c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 centos:centos6
using docker
+ set -o pipefail
+ countisofile=input_1/isoforms.count_table
++ head -n 1 input_1/isoforms.count_table
++ awk '-F\t' '{print NF-1}'
+ numsample=6
++ expr 100 '*' 6
+ histoheight=600
+ cat
+ docker run -v /data/user2/work/89:/data/user2/work/89 -w /data/user2/work/89 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 R --vanilla

R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(reshape2)
> library(Cairo)
> library(ggplot2)
> library(ggridges)

Attaching package: 'ggridges'

The following object is masked from 'package:ggplot2':

    scale_discrete_manual

> data=read.table("input_1/isoforms.count_table",sep="\t",header=T,row.names=1)
> df=melt(data)
No id variables; using all as measure variables
> df=df[df$value>0.1,]
> CairoPNG("histo.count.png",width=800,height=min(600,10000))
> ggplot(df, aes(x = value, y = variable, fill = variable,alpha = 0.5)) + geom_density_ridges2() + scale_x_log10() +
+  theme(legend.justification=c(1,0), legend.position=c(1,1))
Picking joint bandwidth of 0.109
> dev.off()
null device 
          1 
> 
+ '[' -e '' ']'
+ touch histo.temp.sample.txt
+ head -n 1 input_1/isoforms.count_table
+ sed 's/\t/\n/g'
+ tail -n+2
+ awk '-F\t' 'FILENAME==ARGV[1]{cat[$1]=$2} FILENAME==ARGV[2]{if(FNR==1){print "id\tcondition"}; if(cat[$1]==""){cat[$1]=$1}; print $1"\t"cat[$1]}' histo.temp.sample.txt /dev/stdin
+ samplefile=histo.sample.input.txt
++ expr 10 '*' 6 + 600
+ clusterheight=660
++ expr 10 '*' 6 + 700
+ clusterwidth=760
++ expr 300 + 10 '*' 6
+ mdslegwidth=360
+ cat
+ docker run -v /data/user2/work/89:/data/user2/work/89 -w /data/user2/work/89 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 R --vanilla

R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Cairo)
> countData=round(read.table("input_1/isoforms.count_table",sep="\t",header=T,row.names=1))
> colData <- read.csv("histo.sample.input.txt", row.names=1, sep="\t")
> 
> library(RColorBrewer)
> library(pheatmap)
> c=cor(countData)
> for(i in 1:ncol(c)){c[is.na(c[,i]),i]=0}
> sampleDists <- as.dist(1-c)
> sampleDistMatrix <- as.matrix(as.dist(1-c))
> rownames(sampleDistMatrix) <- rownames(colData)
> colnames(sampleDistMatrix) <- rownames(colData)
> colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255)
> CairoPNG(paste("sampleDist.png",sep=""),width=min(760,5000),height = min(660,5100))
> pheatmap(sampleDistMatrix, clustering_distance_rows=sampleDists, clustering_distance_cols=sampleDists, col=colors)
> dev.off()
null device 
          1 
> 
> library(vegan)
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-5
> mds1<-monoMDS(as.dist(1-c))
> library(ggplot2)
> shape=rownames(colData)
> if(length(shape)>6){
+  for(i in 1:6){shape[seq(i,length(shape),6)]=paste(shape[seq(i,length(shape),6)],collapse=",")}
+ }
> mdslegwidth=min(360,4000)
> color=colData[,1]
> p = ggplot(as.data.frame(mds1$points), aes(x=MDS1, y=MDS2, shape=shape, colour=color))
> p = p + geom_point(size=5)
> p = p + theme_bw(base_size=35)
> p = p + theme(legend.justification=c(0,1), legend.position=c(1,1))+theme(plot.margin = margin(0, mdslegwidth, 0, 0, "pt"))
> library(Cairo)
> CairoPNG(filename = paste("MDSdetail.png",sep=""),width=min(760,2000)+mdslegwidth,height = min(660,2100))
> plot(p)
> dev.off()
null device 
          1 
> p = ggplot(as.data.frame(mds1$points), aes(x=MDS1, y=MDS2, colour=color))
> p = p + geom_point(size=5)
> p = p + theme_bw(base_size=35)
> p = p + theme(legend.justification=c(0,1), legend.position=c(1,1))+theme(plot.margin = margin(0, mdslegwidth, 0, 0, "pt"))
> library(Cairo)
> CairoPNG(filename = paste("MDS.png",sep=""),width=min(760,2000)+mdslegwidth,height = min(660,2100))
> plot(p)
> dev.off()
null device 
          1 
> 
> 
> 
+ post_processing
+ '[' 1 = 1 ']'
+ '[' 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' = 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' ']'
+ docker run -v /data/user2/work/89:/data/user2/work/89 -w /data/user2/work/89 -u root -i --rm centos:centos6 chmod -R a=rXw .
+ echo 0
+ exit