# HG changeset patch
# User iuc
# Date 1684531560 0
# Node ID 2c4e879a81cf4e572bc42272737854fc574fa16f
# Parent  f3fefb6d825468daa611c90b6c45fb78bb3e2ce4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf

diff -r f3fefb6d8254 -r 2c4e879a81cf IsoformSwitchAnalyzeR.R
--- a/IsoformSwitchAnalyzeR.R	Tue Jan 24 18:37:14 2023 +0000
+++ b/IsoformSwitchAnalyzeR.R	Fri May 19 21:26:00 2023 +0000
@@ -4,6 +4,8 @@
         warn.conflicts = FALSE)
 library(argparse, quietly = TRUE, warn.conflicts = FALSE)
 library(dplyr, quietly = TRUE, warn.conflicts = FALSE)
+library(ggplot2, quietly = TRUE, warn.conflicts = FALSE)
+
 
 # setup R error handling to go to stderr
 options(
@@ -740,7 +742,7 @@
       file = outputFile,
       onefile = FALSE,
       height = 6,
-      width = 9
+      width = 12
     )
 
     consequenceSummary <- extractConsequenceSummary(
@@ -835,7 +837,7 @@
       file = outputFile,
       onefile = FALSE,
       height = 6,
-      width = 9
+      width = 12
     )
     splicingSummary <- extractSplicingSummary(
       SwitchList,
@@ -863,34 +865,37 @@
 
     ### Volcano like plot:
     outputFile <- file.path(getwd(), "volcanoPlot.pdf")
+
     pdf(
       file = outputFile,
       onefile = FALSE,
       height = 6,
       width = 9
     )
-    ggplot(data = SwitchList$isoformFeatures, aes(x = dIF, y = -log10(isoform_switch_q_value))) +
-      geom_point(aes(color = abs(dIF) > 0.1 &
-                       isoform_switch_q_value < 0.05), # default cutoff
-                 size = 1) +
+
+    p <- ggplot(data = SwitchList$isoformFeatures, aes(x = dIF, y = -log10(isoform_switch_q_value))) +
+      geom_point(
+        aes(color = abs(dIF) > 0.1 & isoform_switch_q_value < 0.05), # default cutoff
+        size = 1
+      ) +
       geom_hline(yintercept = -log10(0.05), linetype = "dashed") + # default cutoff
       geom_vline(xintercept = c(-0.1, 0.1), linetype = "dashed") + # default cutoff
       facet_wrap(~ condition_2) +
+      #facet_grid(condition_1 ~ condition_2) + # alternative to facet_wrap if you have overlapping conditions
       scale_color_manual("Signficant\nIsoform Switch", values = c("black", "red")) +
       labs(x = "dIF", y = "-Log10 ( Isoform Switch Q Value )") +
       theme_bw()
+    print(p)
     dev.off()
 
-
     ### Switch vs Gene changes:
     outputFile <- file.path(getwd(), "switchGene.pdf")
     pdf(
       file = outputFile,
-      onefile = FALSE,
       height = 6,
       width = 9
     )
-    ggplot(data = SwitchList$isoformFeatures,
+    p <- ggplot(data = SwitchList$isoformFeatures,
            aes(x = gene_log2_fold_change, y = dIF)) +
       geom_point(aes(color = abs(dIF) > 0.1 &
                        isoform_switch_q_value < 0.05),
@@ -901,6 +906,7 @@
       scale_color_manual("Signficant\nIsoform Switch", values = c("black", "red")) +
       labs(x = "Gene log2 fold change", y = "dIF") +
       theme_bw()
+    print(p)
     dev.off()
 
     outputFile <- file.path(getwd(), "splicingGenomewide.pdf")
@@ -908,12 +914,12 @@
       file = outputFile,
       onefile = FALSE,
       height = 6,
-      width = 9
+      width = 14
     )
     splicingGenomeWide <- extractSplicingGenomeWide(
       SwitchList,
-      featureToExtract = "all",
-      splicingToAnalyze = c("A3", "MES", "ATSS"),
+      featureToExtract = "isoformUsage",
+      splicingToAnalyze = "all",
       plot = TRUE,
       returnResult = TRUE
     )
diff -r f3fefb6d8254 -r 2c4e879a81cf isoformswitchanalyzer.xml
--- a/isoformswitchanalyzer.xml	Tue Jan 24 18:37:14 2023 +0000
+++ b/isoformswitchanalyzer.xml	Fri May 19 21:26:00 2023 +0000
@@ -25,7 +25,7 @@
                     ln -s '${functionMode.transcriptome}' './transcriptome.fasta.gz' &&
                     #set $transcriptome = './transcriptome.fasta.gz' 
                 #else
-                    ln -s '${functionMode.transcriptome}' './transcriptome.fasta'
+                    ln -s '${functionMode.transcriptome}' './transcriptome.fasta' &&
                     #set $transcriptome = './transcriptome.fasta' 
                 #end if
                 #if $functionMode.genomeAnnotation.is_of_type("gtf.gz"):
@@ -33,7 +33,7 @@
                     #set $annotation = './annotation.gtf.gz' 
                 #else
                     ln -s '${functionMode.genomeAnnotation}' './annotation.gtf' &&
-                        #set $annotation = './annotation.gtf' 
+                    #set $annotation = './annotation.gtf' 
                 #end if
                 mkdir -p 'input_files' &&
                 #if $functionMode.countFiles != 'disabled':
@@ -766,7 +766,7 @@
                 </element>
                 <element name="splicingGenomewide" ftype="pdf">
                     <assert_contents>
-                        <has_size value="68069" delta="300"/>
+                        <has_size value="165752" delta="300"/>
                     </assert_contents>
                 </element>
                 <element name="splicingSummary" ftype="pdf">
@@ -776,12 +776,12 @@
                 </element>
                 <element name="switchGene" ftype="pdf">
                     <assert_contents>
-                        <has_size value="3611" delta="300"/>
+                        <has_size value="18432" delta="300"/>
                     </assert_contents>
                 </element>
                 <element name="volcanoPlot" ftype="pdf">
                     <assert_contents>
-                        <has_size value="3611" delta="300"/>
+                        <has_size value="20147" delta="300"/>
                     </assert_contents>
                 </element>
             </output_collection>
@@ -895,7 +895,7 @@
                 </element>
                 <element name="splicingGenomewide" ftype="pdf">
                     <assert_contents>
-                        <has_size value="68069" delta="300"/>
+                        <has_size value="165752" delta="300"/>
                     </assert_contents>
                 </element>
                 <element name="splicingSummary" ftype="pdf">
@@ -905,12 +905,12 @@
                 </element>
                 <element name="switchGene" ftype="pdf">
                     <assert_contents>
-                        <has_size value="3611" delta="300"/>
+                        <has_size value="18432" delta="300"/>
                     </assert_contents>
                 </element>
                 <element name="volcanoPlot" ftype="pdf">
                     <assert_contents>
-                        <has_size value="3611" delta="300"/>
+                        <has_size value="20147" delta="300"/>
                     </assert_contents>
                 </element>
             </output_collection>
diff -r f3fefb6d8254 -r 2c4e879a81cf macros.xml
--- a/macros.xml	Tue Jan 24 18:37:14 2023 +0000
+++ b/macros.xml	Fri May 19 21:26:00 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.20.0</token>
-    <token name="@SUFFIX_VERSION@">0</token>
+    <token name="@SUFFIX_VERSION@">1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-isoformswitchanalyzer</requirement>