: 1.5.1
+pandoc: 2.11.4
+pkgdown: 1.6.1
 pkgdown_sha: ~
 articles:
   introduction: introduction.html
-last_built: 2020-09-14T07:52Z
+last_built: 2021-07-11T15:26Z
 
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
new file mode 100644
index 0000000..17a3580
Binary files /dev/null and b/docs/reference/Rplot001.png differ
diff --git a/docs/reference/crossTab-Seurat-method.html b/docs/reference/crossTab-Seurat-method.html
index 3abf811..93408d2 100644
--- a/docs/reference/crossTab-Seurat-method.html
+++ b/docs/reference/crossTab-Seurat-method.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -140,13 +140,13 @@ <h1>Gets contingency table</h1>
     </div>
 
     <pre class="usage"><span class='co'># S4 method for Seurat</span>
-<span class='fu'><a href='crossTab.html'>crossTab</a></span>(
-  <span class='no'>object</span>,
-  <span class='kw'>true</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
-  <span class='kw'>pred</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
-  <span class='kw'>output</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"counts"</span>, <span class='st'>"fraction"</span>, <span class='st'>"prop"</span>),
-  <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>
-)</pre>
+<span class='fu'><a href='crossTab.html'>crossTab</a></span><span class='op'>(</span>
+  <span class='va'>object</span>,
+  true <span class='op'>=</span> <span class='cn'>NULL</span>,
+  pred <span class='op'>=</span> <span class='cn'>NULL</span>,
+  output <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"counts"</span>, <span class='st'>"fraction"</span>, <span class='st'>"prop"</span><span class='op'>)</span>,
+  digits <span class='op'>=</span> <span class='fl'>2</span>
+<span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -177,6 +177,9 @@ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arg
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>A contingency table</p>
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>Jose Alquicira Hernandez</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -193,7 +196,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/crossTab.html b/docs/reference/crossTab.html
index 59b87b9..d19b4cc 100644
--- a/docs/reference/crossTab.html
+++ b/docs/reference/crossTab.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -139,13 +139,13 @@ <h1>Gets contingency table</h1>
     <p>Creates a cross table using two columns from the metadata</p>
     </div>
 
-    <pre class="usage"><span class='fu'>crossTab</span>(
-  <span class='no'>object</span>,
-  <span class='kw'>true</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
-  <span class='kw'>pred</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
-  <span class='kw'>output</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"counts"</span>, <span class='st'>"fraction"</span>, <span class='st'>"prop"</span>),
-  <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>
-)</pre>
+    <pre class="usage"><span class='fu'>crossTab</span><span class='op'>(</span>
+  <span class='va'>object</span>,
+  true <span class='op'>=</span> <span class='cn'>NULL</span>,
+  pred <span class='op'>=</span> <span class='cn'>NULL</span>,
+  output <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"counts"</span>, <span class='st'>"fraction"</span>, <span class='st'>"prop"</span><span class='op'>)</span>,
+  digits <span class='op'>=</span> <span class='fl'>2</span>
+<span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -176,6 +176,9 @@ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arg
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>A contingency table</p>
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>Jose Alquicira Hernandez</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -192,7 +195,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/dot-plot_probabilities.html b/docs/reference/dot-plot_probabilities.html
index c64e3aa..87be360 100644
--- a/docs/reference/dot-plot_probabilities.html
+++ b/docs/reference/dot-plot_probabilities.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -139,7 +139,7 @@ <h1>Plot training probabilities</h1>
     <p>Plots all training probabilities for each cell type</p>
     </div>
 
-    <pre class="usage"><span class='fu'>.plot_probabilities</span>(<span class='no'>object</span>, <span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>0.8</span>)</pre>
+    <pre class="usage"><span class='fu'>.plot_probabilities</span><span class='op'>(</span><span class='va'>object</span>, size <span class='op'>=</span> <span class='fl'>0.8</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -173,7 +173,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/getFeatureSpace.html b/docs/reference/getFeatureSpace.html
index f01573b..ad4123b 100644
--- a/docs/reference/getFeatureSpace.html
+++ b/docs/reference/getFeatureSpace.html
@@ -83,7 +83,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -91,7 +91,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -114,7 +114,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -141,7 +141,7 @@ <h1>Get discriminant feature space</h1>
 explain variance differences between cell types.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>getFeatureSpace</span>(<span class='no'>object</span>, <span class='no'>pvar</span>, <span class='kw'>correction</span> <span class='kw'>=</span> <span class='st'>"fdr"</span>, <span class='kw'>sig</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>reduction</span> <span class='kw'>=</span> <span class='st'>"pca"</span>)</pre>
+    <pre class="usage"><span class='fu'>getFeatureSpace</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>pvar</span>, correction <span class='op'>=</span> <span class='st'>"fdr"</span>, sig <span class='op'>=</span> <span class='fl'>1</span>, reduction <span class='op'>=</span> <span class='st'>"pca"</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -180,11 +180,15 @@ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 This column contains the cumulative variance explained across the ranked principal components</p></li>
 </ul>
 
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>Jose Alquicira Hernandez</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>scPred</span>)
-<span class='no'>pbmc_small</span> <span class='kw'>&lt;-</span> <span class='fu'>getFeatureSpace</span>(<span class='no'>pbmc_small</span>, <span class='st'>"RNA_snn_res.0.8"</span>)</div><div class='output co'>#&gt; <span class='error'>Error in is(object, "Seurat"): object 'pbmc_small' not found</span></div><div class='input'>
+<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://github.com/powellgenomicslab/scPred'>scPred</a></span><span class='op'>)</span>
+<span class='va'>pbmc_small</span> <span class='op'>&lt;-</span> <span class='fu'>getFeatureSpace</span><span class='op'>(</span><span class='va'>pbmc_small</span>, <span class='st'>"RNA_snn_res.0.8"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='error'>Error in is(object, "Seurat"): object 'pbmc_small' not found</span></div><div class='input'>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -201,7 +205,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/get_classifiers-Seurat-method.html b/docs/reference/get_classifiers-Seurat-method.html
index 67b3e0c..05affdb 100644
--- a/docs/reference/get_classifiers-Seurat-method.html
+++ b/docs/reference/get_classifiers-Seurat-method.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -140,7 +140,7 @@ <h1>Get classification models</h1>
     </div>
 
     <pre class="usage"><span class='co'># S4 method for Seurat</span>
-<span class='fu'><a href='get_classifiers.html'>get_classifiers</a></span>(<span class='no'>object</span>)</pre>
+<span class='fu'><a href='get_classifiers.html'>get_classifiers</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -170,7 +170,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/get_classifiers-scPred-method.html b/docs/reference/get_classifiers-scPred-method.html
index b01357c..30d7044 100644
--- a/docs/reference/get_classifiers-scPred-method.html
+++ b/docs/reference/get_classifiers-scPred-method.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -140,7 +140,7 @@ <h1>Get classification models</h1>
     </div>
 
     <pre class="usage"><span class='co'># S4 method for scPred</span>
-<span class='fu'><a href='get_classifiers.html'>get_classifiers</a></span>(<span class='no'>object</span>)</pre>
+<span class='fu'><a href='get_classifiers.html'>get_classifiers</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -170,7 +170,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/get_classifiers.html b/docs/reference/get_classifiers.html
index d7161d1..654b266 100644
--- a/docs/reference/get_classifiers.html
+++ b/docs/reference/get_classifiers.html
@@ -83,7 +83,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -91,7 +91,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -114,7 +114,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -141,7 +141,7 @@ <h1>Get classification models</h1>
 and scPred objects</p>
     </div>
 
-    <pre class="usage"><span class='fu'>get_classifiers</span>(<span class='no'>object</span>)</pre>
+    <pre class="usage"><span class='fu'>get_classifiers</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -171,7 +171,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/get_metadata-Seurat-method.html b/docs/reference/get_metadata-Seurat-method.html
index 94dd829..17b90d0 100644
--- a/docs/reference/get_metadata-Seurat-method.html
+++ b/docs/reference/get_metadata-Seurat-method.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -140,7 +140,7 @@ <h1>Get metadata from scPred object</h1>
     </div>
 
     <pre class="usage"><span class='co'># S4 method for Seurat</span>
-<span class='fu'><a href='get_metadata.html'>get_metadata</a></span>(<span class='no'>object</span>)</pre>
+<span class='fu'><a href='get_metadata.html'>get_metadata</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre>
 
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -163,7 +163,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/get_metadata-scPred-method.html b/docs/reference/get_metadata-scPred-method.html
index df78b4e..5d4a3a4 100644
--- a/docs/reference/get_metadata-scPred-method.html
+++ b/docs/reference/get_metadata-scPred-method.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -140,7 +140,7 @@ <h1>Get metadata from scPred object</h1>
     </div>
 
     <pre class="usage"><span class='co'># S4 method for scPred</span>
-<span class='fu'><a href='get_metadata.html'>get_metadata</a></span>(<span class='no'>object</span>)</pre>
+<span class='fu'><a href='get_metadata.html'>get_metadata</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre>
 
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -163,7 +163,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/get_metadata.html b/docs/reference/get_metadata.html
index cac58f3..d9a9f4b 100644
--- a/docs/reference/get_metadata.html
+++ b/docs/reference/get_metadata.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -139,7 +139,7 @@ <h1>Get metadata from scPred object</h1>
     <p>Accessor function to retrieve metadata from scPred object</p>
     </div>
 
-    <pre class="usage"><span class='fu'>get_metadata</span>(<span class='no'>object</span>)</pre>
+    <pre class="usage"><span class='fu'>get_metadata</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre>
 
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -162,7 +162,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/get_probabilities-Seurat-method.html b/docs/reference/get_probabilities-Seurat-method.html
index 05a0298..c7be6fe 100644
--- a/docs/reference/get_probabilities-Seurat-method.html
+++ b/docs/reference/get_probabilities-Seurat-method.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -140,7 +140,7 @@ <h1>Get training probabilities</h1>
     </div>
 
     <pre class="usage"><span class='co'># S4 method for Seurat</span>
-<span class='fu'><a href='get_probabilities.html'>get_probabilities</a></span>(<span class='no'>object</span>)</pre>
+<span class='fu'><a href='get_probabilities.html'>get_probabilities</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -170,7 +170,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/get_probabilities-scPred-method.html b/docs/reference/get_probabilities-scPred-method.html
index 7e9d726..bb37860 100644
--- a/docs/reference/get_probabilities-scPred-method.html
+++ b/docs/reference/get_probabilities-scPred-method.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -140,7 +140,7 @@ <h1>Get training probabilities</h1>
     </div>
 
     <pre class="usage"><span class='co'># S4 method for scPred</span>
-<span class='fu'><a href='get_probabilities.html'>get_probabilities</a></span>(<span class='no'>object</span>)</pre>
+<span class='fu'><a href='get_probabilities.html'>get_probabilities</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -170,7 +170,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/get_probabilities.html b/docs/reference/get_probabilities.html
index a15ef0c..00fbf4a 100644
--- a/docs/reference/get_probabilities.html
+++ b/docs/reference/get_probabilities.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -139,7 +139,7 @@ <h1>Get training probabilities</h1>
     <p>Gets training probabilities for each cell type</p>
     </div>
 
-    <pre class="usage"><span class='fu'>get_probabilities</span>(<span class='no'>object</span>)</pre>
+    <pre class="usage"><span class='fu'>get_probabilities</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -169,7 +169,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/get_scpred-Seurat-method.html b/docs/reference/get_scpred-Seurat-method.html
index 1add9fc..2b14a50 100644
--- a/docs/reference/get_scpred-Seurat-method.html
+++ b/docs/reference/get_scpred-Seurat-method.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -140,7 +140,7 @@ <h1>Get scPred object</h1>
     </div>
 
     <pre class="usage"><span class='co'># S4 method for Seurat</span>
-<span class='fu'><a href='get_scpred.html'>get_scpred</a></span>(<span class='no'>object</span>)</pre>
+<span class='fu'><a href='get_scpred.html'>get_scpred</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -170,7 +170,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/get_scpred.html b/docs/reference/get_scpred.html
index 407d413..005b2fc 100644
--- a/docs/reference/get_scpred.html
+++ b/docs/reference/get_scpred.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -139,7 +139,7 @@ <h1>Get scPred object</h1>
     <p>Accessor function to retrieve scPred models from Seurat objects</p>
     </div>
 
-    <pre class="usage"><span class='fu'>get_scpred</span>(<span class='no'>object</span>)</pre>
+    <pre class="usage"><span class='fu'>get_scpred</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -169,7 +169,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index cba77fe..adb4b92 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -89,7 +89,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -112,7 +112,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -321,7 +321,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/pbmc_1.html b/docs/reference/pbmc_1.html
index d117fd2..9348cb7 100644
--- a/docs/reference/pbmc_1.html
+++ b/docs/reference/pbmc_1.html
@@ -83,7 +83,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -91,7 +91,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -114,7 +114,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -141,7 +141,7 @@ <h1>A random sample of PBMCs from individual 1</h1>
 Illumina sequencing technology for single-cell RNA-sequencing</p>
     </div>
 
-    <pre class="usage"><span class='no'>pbmc_1</span></pre>
+    <pre class="usage"><span class='va'>pbmc_1</span></pre>
 
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -166,7 +166,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/pbmc_2.html b/docs/reference/pbmc_2.html
index 96c2389..cb30e4e 100644
--- a/docs/reference/pbmc_2.html
+++ b/docs/reference/pbmc_2.html
@@ -83,7 +83,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -91,7 +91,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -114,7 +114,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -141,7 +141,7 @@ <h1>A random sample of PBMCs from individual 2</h1>
 Illumina sequencing technology for single-cell RNA-sequencing</p>
     </div>
 
-    <pre class="usage"><span class='no'>pbmc_2</span></pre>
+    <pre class="usage"><span class='va'>pbmc_2</span></pre>
 
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -166,7 +166,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/plot_probabilities-Seurat-method.html b/docs/reference/plot_probabilities-Seurat-method.html
index c26e97c..9a1be4b 100644
--- a/docs/reference/plot_probabilities-Seurat-method.html
+++ b/docs/reference/plot_probabilities-Seurat-method.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -140,7 +140,7 @@ <h1>Plot training probabilities</h1>
     </div>
 
     <pre class="usage"><span class='co'># S4 method for Seurat</span>
-<span class='fu'><a href='plot_probabilities.html'>plot_probabilities</a></span>(<span class='no'>object</span>, <span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>0.8</span>)</pre>
+<span class='fu'><a href='plot_probabilities.html'>plot_probabilities</a></span><span class='op'>(</span><span class='va'>object</span>, size <span class='op'>=</span> <span class='fl'>0.8</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -174,7 +174,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/plot_probabilities-scPred-method.html b/docs/reference/plot_probabilities-scPred-method.html
index 30d3890..74e93c4 100644
--- a/docs/reference/plot_probabilities-scPred-method.html
+++ b/docs/reference/plot_probabilities-scPred-method.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -140,7 +140,7 @@ <h1>Plot training probabilities</h1>
     </div>
 
     <pre class="usage"><span class='co'># S4 method for scPred</span>
-<span class='fu'><a href='plot_probabilities.html'>plot_probabilities</a></span>(<span class='no'>object</span>, <span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>0.8</span>)</pre>
+<span class='fu'><a href='plot_probabilities.html'>plot_probabilities</a></span><span class='op'>(</span><span class='va'>object</span>, size <span class='op'>=</span> <span class='fl'>0.8</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -174,7 +174,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/plot_probabilities.html b/docs/reference/plot_probabilities.html
index efc5e39..1d90ef5 100644
--- a/docs/reference/plot_probabilities.html
+++ b/docs/reference/plot_probabilities.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -139,7 +139,7 @@ <h1>Plot training probabilities</h1>
     <p>Plots all training probabilities for each cell type</p>
     </div>
 
-    <pre class="usage"><span class='fu'>plot_probabilities</span>(<span class='no'>object</span>, <span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>0.8</span>)</pre>
+    <pre class="usage"><span class='fu'>plot_probabilities</span><span class='op'>(</span><span class='va'>object</span>, size <span class='op'>=</span> <span class='fl'>0.8</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -173,7 +173,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/print.scPred.html b/docs/reference/print.scPred.html
index 81a695e..84c95ec 100644
--- a/docs/reference/print.scPred.html
+++ b/docs/reference/print.scPred.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -140,7 +140,7 @@ <h1>show</h1>
     </div>
 
     <pre class="usage"><span class='co'># S3 method for scPred</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>string</span>)</pre>
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>string</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -170,7 +170,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/scPred.html b/docs/reference/scPred.html
index db2dc4b..7a7f7ca 100644
--- a/docs/reference/scPred.html
+++ b/docs/reference/scPred.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -145,7 +145,7 @@ <h2 class="hasAnchor" id="slots"><a class="anchor" href="#slots"></a>Slots</h2>
 
     
 
-<dl'>
+<dl>
 <dt><code>pvar</code></dt><dd><p>Column name from metadata to use as the variable to predict using</p></dd>
 
 <dt><code>metadata</code></dt><dd><p>A data frame to store metadata including prediction variable (pvar)</p></dd>
@@ -186,7 +186,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/scPredict.html b/docs/reference/scPredict.html
index e994f58..0baef43 100644
--- a/docs/reference/scPredict.html
+++ b/docs/reference/scPredict.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -139,16 +139,15 @@ <h1>Predict cell classes from a new dataset using a trained model</h1>
     <p>Predicts cell classes for a new dataset based on trained model(s)</p>
     </div>
 
-    <pre class="usage"><span class='fu'>scPredict</span>(
-  <span class='no'>new</span>,
-  <span class='no'>reference</span>,
-  <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.55</span>,
-  <span class='kw'>max.iter.harmony</span> <span class='kw'>=</span> <span class='fl'>20</span>,
-  <span class='kw'>recompute_alignment</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>reference_scaling</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>66</span>,
-  <span class='no'>...</span>
-)</pre>
+    <pre class="usage"><span class='fu'>scPredict</span><span class='op'>(</span>
+  <span class='va'>new</span>,
+  <span class='va'>reference</span>,
+  threshold <span class='op'>=</span> <span class='fl'>0.55</span>,
+  max.iter.harmony <span class='op'>=</span> <span class='fl'>20</span>,
+  recompute_alignment <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  seed <span class='op'>=</span> <span class='fl'>66</span>,
+  <span class='va'>...</span>
+<span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -177,25 +176,19 @@ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arg
       <th>recompute_alignment</th>
       <td><p>Recompute alignment? Useful if <code>scPredict()</code> has already been run</p></td>
     </tr>
-    <tr>
-      <th>reference_scaling</th>
-      <td><p>Scale new dataset based on means and stdevs from reference dataset before alignment. 
-Otherwise, data will be independently scaled via <code><a href='https://rdrr.io/pkg/Seurat/man/ScaleData.html'>Seurat::ScaleData()</a></code>.</p></td>
-    </tr>
     <tr>
       <th>seed</th>
       <td><p>Numeric seed for harmony</p></td>
     </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Further parameters passed to <code><a href='https://rdrr.io/pkg/Seurat/man/ScaleData.html'>Seurat::ScaleData()</a></code> if <code>reference_scaling</code> is <code>FALSE</code></p></td>
-    </tr>
     </table>
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>A Seurat object with addtional metadata columns with prediction probabilities associated to each class, a <code>prediction</code> column, 
 indicating the classification based on the provided threshold and a <code>generic_class</code> column without "unassigned" labels.</p>
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>José Alquicira Hernández</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -212,7 +205,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/show-scPred-method.html b/docs/reference/show-scPred-method.html
index 1f822b8..cc0a5fa 100644
--- a/docs/reference/show-scPred-method.html
+++ b/docs/reference/show-scPred-method.html
@@ -83,7 +83,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -91,7 +91,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -114,7 +114,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -142,7 +142,7 @@ <h1>show</h1>
     </div>
 
     <pre class="usage"><span class='co'># S4 method for scPred</span>
-<span class='fu'>show</span>(<span class='no'>object</span>)</pre>
+<span class='fu'>show</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre>
 
 
 
@@ -161,7 +161,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/trainModel.html b/docs/reference/trainModel.html
index 815bbd5..59465c5 100644
--- a/docs/reference/trainModel.html
+++ b/docs/reference/trainModel.html
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scPred</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
       </span>
     </div>
 
@@ -90,7 +90,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -113,7 +113,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/powellgenomicslab/scPred/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -139,20 +139,20 @@ <h1>Train a prediction model</h1>
     <p>Trains a prediction model from an <code>scPred</code> object stored in a <code>Seurat</code> object</p>
     </div>
 
-    <pre class="usage"><span class='fu'>trainModel</span>(
-  <span class='no'>object</span>,
-  <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"svmRadial"</span>,
-  <span class='kw'>preProcess</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"center"</span>, <span class='st'>"scale"</span>),
-  <span class='kw'>resampleMethod</span> <span class='kw'>=</span> <span class='st'>"cv"</span>,
-  <span class='kw'>number</span> <span class='kw'>=</span> <span class='fl'>5</span>,
-  <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>66</span>,
-  <span class='kw'>tuneLength</span> <span class='kw'>=</span> <span class='fl'>3</span>,
-  <span class='kw'>metric</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"ROC"</span>, <span class='st'>"PR"</span>, <span class='st'>"Accuracy"</span>, <span class='st'>"Kappa"</span>),
-  <span class='kw'>returnData</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>savePredictions</span> <span class='kw'>=</span> <span class='st'>"final"</span>,
-  <span class='kw'>allowParallel</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>reclassify</span> <span class='kw'>=</span> <span class='kw'>NULL</span>
-)</pre>
+    <pre class="usage"><span class='fu'>trainModel</span><span class='op'>(</span>
+  <span class='va'>object</span>,
+  model <span class='op'>=</span> <span class='st'>"svmRadial"</span>,
+  preProcess <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"center"</span>, <span class='st'>"scale"</span><span class='op'>)</span>,
+  resampleMethod <span class='op'>=</span> <span class='st'>"cv"</span>,
+  number <span class='op'>=</span> <span class='fl'>5</span>,
+  seed <span class='op'>=</span> <span class='fl'>66</span>,
+  tuneLength <span class='op'>=</span> <span class='fl'>3</span>,
+  metric <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"ROC"</span>, <span class='st'>"PR"</span>, <span class='st'>"Accuracy"</span>, <span class='st'>"Kappa"</span><span class='op'>)</span>,
+  returnData <span class='op'>=</span> <span class='cn'>FALSE</span>,
+  savePredictions <span class='op'>=</span> <span class='st'>"final"</span>,
+  allowParallel <span class='op'>=</span> <span class='cn'>FALSE</span>,
+  reclassify <span class='op'>=</span> <span class='cn'>NULL</span>
+<span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -221,6 +221,9 @@ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arg
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>A list of <code>train</code> objects for each cell class (e.g. cell type). See <code>train</code> function for details.</p>
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>Jose Alquicira Hernandez</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -237,7 +240,7 @@ <h2 data-toc-skip>Contents</h2>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>