From 37a30b845497a7903963303fb9f37a3d4754a090 Mon Sep 17 00:00:00 2001
From: micahpf <micahpfletcher@gmail.com>
Date: Wed, 2 Aug 2023 15:39:31 -0400
Subject: [PATCH 1/2] init convertCLID2Name() to convert cl ids in SingleR
 output and seurat objects into human-readable names

---
 NAMESPACE               |  1 +
 R/runSingleR.R          | 56 ++++++++++++++++++++++++++++++++++++
 man/convertClID2Name.Rd | 64 +++++++++++++++++++++++++++++++++++++++++
 3 files changed, 121 insertions(+)
 create mode 100644 man/convertClID2Name.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 6c9b294..7033494 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -6,6 +6,7 @@ export(IdentName)
 export(NormFindVarFeatScaleData)
 export(addQCfilter)
 export(addQCmetrics)
+export(convertClID2Name)
 export(createAzimuthReference)
 export(demuxAntibodyData)
 export(extractGeneCorrectionsSoupX)
diff --git a/R/runSingleR.R b/R/runSingleR.R
index 144bd52..8d95895 100644
--- a/R/runSingleR.R
+++ b/R/runSingleR.R
@@ -61,3 +61,59 @@ runSingleR <- function(obj.seurat,
 
   return(list(obj.seurat, singleR.out))
 }
+
+#' Convert cell ontology IDs to names in SingleR output
+#'
+#' Convert bare cell ontology IDs used in SingleR to human-readable names
+#'
+#' @param metadata data.frame with labels, pruned.labels and delta.next columns. Typically either:
+#'  - Seurat object metadata (after running SingleR), or
+#'  - SingleR output object
+#' @param cl Cell ontology database
+#'  - Can be btained via: `cl <- ontoProc::getOnto('cellOnto')`
+#' @param old.prefix The prefix used for the original runSingleR call (e.g. "ImmGen.ont")
+#' @param new.prefix The new prefix to use for the human readable column (e.g. "ImmGen.ont.name")
+#'
+#' @returns data.frame with three new columns: `{new.prefix}.labels`, `{new.prefix}.pruned.labels`, `{new.prefix}.delta.next`.
+#'
+#'@examples
+#' \dontrun{
+#' ## Run on bare ontology IDs, then convert to human readable cell type labels
+#' # Get cell ontology names and other info
+#' cl <- ontoProc::getOnto('cellOnto')
+#'
+#' # ImmGen.ont
+#' c(obj.seurat, SingleR.ImmGen.ont) %<-% obj.seurat %>%
+#'   Run.SingleR(obj.seurat=.,
+#'               ref=ref.ImmGen,
+#'               labels=ref.ImmGen$label.ont,
+#'               de.method="classic",
+#'               meta.prefix = "ImmGen.ont")
+#'
+#' # These labels aren't very informative:
+#' SingleR::plotScoreHeatmap(SingleR.ImmGen.ont, show.pruned = TRUE, fontsize=4)
+#'
+#' # Convert bare cell ontology IDs to informative names in seurat object
+#' obj.seurat@meta.data <- clID2clNames(metadata = obj.seurat@meta.data, cl = cl,
+#'                                      old.prefix = "ImmGen.ont", new.prefix = "ImmGen.ont.name")
+#'
+#' # Convert bare cell ontology IDs to informative names in SingleR output and visualize
+#' SingleR.ImmGen.ont.names <- clID2clNames(metadata = SingleR.ImmGen.ont, cl = cl,
+#'                                          old.prefix = "ImmGen.ont", new.prefix = "ImmGen.ont.name")
+#'
+#' SingleR::plotScoreHeatmap(SingleR.ImmGen.ont.names, show.pruned = TRUE, fontsize=4)
+#' }
+#'
+#' @export
+# Run SingleR
+# Convert bare cell ontology IDs to informative names
+convertClID2Name <- function(metadata, cl, old.prefix = "ImmGen.ont", new.prefix = "ImmGen.ont.name") {
+  op <- old.prefix
+  np <- new.prefix
+  md <- metadata
+  md[[paste0(np, ".labels")]] <- unname(cl$name[unname(md[[paste0(op, ".labels")]])])
+  md[[paste0(np, ".pruned.labels")]] <- unname(cl$name[unname(md[[paste0(op, ".pruned.labels")]])])
+  md[[paste0(np, ".delta.next")]] <- md[[paste0(op, ".delta.next")]]
+  metadata <- md
+  return(metadata)
+}
diff --git a/man/convertClID2Name.Rd b/man/convertClID2Name.Rd
new file mode 100644
index 0000000..7981e84
--- /dev/null
+++ b/man/convertClID2Name.Rd
@@ -0,0 +1,64 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/runSingleR.R
+\name{convertClID2Name}
+\alias{convertClID2Name}
+\title{Convert cell ontology IDs to names in SingleR output}
+\usage{
+convertClID2Name(
+  metadata,
+  cl,
+  old.prefix = "ImmGen.ont",
+  new.prefix = "ImmGen.ont.name"
+)
+}
+\arguments{
+\item{metadata}{data.frame with labels, pruned.labels and delta.next columns. Typically either:
+\itemize{
+\item Seurat object metadata (after running SingleR), or
+\item SingleR output object
+}}
+
+\item{cl}{Cell ontology database
+\itemize{
+\item Can be btained via: \code{cl <- ontoProc::getOnto('cellOnto')}
+}}
+
+\item{old.prefix}{The prefix used for the original runSingleR call (e.g. "ImmGen.ont")}
+
+\item{new.prefix}{The new prefix to use for the human readable column (e.g. "ImmGen.ont.name")}
+}
+\value{
+data.frame with three new columns: \verb{\{new.prefix\}.labels}, \verb{\{new.prefix\}.pruned.labels}, \verb{\{new.prefix\}.delta.next}.
+}
+\description{
+Convert bare cell ontology IDs used in SingleR to human-readable names
+}
+\examples{
+\dontrun{
+## Run on bare ontology IDs, then convert to human readable cell type labels
+# Get cell ontology names and other info
+cl <- ontoProc::getOnto('cellOnto')
+
+# ImmGen.ont
+c(obj.seurat, SingleR.ImmGen.ont) \%<-\% obj.seurat \%>\%
+  Run.SingleR(obj.seurat=.,
+              ref=ref.ImmGen,
+              labels=ref.ImmGen$label.ont,
+              de.method="classic",
+              meta.prefix = "ImmGen.ont")
+
+# These labels aren't very informative:
+SingleR::plotScoreHeatmap(SingleR.ImmGen.ont, show.pruned = TRUE, fontsize=4)
+
+# Convert bare cell ontology IDs to informative names in seurat object
+obj.seurat@meta.data <- clID2clNames(metadata = obj.seurat@meta.data, cl = cl,
+                                     old.prefix = "ImmGen.ont", new.prefix = "ImmGen.ont.name")
+
+# Convert bare cell ontology IDs to informative names in SingleR output and visualize
+SingleR.ImmGen.ont.names <- clID2clNames(metadata = SingleR.ImmGen.ont, cl = cl,
+                                         old.prefix = "ImmGen.ont", new.prefix = "ImmGen.ont.name")
+
+SingleR::plotScoreHeatmap(SingleR.ImmGen.ont.names, show.pruned = TRUE, fontsize=4)
+}
+
+}

From 0b3612f2c0a7c10adc61ece56a29fbb11db5161a Mon Sep 17 00:00:00 2001
From: Derrik Gratz <46037149+derrik-gratz@users.noreply.github.com>
Date: Wed, 9 Aug 2023 13:44:54 -0400
Subject: [PATCH 2/2] Update runSingleR.R

fix example function calls to proper function name
---
 R/runSingleR.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/runSingleR.R b/R/runSingleR.R
index 8d95895..7776f33 100644
--- a/R/runSingleR.R
+++ b/R/runSingleR.R
@@ -94,11 +94,11 @@ runSingleR <- function(obj.seurat,
 #' SingleR::plotScoreHeatmap(SingleR.ImmGen.ont, show.pruned = TRUE, fontsize=4)
 #'
 #' # Convert bare cell ontology IDs to informative names in seurat object
-#' obj.seurat@meta.data <- clID2clNames(metadata = obj.seurat@meta.data, cl = cl,
+#' obj.seurat@meta.data <- convertClID2Name(metadata = obj.seurat@meta.data, cl = cl,
 #'                                      old.prefix = "ImmGen.ont", new.prefix = "ImmGen.ont.name")
 #'
 #' # Convert bare cell ontology IDs to informative names in SingleR output and visualize
-#' SingleR.ImmGen.ont.names <- clID2clNames(metadata = SingleR.ImmGen.ont, cl = cl,
+#' SingleR.ImmGen.ont.names <- convertClID2Name(metadata = SingleR.ImmGen.ont, cl = cl,
 #'                                          old.prefix = "ImmGen.ont", new.prefix = "ImmGen.ont.name")
 #'
 #' SingleR::plotScoreHeatmap(SingleR.ImmGen.ont.names, show.pruned = TRUE, fontsize=4)