Mercurial > repos > iuc > mageck_gsea

annotate test-data/out.count.Rnw @ 2:82a180e6b582 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
author iuc
date Wed, 04 Apr 2018 11:03:05 -0400
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82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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1 % This is a template file for Sweave used in MAGeCK
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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2 % Author: Wei Li, Shirley Liu lab
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3 % Do not modify lines beginning with "#__".
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4 \documentclass{article}
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6 \usepackage{amsmath}
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7 \usepackage{amscd}
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8 \usepackage[tableposition=top]{caption}
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9 \usepackage{ifthen}
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10 \usepackage{fullpage}
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11 \usepackage[utf8]{inputenc}
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12 % \usepackage{longtable}
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14 \begin{document}
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15 \setkeys{Gin}{width=0.9\textwidth}
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17 \title{MAGeCK Count Report}
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18 \author{Wei Li}
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20 \maketitle
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23 \tableofcontents
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25 \section{Summary}
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27 %Function definition
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28 <<label=funcdef,include=FALSE,echo=FALSE>>=
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29 genreporttable<-function(filelist,labellist,reads,mappedreads){
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30 xtb=data.frame(Label=labellist,Reads=reads,MappedReads=mappedreads,MappedPercentage=mappedreads/reads);
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31 colnames(xtb)=c("Label","Reads","Mapped","Percentage");
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32 return (xtb);
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33 }
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34 genreporttable2<-function(filelist,labellist,sgrnas,zerocounts,gini){
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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35 xtb=data.frame(Label=labellist,TotalsgRNAs=sgrnas,ZeroCounts=zerocounts,GiniIndex=gini);
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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36 colnames(xtb)=c("Label","TotalsgRNA","ZeroCounts","GiniIndex");
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37 return (xtb);
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38 }
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39 genreporttable3<-function(filelist,labellist){
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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40 xtb=data.frame(File=filelist,Label=labellist);
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41 colnames(xtb)=c("File","Label");
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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42 return (xtb);
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43 }
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46 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
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47 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
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48 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
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49 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F");
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53 genboxplot<-function(filename,...){
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54 #slmed=read.table(filename,header=T)
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55 slmed=read.table(filename,header=T)
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56 slmat=as.matrix(slmed[,c(-1,-2)])
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57 slmat_log=log2(slmat+1)
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58
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59 boxplot(slmat_log,pch='.',las=2,ylab='log2(read counts)',cex.axis=0.8,...)
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60 }
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63 genhistplot<-function(filename,isfile=T,...){
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64 if(isfile){
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65 slmed=read.table(filename,header=T)
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66 }else{
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67 slmed=filename;
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68 }
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69 tabsmat=as.matrix(log2(slmed[,c(-1,-2)]+1))
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70 colnames(tabsmat)=colnames(slmed)[c(-1,-2)]
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71 samplecol=colors[((1:ncol(tabsmat)) %% length(colors)) ]
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72 if(ncol(tabsmat)>=1){
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73 histlist=lapply(1:ncol(tabsmat),function(X){ return (hist(tabsmat[,X],plot=F,breaks=40)) })
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74 xrange=range(unlist(lapply(histlist,function(X){X$mids})))
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75 yrange=range(unlist(lapply(histlist,function(X){X$counts})))
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76 hst1=histlist[[1]]
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77 plot(hst1$mids,hst1$counts,type='b',pch=20,xlim=c(0,xrange[2]*1.2),ylim=c(0,yrange[2]*1.2),xlab='log2(counts)',ylab='Frequency',main='Distribution of read counts',col = samplecol[1], ... )
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78 }
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79 if(ncol(tabsmat)>=2){
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80 for(i in 2:ncol(tabsmat)){
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81 hstn=histlist[[i]]
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82 lines(hstn$mids,hstn$counts,type='b',pch=20,col=samplecol[i])
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83 }
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84 }
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85 legend('topright',colnames(tabsmat),pch=20,lwd=1,col=samplecol)
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86 }
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87
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89
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90 genclustering<-function(filename,...){
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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91 #slmed=read.table(filename,header=T)
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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92 slmed=read.table(filename,header=T)
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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93 slmat=as.matrix(slmed[,c(-1,-2)])
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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94 slmat_log=log2(slmat+1)
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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95
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96 result=tryCatch({
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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97 library(gplots);
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98 heatmap.2(cor(slmat_log),trace = 'none',density.info = 'none',cexRow = 0.8,cexCol = 0.8,offsetRow = -0.2,offsetCol = -0.2)
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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99 }, error=function(e){
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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100 heatmap(cor(slmat_log),scale='none',cexRow = 0.8,cexCol = 0.8,cex.axis=0.8,...)
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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101 });
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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102 }
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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103
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104 ctfit_tx=0;
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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105
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106
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107 panel.plot<-function(x,y,textnames=names(x),...){
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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108 par(new=TRUE)
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109 m<-cbind(x,y)
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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110 plot(m,pch=20,xlim = range(x)*1.1,ylim=range(y)*1.1,...)
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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111 text(x,y,textnames,...)
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112 }
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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113
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114
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115 genpcaplot<-function(filename,...){
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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116 #slmed=read.table(filename,header=T)
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117 slmed=read.table(filename,header=T)
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118 slmat=as.matrix(slmed[,c(-1,-2)])
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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119 slmat_log=log2(slmat+1)
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120 ctfit_tx<<-prcomp(t(slmat_log),center=TRUE)
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121
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122 # par(mfrow=c(2,1));
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123 samplecol=colors[((1:ncol(slmat)) %% length(colors)) ]
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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124 # first 2 PCA
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125 #plot(ctfit_tx$x[,1],ctfit_tx$x[,2],xlab='PC1',ylab='PC2',main='First 2 PCs',col=samplecol,xlim=1.1*range(ctfit_tx$x[,1]),ylim=1.1*range(ctfit_tx$x[,2]));
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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126 #text(ctfit_tx$x[,1],ctfit_tx$x[,2],rownames(ctfit_tx$x),col=samplecol);
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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127 # par(mfrow=c(1,1));
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128 if(length(samplecol)>2){
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129 pairs(ctfit_tx$x[,1:3],panel=panel.plot,textnames=rownames(ctfit_tx$x),main='First 3 principle components',col=samplecol)
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130 }else{
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131 if(length(samplecol)>1){
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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132 pairs(ctfit_tx$x[,1:2],panel=panel.plot,textnames=rownames(ctfit_tx$x),main='First 2 principle components',col=samplecol)
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133 }
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134 }
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135
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136
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137 }
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138
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139 genpcavar<-function(){
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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140 # % variance
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141 varpca=ctfit_tx$sdev^2
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iuc
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142 varpca=varpca/sum(varpca)*100;
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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143 if(length(varpca)>10){
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144 varpca=varpca[1:10];
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145 }
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146 plot(varpca,type='b',lwd=2,pch=20,xlab='PCs',ylab='% Variance explained');
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147 }
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148
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149 @
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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150
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151 %__FILE_SUMMARY__
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152
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153 The statistics of comparisons are listed in Table 1 and Table 2.
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154 The corresponding fastq files in each row are listed in Table 3.
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155
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156 <<label=tab1,echo=FALSE,results=tex>>=
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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157 library(xtable)
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158 filelist=c("input_0.gz");
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159 labellist=c("test1_fastq_gz");
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160 reads=c(2500);
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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161 mappedreads=c(1453);
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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162 totalsgrnas=c(2550);
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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163 zerocounts=c(1276);
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164 giniindex=c(0.5266899931488773);
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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165
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166 cptable=genreporttable(filelist,labellist,reads,mappedreads);
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167 print(xtable(cptable, caption = "Summary of comparisons", label = "tab:one",
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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168 digits = c(0, 0, 0, 0,2),
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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169 align=c('c', 'c','c', 'c', 'c'),
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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170 table.placement = "tbp",
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171 caption.placement = "top"))
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172 @
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173
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174 <<label=tab2,echo=FALSE,results=tex>>=
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175 library(xtable)
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176 cptable=genreporttable2(filelist,labellist,totalsgrnas,zerocounts,giniindex);
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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177 print(xtable(cptable, caption = "Summary of comparisons", label = "tab:two",
82a180e6b582 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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178 digits = c(0, 0,0, 0,2),
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179 align=c('c', 'c','c', 'c', 'c'),
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180 table.placement = "tbp",
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181 caption.placement = "top"))
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182 @
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188 <<label=tab3,echo=FALSE,results=tex>>=
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189 library(xtable)
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190 cptable=genreporttable3(filelist,labellist);
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191 print(xtable(cptable, caption = "Summary of samples", label = "tab:three",
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192 digits = c(0,0, 0),
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193 align=c('c', 'p{9cm}', 'c'),
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194 table.placement = "tbp",
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195 caption.placement = "top"))
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196 @
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201 The meanings of the columns are as follows.
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202
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203 \begin{itemize}
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204 \item \textbf{Row}: The row number in the table;
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205 \item \textbf{File}: The filename of fastq file;
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206 \item \textbf{Label}: Assigned label;
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207 \item \textbf{Reads}: The total read count in the fastq file;
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208 \item \textbf{Mapped}: Reads that can be mapped to gRNA library;
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209 \item \textbf{Percentage}: The percentage of mapped reads;
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210 \item \textbf{TotalsgRNAs}: The number of sgRNAs in the library;
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211 \item \textbf{ZeroCounts}: The number of sgRNA with 0 read counts;
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212 \item \textbf{GiniIndex}: The Gini Index of the read count distribution. Gini index can be used to measure the evenness of the read counts, and a smaller value means a more even distribution of the read counts.
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213 \end{itemize}
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214
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217 \newpage\section{Normalized read count distribution of all samples}
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218 The following figure shows the distribution of median-normalized read counts in all samples.
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221 <<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>=
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222 genboxplot("output.count_normalized.txt");
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223 @
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224
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225 The following figure shows the histogram of median-normalized read counts in all samples.
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228 <<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>=
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229 genhistplot("output.count_normalized.txt");
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230 @
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232 %__INDIVIDUAL_PAGE__
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236 \end{document}
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237