# HG changeset patch
# User iuc
# Date 1733760264 0
# Node ID ab01e379d29ec4f9bffd333eda6b951913f196b6
# Parent 2f557f6abbfbf76cf93b60acc6b957125fb3748c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 060f6734402e7d2eced6227663cc61d2cb865ae5
diff -r 2f557f6abbfb -r ab01e379d29e test-data/category.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/category.tab Mon Dec 09 16:04:24 2024 +0000
@@ -0,0 +1,11 @@
+Gene log2FoldChange pvalue padj category
+DOK6 0.51 1.861e-08 0.0003053 Category A
+TBX5 -2.129 5.655e-08 0.0004191 Category B
+SLC32A1 0.9003 7.664e-08 0.0004191 Category C
+IFITM1 -1.687 3.735e-06 0.006809 Category A
+NUP93 0.3659 3.373e-06 0.006809 Category B
+EMILIN2 1.534 2.976e-06 0.006809 Category C
+TPX2 -0.9974 2.097e-06 0.006809 Category A
+LAMA2 -1.425 2.39e-06 0.006809 Category B
+CAV2 -1.052 3.213e-06 0.006809 Category C
+TNN -1.658 8.973e-06 0.01472 Category A
\ No newline at end of file
diff -r 2f557f6abbfb -r ab01e379d29e test-data/out.rscript
--- a/test-data/out.rscript Wed Jun 05 15:03:07 2024 +0000
+++ b/test-data/out.rscript Mon Dec 09 16:04:24 2024 +0000
@@ -20,16 +20,20 @@
# Import data ------------------------------------------------------------
-results <- read.delim('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmprh4qip75/files/d/2/2/dataset_d2255b46-f0f6-4900-8b9e-bd352e34f303.dat', header = TRUE)
+results <- read.delim('/tmp/tmpl4o1f_bf/files/5/2/5/dataset_52538741-d085-42da-817b-263bd4f7cf98.dat', header = TRUE)
# Format data ------------------------------------------------------------
-# Create columns from the column numbers specified
-results <- results %>% mutate(fdr = .[[4]],
- pvalue = .[[3]],
- logfc = .[[2]],
- labels = .[[1]])
+# Create columns from the column numbers specified and use the existing category_symbol column for shapes
+results <- results %>% mutate(
+ fdr = .[[4]],
+ pvalue = .[[3]],
+ logfc = .[[2]],
+ labels = .[[1]],
+)
+
+# Check if shape_col is provided
# Get names for legend
down <- unlist(strsplit('Down,Not Sig,Up', split = ","))[1]
@@ -49,7 +53,7 @@
# Specify genes to label --------------------------------------------------
# Import file with genes of interest
-labelfile <- read.delim('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmprh4qip75/files/5/e/5/dataset_5e5b8fb0-bf65-438e-9b5b-03a540d9aa5d.dat', header = TRUE)
+labelfile <- read.delim('/tmp/tmpl4o1f_bf/files/5/d/4/dataset_5d401b02-f6af-4ed9-b853-992fd4a4d044.dat', header = TRUE)
# Label the genes of interest in results table
results <- mutate(results, labels = ifelse(labels %in% labelfile[, 1], labels, ""))
@@ -61,15 +65,17 @@
# Open file to save plot as PDF
pdf("volcano_plot.pdf")
-# Set up base plot
+# Set up base plot with faceting by category_symbol instead of shapes
p <- ggplot(data = results, aes(x = logfc, y = -log10(pvalue))) +
- geom_point(aes(colour = sig)) +
scale_color_manual(values = colours) +
theme(panel.grid.major = element_blank(),
- panel.grid.minor = element_blank(),
- panel.background = element_blank(),
- axis.line = element_line(colour = "black"),
- legend.key = element_blank())
+ panel.grid.minor = element_blank(),
+ panel.background = element_blank(),
+ axis.line = element_line(colour = "black"),
+ legend.key = element_blank())
+
+# Conditional logic to use either shape or facet based on user selection
+p <- p + geom_point(aes(colour = sig)) #only add color
# Add gene labels
p <- p + geom_text_repel(data = filter(results, labels != ""), aes(label = labels),
diff -r 2f557f6abbfb -r ab01e379d29e volcanoplot.xml
--- a/volcanoplot.xml Wed Jun 05 15:03:07 2024 +0000
+++ b/volcanoplot.xml Mon Dec 09 16:04:24 2024 +0000
@@ -64,11 +64,18 @@
# Format data ------------------------------------------------------------
-# Create columns from the column numbers specified
-results <- results %>% mutate(fdr = .[[$fdr_col]],
- pvalue = .[[$pval_col]],
- logfc = .[[$lfc_col]],
- labels = .[[$label_col]])
+# Create columns from the column numbers specified and use the existing category_symbol column for shapes
+results <- results %>% mutate(
+ fdr = .[[$fdr_col]],
+ pvalue = .[[$pval_col]],
+ logfc = .[[$lfc_col]],
+ labels = .[[$label_col]],
+)
+
+# Check if shape_col is provided
+#if $shape_col:
+results <- results %>% mutate(category_symbol = .[[$shape_col]]) # Use the shape column if it exists
+#end if
# Get names for legend
down <- unlist(strsplit('$plot_options.legend_labs', split = ","))[1]
@@ -120,15 +127,25 @@
# Open file to save plot as PDF
pdf("volcano_plot.pdf")
-# Set up base plot
+# Set up base plot with faceting by category_symbol instead of shapes
p <- ggplot(data = results, aes(x = logfc, y = -log10(pvalue))) +
- geom_point(aes(colour = sig)) +
scale_color_manual(values = colours) +
theme(panel.grid.major = element_blank(),
- panel.grid.minor = element_blank(),
- panel.background = element_blank(),
- axis.line = element_line(colour = "black"),
- legend.key = element_blank())
+ panel.grid.minor = element_blank(),
+ panel.background = element_blank(),
+ axis.line = element_line(colour = "black"),
+ legend.key = element_blank())
+
+# Conditional logic to use either shape or facet based on user selection
+#if $shape_col:
+if ('$shape_or_facet' == 'facet') {
+ p <- p + facet_wrap(~ category_symbol) # Facet the plot based on category_symbol
+} else {
+ p <- p + geom_point(aes(colour = sig, shape = factor(category_symbol))) # Use shapes for categories
+}
+#else:
+p <- p + geom_point(aes(colour = sig)) #only add color
+#end if
#if $labels.label_select != "none"
# Add gene labels
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10.1007/978-3-319-24277-4