Mercurial > repos > youngkim > ezbamqc

comparison ezBAMQC/ezBAMQC @ 9:6610eedd9fae

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Uploaded
author cshl-bsr
date Wed, 30 Mar 2016 12:11:46 -0400
parents dfa3745e5fd8
children
comparison
equal deleted inserted replaced
8:82bb8c455761 9:6610eedd9fae
10 10
11 @contact: yjin@cshl.edu 11 @contact: yjin@cshl.edu
12 12
13 @status: 13 @status:
14 14
15 @version: 0.6.6 15 @version: 0.6.7
16 16
17 ''' 17 '''
18 18
19 import argparse, subprocess,traceback 19 import argparse, subprocess,traceback
20 20
870 870
871 f.write("for(i in 1:length(M1[1,])) { \n") 871 f.write("for(i in 1:length(M1[1,])) { \n")
872 872
873 f.write("nz_gene_mm[i] = length(which(M1[,i]>0))/nz_genes * 100 } \n") 873 f.write("nz_gene_mm[i] = length(which(M1[,i]>0))/nz_genes * 100 } \n")
874 874
875 f.write("bplt <- barplot(nz_gene_mm,beside=T,border='NA',space=1.5,ylim=c(0,100),ylab='Genes reproducibly detected (%)',col='blue',names.arg=colnames(MM))\n") 875 f.write("bplt <- barplot(nz_gene_mm,beside=T,border='NA',space=1.5,ylim=c(0,100),ylab='Genes reproducibly detected (%)',col='blue',names.arg=colnames(MM),las=2)\n")
876 876
877 f.write("text(y= nz_gene_mm+2, x= bplt, labels=paste(as.character(round(nz_gene_mm,digits=1)),'%',sep=''), xpd=TRUE)\n") 877 f.write("text(y= nz_gene_mm+2, x= bplt, labels=paste(as.character(round(nz_gene_mm,digits=1)),'%',sep=''), xpd=TRUE)\n")
878 878
879 f.write("dev.state = dev.off()}\n") 879 f.write("dev.state = dev.off()}\n")
880 880
954 954
955 f.write('Fn_mm[4,i] = length(which(M1[,i]>=100)) }\n') 955 f.write('Fn_mm[4,i] = length(which(M1[,i]>=100)) }\n')
956 956
957 957
958 958
959 f.write('barplot(Fn_mm,main="Gene abundance (RPM)",xlab="Sample",ylab="Frequency",col=c("green","blue","red","yellow"),legend=xname)\n') 959 f.write('barplot(Fn_mm,main="Gene abundance (RPM)",xlab="Sample",ylab="Frequency",col=c("green","blue","red","yellow"),legend=xname,las=2)\n')
960 960
961 f.write("dev.state = dev.off()\n") 961 f.write("dev.state = dev.off()\n")
962 962
963 if pe_smp_cnt > 0 : 963 if pe_smp_cnt > 0 :
964 964
1020 1020
1021 f.write('if(length(which(f[,1]>=30)) >0) {Fn_mm[5,i] = sum(f[which(f[,1]>=30),3])/f[1,2] }} \n') 1021 f.write('if(length(which(f[,1]>=30)) >0) {Fn_mm[5,i] = sum(f[which(f[,1]>=30),3])/f[1,2] }} \n')
1022 1022
1023 1023
1024 1024
1025 f.write('barplot(Fn_mm,xlab="Sample",main="Mapping Quality",ylim=c(0,1),ylab="Frequency",col=c("blue","green","yellow","orange","red"),legend=xname)\n') 1025 f.write('barplot(Fn_mm,xlab="Sample",main="Mapping Quality",ylim=c(0,1),ylab="Frequency",col=c("blue","green","yellow","orange","red"),legend=xname,las=2)\n')
1026 1026
1027 f.write("dev.state = dev.off()\n") 1027 f.write("dev.state = dev.off()\n")
1028 1028
1029 1029
1030 1030