From 8ce744dcc6f96c3eb7ba92980741b4832237bad0 Mon Sep 17 00:00:00 2001
From: MaraBesemer <deine.email@beispiel.com>
Date: Wed, 27 Nov 2024 09:24:27 +0100
Subject: [PATCH] add ggplot2 to macros and R linting fixing

---
 tools/phyloseq/macros.xml          |  1 +
 tools/phyloseq/phyloseq_plot_bar.R | 54 +++++++++++++++---------------
 2 files changed, 28 insertions(+), 27 deletions(-)

diff --git a/tools/phyloseq/macros.xml b/tools/phyloseq/macros.xml
index ebe365840ac..312bcccd9a3 100644
--- a/tools/phyloseq/macros.xml
+++ b/tools/phyloseq/macros.xml
@@ -12,6 +12,7 @@
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-phyloseq</requirement>
             <requirement type="package" version="1.7.3">r-optparse</requirement>
             <requirement type="package" version="2.0.0">r-tidyverse</requirement>
+            <requirement type="package" version="3.3.0">r-ggplot2</requirement>
         </requirements>
     </xml>
     <xml name="phyloseq_input">
diff --git a/tools/phyloseq/phyloseq_plot_bar.R b/tools/phyloseq/phyloseq_plot_bar.R
index 237abf2d658..0a3aba58490 100755
--- a/tools/phyloseq/phyloseq_plot_bar.R
+++ b/tools/phyloseq/phyloseq_plot_bar.R
@@ -7,26 +7,26 @@ suppressPackageStartupMessages(library("ggplot2"))
 
 # Define options
 option_list <- list(
-  make_option(c("--input"),
-    action = "store", dest = "input",
-    help = "Input file containing a phyloseq object"
-  ),
-  make_option(c("--x"),
-    action = "store", dest = "x",
-    help = "Variable for x-axis (e.g., 'Sample', 'Phylum')"
-  ),
-  make_option(c("--fill"),
-    action = "store", dest = "fill",
-    help = "Variable for fill color (e.g., 'Genus', 'Order')"
-  ),
-  make_option(c("--facet"),
-    action = "store", dest = "facet", default = NULL,
-    help = "Facet by variable (optional)"
-  ),
-  make_option(c("--output"),
-    action = "store", dest = "output",
-    help = "Output file (PDF)"
-  )
+    make_option(c("--input"),
+        action = "store", dest = "input",
+        help = "Input file containing a phyloseq object"
+    ),
+    make_option(c("--x"),
+        action = "store", dest = "x",
+        help = "Variable for x-axis (e.g., 'Sample', 'Phylum')"
+    ),
+    make_option(c("--fill"),
+        action = "store", dest = "fill",
+        help = "Variable for fill color (e.g., 'Genus', 'Order')"
+    ),
+    make_option(c("--facet"),
+        action = "store", dest = "facet", default = NULL,
+        help = "Facet by variable (optional)"
+    ),
+    make_option(c("--output"),
+        action = "store", dest = "output",
+        help = "Output file (PDF)"
+    )
 )
 
 # Parse arguments
@@ -40,11 +40,11 @@ physeq <- readRDS(opt$input)
 
 # Check if the 'x' and 'fill' variables are valid
 if (!opt$x %in% colnames(sample_data(physeq))) {
-  stop(paste("Error: x variable", opt$x, "does not exist in the sample data."))
+    stop(paste("Error: x variable", opt$x, "does not exist in the sample data."))
 }
 
 if (!opt$fill %in% colnames(sample_data(physeq))) {
-  stop(paste("Error: fill variable", opt$fill, "does not exist in the sample data."))
+    stop(paste("Error: fill variable", opt$fill, "does not exist in the sample data."))
 }
 
 # Generate bar plot
@@ -52,11 +52,11 @@ p <- plot_bar(physeq, x = opt$x, fill = opt$fill)
 
 # Only facet if the facet variable is provided and exists in the sample data
 if (!is.null(opt$facet)) {
-  if (opt$facet %in% colnames(sample_data(physeq))) {
-    p <- p + facet_wrap(as.formula(paste("~", opt$facet)))
-  } else {
-    warning(paste("Facet variable", opt$facet, "does not exist in the sample data. Faceting will be skipped."))
-  }
+    if (opt$facet %in% colnames(sample_data(physeq))) {
+        p <- p + facet_wrap(as.formula(paste("~", opt$facet)))
+    } else {
+        warning(paste("Facet variable", opt$facet, "does not exist in the sample data. Faceting will be skipped."))
+    }
 }
 
 # Save to output file