Mercurial > repos > proteore > proteore_clusterprofiler

changeset 9:60a3897346e0 draft

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planemo upload commit eb8dd48804bfbeb0f0c8076458de65d66d7f075b-dirty
author proteore
date Tue, 18 Sep 2018 10:44:34 -0400
parents ea5fecd4aa69
children 6604d9aa7cf3
files GO-enrich.R cluster_profiler.xml
diffstat 2 files changed, 11 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/GO-enrich.R	Tue Sep 18 09:49:55 2018 -0400
+++ b/GO-enrich.R	Tue Sep 18 10:44:34 2018 -0400
@@ -28,6 +28,7 @@
   return(max(nchar(vector[1:nb_description])))
 }
 
+#used before the limit was set to 50 characters
 width_by_max_char <- function (nb_max_char) {
   if (nb_max_char < 50 ){
     width=600
@@ -49,11 +50,11 @@
                readable=TRUE)
 
   if (length(ggo@result$ID) > 0 ) {
-    ggo@result$Description <- sapply(as.vector(ggo@result$Description), function(x) {ifelse(nchar(x)>100, substr(x,1,100),x)},USE.NAMES = FALSE)
-    nb_max_char = max_str_length_10_first(ggo$Description)
-    width = width_by_max_char(nb_max_char)
+    ggo@result$Description <- sapply(as.vector(ggo@result$Description), function(x) {ifelse(nchar(x)>50, substr(x,1,50),x)},USE.NAMES = FALSE)
+    #nb_max_char = max_str_length_10_first(ggo$Description)
+    #width = width_by_max_char(nb_max_char)
     name <- paste("GGO_", ontology, "_bar-plot", sep = "")
-    png(name,height = 720, width = width)
+    png(name,height = 720, width = 600)
     p <- barplot(ggo, showCategory=10)
     print(p)
     dev.off()
@@ -77,13 +78,13 @@
   #if there are enriched GopTerms
   if (length(ego$ID)>0){
     
-    ego@result$Description <- sapply(ego@result$Description, function(x) {ifelse(nchar(x)>100, substr(x,1,100),x)},USE.NAMES = FALSE)
-    nb_max_char = max_str_length_10_first(ego$Description)
-    width = width_by_max_char(nb_max_char)
+    ego@result$Description <- sapply(ego@result$Description, function(x) {ifelse(nchar(x)>50, substr(x,1,50),x)},USE.NAMES = FALSE)
+    #nb_max_char = max_str_length_10_first(ego$Description)
+    #width = width_by_max_char(nb_max_char)
     
     if ("dotplot" %in% plot ){
     dot_name <- paste("EGO_", ontology, "_dot-plot", sep = "")
-    png(dot_name,height = 720, width = width)
+    png(dot_name,height = 720, width = 600)
     p <- dotplot(ego, showCategory=10)
     print(p)
     dev.off()
@@ -91,7 +92,7 @@
 
     if ("barplot" %in% plot ){
     bar_name <- paste("EGO_", ontology, "_bar-plot", sep = "")
-    png(bar_name,height = 720, width = width)
+    png(bar_name,height = 720, width = 600)
     p <- barplot(ego)
     print(p)
     dev.off()
--- a/cluster_profiler.xml	Tue Sep 18 09:49:55 2018 -0400
+++ b/cluster_profiler.xml	Tue Sep 18 10:44:34 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="cluter_profiler" name="clusterProfiler" version="2018.09.18.4">
+<tool id="cluter_profiler" name="clusterProfiler" version="2018.09.18.5">
     <description>
     GO terms classification and enrichment analysis
     </description>