Commit 0cf89e92 authored by Christoph Ziegenhain's avatar Christoph Ziegenhain
Browse files

fix NA in summary plots

parent b2915bcc

statsFUN.R

+2 −2
Original line number Diff line number Diff line
@@ -84,7 +84,7 @@ totReadCountBarplot<-function(typeCount,fillcol){ 
    mutate(perc=100*tot/sum(tot))



  sumBar$type<-factor(sumBar$type,

                      levels=rev(c("Exon","Intron","Intergenic","Ambiguity",

                      levels=rev(c("Exon","Intron","Intergenic","Ambiguity","MultiMapping",

                                   "Unmapped","User","Unused BC")))



  bar <- ggplot(sumBar, aes(x=1, y=perc, fill=type))+
@@ -113,7 +113,7 @@ totReadBoxplot<-function(typeCount,fillcol){ 
         mutate( perc = 100*N/sum(N))



  dpf$type<-factor(dpf$type,

              levels = c("Exon","Intron" ,"Intergenic" ,"Ambiguity","Unmapped","User"))

              levels = c("Exon","Intron" ,"Intergenic" ,"Ambiguity","MultiMapping","Unmapped","User"))



  box<-ggplot(dpf, aes(x=type, y=perc , fill=type))  +

        geom_boxplot()+

zUMIs-stats2.R

+2 −2
Original line number Diff line number Diff line
@@ -15,8 +15,8 @@ suppressMessages(library(cowplot)) 
myYaml<-commandArgs(trailingOnly = T)

opt   <-read_yaml(myYaml)

setwd(opt$out_dir)

featColors<-c("#1A5084", "#914614" ,"#118730","grey33","tan1","gold1","grey73","firebrick3")

names(featColors)<-c("Exon","Intron+Exon","Intron","Unmapped","Ambiguity","Intergenic","Unused BC","User")

featColors<-c("#1A5084", "#914614" ,"#118730","grey33","tan1","#631879FF","gold1","grey73","firebrick3")

names(featColors)<-c("Exon","Intron+Exon","Intron","Unmapped","Ambiguity","MultiMapping","Intergenic","Unused BC","User")

#####################################



source(paste0(opt$zUMIs_directory,"/statsFUN.R"))

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