Mercurial > repos > iuc > mageck_count

annotate test-data/output_summary.Rnw @ 3:d8f26ae1e909 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
author iuc
date Thu, 19 Apr 2018 05:34:34 -0400
parents 9527a3d6ebd2
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1 % This is a template file for Sweave used in MAGeCK
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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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13 \begin{document}
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14 \setkeys{Gin}{width=0.9\textwidth}
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16 \title{MAGeCK Comparison Report}
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17 \author{Wei Li}
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19 \maketitle
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22 \tableofcontents
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24 \section{Summary}
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26 %Function definition
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27 <<label=funcdef,include=FALSE,echo=FALSE>>=
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28 genreporttable<-function(comparisons,ngenes,direction,fdr1,fdr5,fdr25){
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29 xtb=data.frame(Comparison=comparisons,Genes=ngenes,Selection=direction,FDR1=fdr1,FDR5=fdr5,FDR25=fdr25);
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30 colnames(xtb)=c("Comparison","Genes","Selection","FDR1%","FDR5%","FDR25%");
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31 return (xtb);
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32 }
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33 @
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35 The statistics of comparisons is as indicated in the following table.
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37 <<label=tab1,echo=FALSE,results=tex>>=
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38 library(xtable)
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39 comparisons=c("HL60_final,KBM7_final_vs_HL60_initial,KBM7_initial neg.","HL60_final,KBM7_final_vs_HL60_initial,KBM7_initial pos.");
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40 ngenes=c(100,100);
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41 direction=c("negative","positive");
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42 fdr1=c(0,0);
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43 fdr5=c(2,0);
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44 fdr25=c(9,1);
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46 cptable=genreporttable(comparisons,ngenes,direction,fdr1,fdr5,fdr25);
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47 print(xtable(cptable, caption = "Summary of comparisons", label = "tab:one",
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48 digits = c(0, 0, 0, 0, 0, 0, 0),
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49 table.placement = "tbp",
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50 caption.placement = "top"))
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51 @
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52
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53 The meanings of the columns are as follows.
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54
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55 \begin{itemize}
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56 \item \textbf{Comparison}: The label for comparisons;
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57 \item \textbf{Genes}: The number of genes in the library;
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58 \item \textbf{Selection}: The direction of selection, either positive selection or negative selection;
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59 \item \textbf{FDR1\%}: The number of genes with FDR $<$ 1\%;
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60 \item \textbf{FDR5\%}: The number of genes with FDR $<$ 5\%;
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61 \item \textbf{FDR25\%}: The number of genes with FDR $<$ 25\%;
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62 \end{itemize}
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63
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64 The following figures show:
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65
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66 \begin{itemize}
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67 \item Individual sgRNA read counts of selected genes in selected samples;
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68 \item The distribution of RRA scores and p values of all genes; and
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69 \item The RRA scores and p values of selected genes.
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70 \end{itemize}
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71
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73 \newpage\section{Comparison results of HL60 final,KBM7 final vs HL60 initial,KBM7 initial neg.}
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74
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75 The following figure shows the distribution of RRA score in the comparison HL60 final,KBM7 final vs HL60 initial,KBM7 initial neg., and the RRA scores of 10 genes.
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76
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77 <<echo=FALSE>>=
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78 gstable=read.table('output.gene_summary.txt',header=T)
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79 @
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80 %
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81
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83 <<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>=#
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84 #
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85 # parameters
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86 # Do not modify the variables beginning with "__"
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87
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88 # gstablename='__GENE_SUMMARY_FILE__'
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89 startindex=3
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90 # outputfile='__OUTPUT_FILE__'
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91 targetgenelist=c("ACIN1","ACTR8","AHCY","ACLY","AATF","AGBL5","AHCTF1","ABT1","ADIRF","ABCF1")
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92 # samplelabel=sub('.\w+.\w+$','',colnames(gstable)[startindex]);
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93 samplelabel='HL60_final,KBM7_final_vs_HL60_initial,KBM7_initial neg.'
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94
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95
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96 # You need to write some codes in front of this code:
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97 # gstable=read.table(gstablename,header=T)
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98 # pdf(file=outputfile,width=6,height=6)
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99
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100
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101 # set up color using RColorBrewer
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102 #library(RColorBrewer)
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103 #colors <- brewer.pal(length(targetgenelist), "Set1")
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104
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105 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
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106 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
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107 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
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108 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
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109
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110 ######
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111 # function definition
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112
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113 plotrankedvalues<-function(val, tglist, ...){
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114
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115 plot(val,log='y',ylim=c(max(val),min(val)),type='l',lwd=2, ...)
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116 if(length(tglist)>0){
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117 for(i in 1:length(tglist)){
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118 targetgene=tglist[i];
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119 tx=which(names(val)==targetgene);ty=val[targetgene];
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120 points(tx,ty,col=colors[(i %% length(colors)) ],cex=2,pch=20)
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121 # text(tx+50,ty,targetgene,col=colors[i])
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122 }
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123 legend('topright',tglist,pch=20,pt.cex = 2,cex=1,col=colors)
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124 }
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125 }
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126
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127
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128
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129 plotrandvalues<-function(val,targetgenelist, ...){
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130 # choose the one with the best distance distribution
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131
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132 mindiffvalue=0;
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133 randval=val;
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134 for(i in 1:20){
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135 randval0=sample(val)
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136 vindex=sort(which(names(randval0) %in% targetgenelist))
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137 if(max(vindex)>0.9*length(val)){
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138 # print('pass...')
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139 next;
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140 }
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141 mindiffind=min(diff(vindex));
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142 if (mindiffind > mindiffvalue){
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143 mindiffvalue=mindiffind;
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144 randval=randval0;
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145 # print(paste('Diff: ',mindiffvalue))
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146 }
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147 }
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148 plot(randval,log='y',ylim=c(max(randval),min(randval)),pch=20,col='grey', ...)
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149
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150 if(length(targetgenelist)>0){
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151 for(i in 1:length(targetgenelist)){
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152 targetgene=targetgenelist[i];
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153 tx=which(names(randval)==targetgene);ty=randval[targetgene];
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154 points(tx,ty,col=colors[(i %% length(colors)) ],cex=2,pch=20)
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155 text(tx+50,ty,targetgene,col=colors[i])
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156 }
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157 }
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158
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159 }
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160
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161
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162
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163
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164 # set.seed(1235)
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165
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166
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167
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168 pvec=gstable[,startindex]
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169 names(pvec)=gstable[,'id']
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170 pvec=sort(pvec);
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171
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172 plotrankedvalues(pvec,targetgenelist,xlab='Genes',ylab='RRA score',main=paste('Distribution of RRA scores in \n',samplelabel))
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173
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174 # plotrandvalues(pvec,targetgenelist,xlab='Genes',ylab='RRA score',main=paste('Distribution of RRA scores in \n',samplelabel))
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175
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176
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177 pvec=gstable[,startindex+1]
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178 names(pvec)=gstable[,'id']
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179 pvec=sort(pvec);
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180
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181 plotrankedvalues(pvec,targetgenelist,xlab='Genes',ylab='p value',main=paste('Distribution of p values in \n',samplelabel))
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182
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183 # plotrandvalues(pvec,targetgenelist,xlab='Genes',ylab='p value',main=paste('Distribution of p values in \n',samplelabel))
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184
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185
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186
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187 # you need to write after this code:
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188 # dev.off()
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189
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190
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191
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192
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193 @
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194 %%
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195 \clearpage
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196 \newpage
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197 The following figures show the distribution of sgRNA read counts (normalized) of selected genes in selected samples.
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198 %
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199
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200
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201 <<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>=
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202 par(mfrow=c(2,2));
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203
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204 # parameters
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205 # Do not modify the variables beginning with "__"
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206 targetmat=list(c(561.4907165816957,824.0396348113272,428.37415340969943,579.047491896501),c(3424.79939695118,3818.2871009576584,1992.3498917052,690.0506672205338),c(846.6456878299913,985.6508562937211,335.0024675413113,415.97581680707134),c(2432.636481525409,2122.257249136931,1067.465489792653,155.6333179800872),c(1308.1851773762019,2186.1913587343615,1482.5909580453515,997.3120339679854),c(405.68439208520414,268.16807081144486,170.34023773287015,109.85881269182627),c(640.8637498157573,559.4234589775174,711.6436598617687,632.2603542941043),c(946.5969148654764,470.6260845366416,663.0651476194316,457.74505288260946),c(246.9383256170808,177.59474888175154,28.39003962214503,0.0),c(568.8400715107754,612.7018836420428,564.0154538266146,270.64176251684285))
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207 targetgene="ACIN1"
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208 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
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209
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210 # set up color using RColorBrewer
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211 #library(RColorBrewer)
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212 #colors <- brewer.pal(length(targetgenelist), "Set1")
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213
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214 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
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215 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
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216 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
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217 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
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218
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219
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220 ## code
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221
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222 targetmatvec=unlist(targetmat)+1
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223 yrange=range(targetmatvec[targetmatvec>0]);
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224 # yrange[1]=1; # set the minimum value to 1
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225 for(i in 1:length(targetmat)){
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226 vali=targetmat[[i]]+1;
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227 if(i==1){
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228 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
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229 axis(1,at=1:length(vali),labels=(collabel),las=2)
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230 # lines(0:100,rep(1,101),col='black');
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231 }else{
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232 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
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233 }
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234 }
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235
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236
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237
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238 # parameters
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239 # Do not modify the variables beginning with "__"
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240 targetmat=list(c(2484.0819660289676,2349.578527705573,2172.7843657481662,910.9126552363929),c(992.1629154257711,1005.1862786707138,743.8190381001997,200.26346063614164),c(1267.0287897733551,1156.1418152202027,251.09412821363824,42.34141739164138),c(1500.738276518092,1315.977089213779,800.5991173444897,1476.2277955464156),c(1925.5309914189038,2054.7712445618654,194.94493873872918,235.16652091844063),c(351.29916561001374,781.4168950797068,227.75120674654121,624.2498158686586),c(1719.74905340467,1006.9622261595313,356.45271970026533,222.0063506480656),c(903.9706562768137,1445.6212558974576,1482.5909580453515,1055.1023468944147),c(651.152846716469,1081.552020689867,576.0023594448536,1072.2677863775127),c(285.1549712482957,408.46792242802854,99.0496937928171,44.630142656054424))
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241 targetgene="ACTR8"
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242 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
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243
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244 # set up color using RColorBrewer
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245 #library(RColorBrewer)
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246 #colors <- brewer.pal(length(targetgenelist), "Set1")
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247
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248 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
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249 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
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250 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
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251 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
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252
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253
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254 ## code
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255
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256 targetmatvec=unlist(targetmat)+1
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257 yrange=range(targetmatvec[targetmatvec>0]);
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258 # yrange[1]=1; # set the minimum value to 1
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259 for(i in 1:length(targetmat)){
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260 vali=targetmat[[i]]+1;
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261 if(i==1){
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262 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
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263 axis(1,at=1:length(vali),labels=(collabel),las=2)
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264 # lines(0:100,rep(1,101),col='black');
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265 }else{
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266 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
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267 }
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268 }
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269
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270
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271
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272 # parameters
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273 # Do not modify the variables beginning with "__"
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274 targetmat=list(c(301.3235520922712,657.1005708624807,228.38209651592223,137.32351586478285),c(1142.0897559789987,1099.311495578042,112.92926871919911,100.70391163417409),c(789.3207193831689,671.3081507730209,723.6305654800077,588.7745742702564),c(392.45555321286054,412.0198174056636,334.37157777193033,213.99581222261992),c(2009.3136376104133,2235.917888421252,2437.1271791188055,1937.9781176417478),c(1071.5359486598327,406.69197493921104,645.4002340767636,349.602784139093),c(61.7345814042702,218.44154112455442,614.4866353770946,452.5954210376801),c(651.152846716469,879.0940069646701,237.21455328725622,18.88198343140764),c(1625.6773103124485,1410.1023061211074,2146.286995434164,1986.613529510525),c(1053.8974968300413,882.6459019423052,106.6203710253891,105.85354347910344))
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275 targetgene="AHCY"
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276 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
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277
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278 # set up color using RColorBrewer
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279 #library(RColorBrewer)
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280 #colors <- brewer.pal(length(targetgenelist), "Set1")
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281
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282 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
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283 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
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284 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
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285 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
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286
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287
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288 ## code
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289
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290 targetmatvec=unlist(targetmat)+1
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291 yrange=range(targetmatvec[targetmatvec>0]);
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292 # yrange[1]=1; # set the minimum value to 1
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293 for(i in 1:length(targetmat)){
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294 vali=targetmat[[i]]+1;
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295 if(i==1){
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296 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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297 axis(1,at=1:length(vali),labels=(collabel),las=2)
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298 # lines(0:100,rep(1,101),col='black');
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299 }else{
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300 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
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301 }
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302 }
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303
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304
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305
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306 # parameters
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307 # Do not modify the variables beginning with "__"
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308 targetmat=list(c(1268.498660759171,1411.8782536099247,1136.2324746551822,603.6512884889412),c(327.78122983695846,454.642557137284,51.73296108924205,24.031615276336996),c(132.28838872343613,241.5288584791821,123.02350502929512,65.80085135187511),c(495.34652221997754,586.0626713097802,279.4841678357833,243.74924065998954),c(1009.8013672555626,1102.8633905556771,1237.174837756142,1004.7503910773278),c(877.5129785321263,715.7068379934587,538.1489732819936,594.496387431289),c(1594.8100196103135,1108.1912330221296,605.6541786057605,127.59643349102738),c(314.5523909646148,252.1845434120872,88.95545748272109,359.9020478289517),c(512.984974049769,269.94401830026237,205.67006481820619,126.45207085882086),c(761.3931706526657,475.9539270030942,559.5992254409475,596.7851126957021))
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309 targetgene="ACLY"
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310 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
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311
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312 # set up color using RColorBrewer
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313 #library(RColorBrewer)
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314 #colors <- brewer.pal(length(targetgenelist), "Set1")
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315
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316 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
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317 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
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318 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
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319 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
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320
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321
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322 ## code
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323
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324 targetmatvec=unlist(targetmat)+1
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325 yrange=range(targetmatvec[targetmatvec>0]);
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326 # yrange[1]=1; # set the minimum value to 1
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327 for(i in 1:length(targetmat)){
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328 vali=targetmat[[i]]+1;
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329 if(i==1){
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330 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
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331 axis(1,at=1:length(vali),labels=(collabel),las=2)
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332 # lines(0:100,rep(1,101),col='black');
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333 }else{
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334 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
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335 }
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336 }
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337
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338
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339
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340 par(mfrow=c(1,1));
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341 @
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342 %
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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343
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344
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345 <<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>=
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346 par(mfrow=c(2,2));
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347
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348 # parameters
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349 # Do not modify the variables beginning with "__"
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350 targetmat=list(c(659.9720726313648,809.832054900787,880.7221180558769,802.1982051767731),c(724.6463960072668,1086.8798631563195,695.2405258578626,307.26136674745163),c(836.3565909292796,1289.3378768815162,468.75109865008346,177.94838930811443),c(367.46774645398926,571.85509139924,300.30353022535627,116.72498848506541),c(518.8644579930328,632.2373060190355,627.7353205340956,308.9779106957614),c(405.68439208520414,259.28833336735727,324.27734146183434,166.5047629860492),c(2096.0360257735547,1960.6460276545372,1573.4390848362154,629.9716290296913),c(277.8056163192159,435.1071347602913,182.32714335110919,0.0),c(995.1026573974029,477.7298744919117,728.0467938656747,275.21921304566894),c(2185.6981559083283,1482.9161531626255,1741.8866532609427,1862.4501839161173))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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351 targetgene="AATF"
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352 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
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353
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354 # set up color using RColorBrewer
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355 #library(RColorBrewer)
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356 #colors <- brewer.pal(length(targetgenelist), "Set1")
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357
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358 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
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359 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
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360 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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361 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
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362
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363
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364 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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365
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366 targetmatvec=unlist(targetmat)+1
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367 yrange=range(targetmatvec[targetmatvec>0]);
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368 # yrange[1]=1; # set the minimum value to 1
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369 for(i in 1:length(targetmat)){
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370 vali=targetmat[[i]]+1;
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371 if(i==1){
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372 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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373 axis(1,at=1:length(vali),labels=(collabel),las=2)
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374 # lines(0:100,rep(1,101),col='black');
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375 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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376 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
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377 }
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378 }
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379
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380
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381
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382 # parameters
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383 # Do not modify the variables beginning with "__"
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384 targetmat=list(c(640.8637498157573,602.0461987091378,307.2433176885473,192.82510352679924),c(354.23890758164566,280.5997032331675,204.4082852794442,275.79139436177223),c(779.0316224824572,932.3724316291956,778.5179754161547,905.1908420753603),c(624.6951689717818,554.0956165110648,370.96318439602834,558.4489645167836),c(1133.270530064103,1394.1187787217498,639.0913363829536,1131.2024619361487),c(423.32284391499564,412.0198174056636,224.59675789963623,426.84726181303336),c(296.91393913482335,829.3674772777797,489.5704610396565,1233.0507362025292),c(684.959879390236,546.9918265557948,394.30610586312537,566.4595029422292),c(440.96129574478715,630.461358530218,434.6830511035094,457.1728715665062),c(1108.2827233052317,1969.5257650986248,1066.2037102538911,1333.7546478367033))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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385 targetgene="AGBL5"
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386 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
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387
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388 # set up color using RColorBrewer
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389 #library(RColorBrewer)
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390 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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391
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392 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
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393 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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394 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
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395 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
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396
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397
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398 ## code
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399
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400 targetmatvec=unlist(targetmat)+1
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401 yrange=range(targetmatvec[targetmatvec>0]);
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402 # yrange[1]=1; # set the minimum value to 1
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403 for(i in 1:length(targetmat)){
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404 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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405 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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406 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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407 axis(1,at=1:length(vali),labels=(collabel),las=2)
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408 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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409 }else{
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410 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
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411 }
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412 }
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413
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414
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415
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416 # parameters
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417 # Do not modify the variables beginning with "__"
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418 targetmat=list(c(196.96271209933826,301.9110730989776,423.9579250240324,34.33087896619571),c(1106.8128523194157,1056.6887558464218,1743.1484327997048,807.3478370217025),c(748.1643317803222,488.3855594248168,239.73811236478022,477.77139894622366),c(1095.053884432888,882.6459019423052,837.8216137379688,365.05167967388104),c(677.6105244611563,316.11865300951774,613.8557456077136,819.3636446598709),c(1078.8853035889126,1609.008424868669,348.88204246769334,193.96946615900578),c(1437.533824128006,1095.759600600407,320.4920028455483,161.35513114111984),c(845.1758168441753,660.6524658401157,541.3034221288985,640.8430740356532),c(551.2016196809839,740.570102836904,1103.42620664737,622.5332719203489),c(601.1772331987264,900.4053768304803,735.6174710982467,754.1349746240991))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
419 targetgene="AHCTF1"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
420 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
421
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
422 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
423 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
424 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
425
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
426 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
427 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
428 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
429 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
430
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
431
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
432 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
433
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
434 targetmatvec=unlist(targetmat)+1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
435 yrange=range(targetmatvec[targetmatvec>0]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
436 # yrange[1]=1; # set the minimum value to 1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
437 for(i in 1:length(targetmat)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
438 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
439 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
440 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
441 axis(1,at=1:length(vali),labels=(collabel),las=2)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
442 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
443 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
444 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
445 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
446 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
447
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
448
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
449
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
450 # parameters
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
451 # Do not modify the variables beginning with "__"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
452 targetmat=list(c(487.9971672908978,367.6211301852257,312.2904358435953,441.15179471561487),c(358.6485205390935,394.2603425174884,593.0363832181406,268.35303725242983),c(1743.266989177725,1980.1814500315297,837.1907239685878,281.5132075228048),c(1597.7497615819454,1465.1566782744503,1065.57282048451,992.7345834391593),c(119.05954985109253,378.2768151181308,185.48159219801417,128.7407961232339),c(986.2834314825072,745.8979453033566,328.0626800781203,302.11173490252224),c(523.2740709504807,694.3954681276485,336.89513684945433,597.9294753279087),c(1562.4728579223624,763.6574201915316,422.0652557158894,220.28980669975581),c(30.8672907021351,179.37069637056908,238.47633282601822,184.81456510135357),c(339.5401977234861,447.5387671820139,310.3977665354523,205.98527379717427))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
453 targetgene="ABT1"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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diff changeset
454 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
455
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
456 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
457 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
458 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
459
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
460 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
461 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
462 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
463 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
464
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
465
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
466 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
467
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
468 targetmatvec=unlist(targetmat)+1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
469 yrange=range(targetmatvec[targetmatvec>0]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
470 # yrange[1]=1; # set the minimum value to 1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
471 for(i in 1:length(targetmat)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
472 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
473 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
474 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
475 axis(1,at=1:length(vali),labels=(collabel),las=2)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
476 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
477 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
478 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
479 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
480 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
481
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
482
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
483
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
484 par(mfrow=c(1,1));
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
485 @
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
486 %
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
487
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
488
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
489 <<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>=
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
490 par(mfrow=c(2,2));
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
491
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
492 # parameters
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
493 # Do not modify the variables beginning with "__"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
494 targetmat=list(c(492.4067802483456,221.99343610218943,309.7668767660713,102.99263689858714),c(243.9985836454489,239.7529109903646,130.59418226186713,174.51530141149487),c(734.9354929079785,673.0840982618383,620.7955330709046,470.9052231529845),c(1074.4756906314647,950.1319065173708,1100.902647569846,743.8357109342404),c(702.5983312200275,1010.5141211371663,1291.4313579229083,1017.3383800315995),c(1647.7253750996879,760.1055252138966,685.7771793171477,608.2287390177673),c(951.0065278229242,864.8864270541301,606.9159581445226,769.0116888427839),c(435.0818118015233,435.1071347602913,275.69882921949727,339.8757017653375),c(89.66213013477338,209.56180368046682,208.8245136651112,304.4004601669353),c(1328.7633711776252,1571.7135276035012,1122.983789498181,1356.6419004808338))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
495 targetgene="ADIRF"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
496 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
497
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
498 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
499 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
500 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
501
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
502 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
503 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
504 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
505 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
506
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
507
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
508 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
509
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
510 targetmatvec=unlist(targetmat)+1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
511 yrange=range(targetmatvec[targetmatvec>0]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
512 # yrange[1]=1; # set the minimum value to 1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
513 for(i in 1:length(targetmat)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
514 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
515 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
516 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
517 axis(1,at=1:length(vali),labels=(collabel),las=2)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
518 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
519 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
520 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
521 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
522 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
523
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
524
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
525
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
526 # parameters
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
527 # Do not modify the variables beginning with "__"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
528 targetmat=list(c(216.0710349149457,289.479440677255,192.42137966120518,498.36992632594104),c(1127.391046120839,1198.764554951823,371.5940741654094,370.2013115188104),c(1111.2224652768637,1038.9292809582466,948.227323379644,922.3562815584581),c(1164.137820766238,1204.0923974182756,1686.9992433247955,2089.033985093009),c(48.505742531926586,248.63264843445216,665.5887066969557,248.8988725049189),c(501.2260061632414,387.1565525622184,436.5757204116524,314.69972385679404),c(1975.5066049366465,1797.2588586833258,1628.3264947723626,1289.6966864967521),c(213.13129294331378,376.5008676293133,404.4003421732214,482.921030791153),c(2012.2533795820452,1989.0611874756173,1064.3110409457481,431.9968936579627),c(264.57677744687226,353.4135502746856,442.25372833608145,191.6807408945927))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
529 targetgene="ABCF1"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
530 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
531
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
532 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
533 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
534 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
535
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
536 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
537 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
538 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
539 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
540
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
541
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
542 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
543
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
544 targetmatvec=unlist(targetmat)+1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
545 yrange=range(targetmatvec[targetmatvec>0]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
546 # yrange[1]=1; # set the minimum value to 1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
547 for(i in 1:length(targetmat)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
548 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
549 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
550 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
551 axis(1,at=1:length(vali),labels=(collabel),las=2)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
552 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
553 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
554 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
555 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
556 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
557
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
558
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
559
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
560 par(mfrow=c(1,1));
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
561 @
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
562
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
563 \newpage\section{Comparison results of HL60 final,KBM7 final vs HL60 initial,KBM7 initial pos.}
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
564
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
565 The following figure shows the distribution of RRA score in the comparison HL60 final,KBM7 final vs HL60 initial,KBM7 initial pos., and the RRA scores of 10 genes.
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
566
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
567 <<echo=FALSE>>=
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
568 gstable=read.table('output.gene_summary.txt',header=T)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
569 @
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
570 %
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
571
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
572
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
573 <<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>=#
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
574 #
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
575 # parameters
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
576 # Do not modify the variables beginning with "__"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
577
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
578 # gstablename='__GENE_SUMMARY_FILE__'
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
579 startindex=9
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
580 # outputfile='__OUTPUT_FILE__'
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
581 targetgenelist=c("ACRC","AGAP3","ADCK4","AHRR","ADRBK1","ADK","ADCK1","ADARB2","ACSS2","ADNP")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
582 # samplelabel=sub('.\w+.\w+$','',colnames(gstable)[startindex]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
583 samplelabel='HL60_final,KBM7_final_vs_HL60_initial,KBM7_initial pos.'
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
584
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
585
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
586 # You need to write some codes in front of this code:
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
587 # gstable=read.table(gstablename,header=T)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
588 # pdf(file=outputfile,width=6,height=6)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
589
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
590
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
591 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
592 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
593 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
594
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
595 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
596 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
597 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
598 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
599
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
600 ######
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
601 # function definition
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
602
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
603 plotrankedvalues<-function(val, tglist, ...){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
604
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
605 plot(val,log='y',ylim=c(max(val),min(val)),type='l',lwd=2, ...)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
606 if(length(tglist)>0){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
607 for(i in 1:length(tglist)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
608 targetgene=tglist[i];
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
609 tx=which(names(val)==targetgene);ty=val[targetgene];
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
610 points(tx,ty,col=colors[(i %% length(colors)) ],cex=2,pch=20)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
611 # text(tx+50,ty,targetgene,col=colors[i])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
612 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
613 legend('topright',tglist,pch=20,pt.cex = 2,cex=1,col=colors)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
614 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
615 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
616
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
617
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
618
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
619 plotrandvalues<-function(val,targetgenelist, ...){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
620 # choose the one with the best distance distribution
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
621
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
622 mindiffvalue=0;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
623 randval=val;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
624 for(i in 1:20){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
625 randval0=sample(val)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
626 vindex=sort(which(names(randval0) %in% targetgenelist))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
627 if(max(vindex)>0.9*length(val)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
628 # print('pass...')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
629 next;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
630 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
631 mindiffind=min(diff(vindex));
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
632 if (mindiffind > mindiffvalue){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
633 mindiffvalue=mindiffind;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
634 randval=randval0;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
635 # print(paste('Diff: ',mindiffvalue))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
636 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
637 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
638 plot(randval,log='y',ylim=c(max(randval),min(randval)),pch=20,col='grey', ...)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
639
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
640 if(length(targetgenelist)>0){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
641 for(i in 1:length(targetgenelist)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
642 targetgene=targetgenelist[i];
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
643 tx=which(names(randval)==targetgene);ty=randval[targetgene];
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
644 points(tx,ty,col=colors[(i %% length(colors)) ],cex=2,pch=20)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
645 text(tx+50,ty,targetgene,col=colors[i])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
646 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
647 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
648
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
649 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
650
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
651
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
652
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
653
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
654 # set.seed(1235)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
655
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
656
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
657
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
658 pvec=gstable[,startindex]
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
659 names(pvec)=gstable[,'id']
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
660 pvec=sort(pvec);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
661
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
662 plotrankedvalues(pvec,targetgenelist,xlab='Genes',ylab='RRA score',main=paste('Distribution of RRA scores in \n',samplelabel))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
663
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
664 # plotrandvalues(pvec,targetgenelist,xlab='Genes',ylab='RRA score',main=paste('Distribution of RRA scores in \n',samplelabel))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
665
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
666
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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diff changeset
667 pvec=gstable[,startindex+1]
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
668 names(pvec)=gstable[,'id']
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
669 pvec=sort(pvec);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
670
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
671 plotrankedvalues(pvec,targetgenelist,xlab='Genes',ylab='p value',main=paste('Distribution of p values in \n',samplelabel))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
672
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
673 # plotrandvalues(pvec,targetgenelist,xlab='Genes',ylab='p value',main=paste('Distribution of p values in \n',samplelabel))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
674
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
675
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
676
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
677 # you need to write after this code:
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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diff changeset
678 # dev.off()
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
679
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
680
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
681
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
682
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
683 @
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
684 %%
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
685 \clearpage
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
686 \newpage
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
687 The following figures show the distribution of sgRNA read counts (normalized) of selected genes in selected samples.
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
688 %
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
689
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
690
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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diff changeset
691 <<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>=
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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diff changeset
692 par(mfrow=c(2,2));
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
693
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
694 # parameters
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
695 # Do not modify the variables beginning with "__"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
696 targetmat=list(c(461.5394895462105,502.5931393353569,445.40817718298644,889.1697652244688),c(76.43329126242978,90.5733219296933,447.30084649112945,357.0411412484354),c(258.6972935036084,685.515730683561,533.7327448963265,560.7376897811967),c(232.23961575892122,681.9638357059259,275.69882921949727,467.47213525636494),c(1393.4376945535273,1472.2604682297203,1039.706339939889,532.7008052921368),c(2395.88970688001,2441.927797124084,2462.9936596634266,2461.5240218762324),c(495.34652221997754,605.5980936867728,1159.575396122279,1617.5565806239213),c(682.0201374186041,822.2636873225097,1572.1773052974536,1333.7546478367033),c(961.2956247236359,1097.5355480892247,959.5833392285019,905.1908420753603),c(1940.2297012770634,1289.3378768815162,942.5493154552149,1103.737758763192))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
697 targetgene="ACRC"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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diff changeset
698 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
699
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
700 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
701 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
702 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
703
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
704 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
705 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
706 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
707 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
708
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
709
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
710 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
711
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
712 targetmatvec=unlist(targetmat)+1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
713 yrange=range(targetmatvec[targetmatvec>0]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
714 # yrange[1]=1; # set the minimum value to 1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
715 for(i in 1:length(targetmat)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
716 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
717 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
718 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
719 axis(1,at=1:length(vali),labels=(collabel),las=2)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
720 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
721 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
722 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
723 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
724 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
725
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
726
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
727
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
728 # parameters
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
729 # Do not modify the variables beginning with "__"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
730 targetmat=list(c(1387.5582106102636,1120.6228654438523,1214.4628060584262,1111.1761158725344),c(388.0459402554127,509.69692929062694,933.0859689144999,750.1297054113762),c(326.3113588511425,635.7892009966705,960.8451187672639,615.6670961271097),c(1328.7633711776252,1038.9292809582466,1346.3187678590552,1596.3858719281006),c(352.7690365958297,234.42506852391205,310.3977665354523,429.1359870774464),c(693.7791053051318,678.4119407282909,784.1959833405838,895.4637597016048),c(837.8264619150956,719.2587329710938,374.74852301231437,993.8789460713658),c(365.99787546817333,369.3970776740432,333.74068800254935,746.6966175147567),c(707.0079441774753,635.7892009966705,837.1907239685878,1465.3563505404536),c(486.5272963050818,673.0840982618383,784.8268731099647,734.6808098765882))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
731 targetgene="AGAP3"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
732 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
733
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
734 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
735 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
736 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
737
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
738 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
739 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
740 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
741 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
742
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
743
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
744 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
745
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
746 targetmatvec=unlist(targetmat)+1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
747 yrange=range(targetmatvec[targetmatvec>0]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
748 # yrange[1]=1; # set the minimum value to 1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
749 for(i in 1:length(targetmat)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
750 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
751 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
752 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
753 axis(1,at=1:length(vali),labels=(collabel),las=2)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
754 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
755 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
756 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
757 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
758 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
759
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
760
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
761
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
762 # parameters
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
763 # Do not modify the variables beginning with "__"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
764 targetmat=list(c(830.4771069860158,864.8864270541301,1349.4732167059603,740.974804353724),c(1481.6299537024847,1994.38902994207,2044.082852794442,1810.9538654668238),c(1234.6916280854039,1299.9935618144214,1357.6747837079133,2232.6514954349277),c(224.89026082984142,188.25043381465665,700.2876440129107,81.24974688666317),c(812.8386551562243,845.3510046771374,946.334654071501,999.6007592323984),c(1978.4463469082782,1751.0842239740703,2659.2003779409174,2851.1794981425537),c(565.9003295391435,776.0890526132542,878.1985589783528,445.72924524444096),c(680.5502664327881,534.5601941340722,550.7667686696135,1025.9210997731484),c(161.68580843975528,333.87812789769293,275.0679394501163,465.18340999195186),c(2523.768482645998,2445.4796921017187,2153.226782897355,1516.8526689897471))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
765 targetgene="ADCK4"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
766 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
767
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
768 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
769 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
770 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
771
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
772 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
773 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
774 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
775 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
776
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
777
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
778 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
779
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
780 targetmatvec=unlist(targetmat)+1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
781 yrange=range(targetmatvec[targetmatvec>0]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
782 # yrange[1]=1; # set the minimum value to 1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
783 for(i in 1:length(targetmat)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
784 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
785 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
786 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
787 axis(1,at=1:length(vali),labels=(collabel),las=2)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
788 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
789 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
790 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
791 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
792 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
793
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
794
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
795
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
796 # parameters
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
797 # Do not modify the variables beginning with "__"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
798 targetmat=list(c(345.4196816667499,163.38716897121142,474.42910657451245,481.2044868428432),c(415.9734889859159,372.9489726516783,212.6098522813972,349.03060282298975),c(1.469870985815957,83.46953197442323,0.0,62.9399447713588),c(351.29916561001374,150.9555365494888,288.9475143764983,416.54799812317464),c(561.4907165816957,170.49095892648148,199.3611671243962,411.97054759434855),c(251.34793857452865,221.99343610218943,1564.6066280648815,1502.5481360871656),c(736.4053638937945,893.3015868752103,1114.782222496228,459.46159683091923),c(338.07032673767014,607.3740411755903,378.5338616286004,65.22867003577186),c(1230.2820151279561,525.6804566899846,837.1907239685878,945.2435342025885))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
799 targetgene="AHRR"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
800 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
801
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
802 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
803 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
804 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
805
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
806 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
807 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
808 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
809 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
810
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
811
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
812 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
813
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
814 targetmatvec=unlist(targetmat)+1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
815 yrange=range(targetmatvec[targetmatvec>0]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
816 # yrange[1]=1; # set the minimum value to 1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
817 for(i in 1:length(targetmat)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
818 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
819 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
820 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
821 axis(1,at=1:length(vali),labels=(collabel),las=2)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
822 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
823 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
824 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
825 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
826 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
827
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
828
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
829
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
830 par(mfrow=c(1,1));
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
831 @
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
832 %
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
833
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
834
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
835 <<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>=
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
836 par(mfrow=c(2,2));
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
837
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
838 # parameters
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
839 # Do not modify the variables beginning with "__"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
840 targetmat=list(c(371.87735941143717,877.3180594758527,2395.4884543396593,1564.9158995424211),c(1109.7525942910477,1138.3823403320275,970.308465307979,999.0285779162951),c(1462.5216308868773,1209.420239884728,1537.4783679814984,1519.14139425416),c(586.4785233405669,987.4268037825386,743.8190381001997,1312.0117578247794),c(1018.6205931704583,717.4827854822763,1070.619938639558,1144.3626322065236),c(1269.9685317449869,1212.9721348623632,1591.1039983788835,1624.9949377332637),c(1321.4140162485455,1795.4829111945082,1478.8056194290655,1237.056005415252),c(908.3802692342615,832.9193722554148,1639.6825106212207,1268.5259778009315),c(923.078979092421,758.3295777250792,1479.4365091984464,1275.964334910274),c(680.5502664327881,634.013253507853,318.5993335374053,631.1159916618979))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
841 targetgene="ADRBK1"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
842 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
843
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
844 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
845 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
846 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
847
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
848 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
849 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
850 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
851 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
852
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
853
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
854 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
855
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
856 targetmatvec=unlist(targetmat)+1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
857 yrange=range(targetmatvec[targetmatvec>0]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
858 # yrange[1]=1; # set the minimum value to 1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
859 for(i in 1:length(targetmat)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
860 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
861 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
862 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
863 axis(1,at=1:length(vali),labels=(collabel),las=2)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
864 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
865 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
866 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
867 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
868 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
869
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
870
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
871
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
872 # parameters
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
873 # Do not modify the variables beginning with "__"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
874 targetmat=list(c(1472.810727787589,1829.225913482041,1263.0413183007631,1315.444845721399),c(208.7216799858659,65.71005708624807,292.1019632234033,350.17496545519623),c(1011.2712382413785,1166.7975001531076,652.9709113093356,860.5606994193058),c(557.0811036242477,685.515730683561,875.0441101314478,1019.6271052960126),c(363.0581334965414,825.8155823001447,736.8792506370087,349.602784139093),c(1505.14788947554,451.09066215964896,653.6018010787167,991.0180394908496),c(198.43258308515422,28.41515982108025,249.83234867487624,114.43626322065236),c(438.02155377315523,74.58979453033565,254.87946682992424,231.16125170571777),c(804.0194292413286,472.4020320254591,1336.2245315489592,1203.2973077651598),c(454.19013461713075,490.1615069136343,896.4943622904019,685.4732166917076))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
875 targetgene="ADK"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
876 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
877
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
878 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
879 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
880 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
881
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
882 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
883 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
884 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
885 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
886
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
887
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
888 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
889
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
890 targetmatvec=unlist(targetmat)+1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
891 yrange=range(targetmatvec[targetmatvec>0]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
892 # yrange[1]=1; # set the minimum value to 1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
893 for(i in 1:length(targetmat)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
894 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
895 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
896 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
897 axis(1,at=1:length(vali),labels=(collabel),las=2)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
898 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
899 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
900 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
901 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
902 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
903
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
904
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
905
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
906 # parameters
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
907 # Do not modify the variables beginning with "__"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
908 targetmat=list(c(662.9118146029966,1008.7381736483488,1101.533537339227,1694.8010582978616),c(1547.7741480642028,1965.9738701209897,1869.9572764452857,2353.9539344488194),c(1459.5818889152454,1179.2291325748304,1296.4784760779562,1222.1792911965672),c(1193.5352404825571,1355.0479339677643,1622.0175970785526,1905.9359639399652),c(868.6937526172306,701.4992580829187,720.4761166331027,603.6512884889412),c(798.1399452980647,768.9852626579842,1478.8056194290655,1756.0244591209105),c(1168.5474337236858,907.5091667857504,879.4603385171149,977.8578692204745),c(809.8989131845924,687.2916781723785,678.8373918539567,865.7103312642352),c(1246.4505959719315,753.0017352586266,1301.5255942330043,1264.5207085882087),c(826.0674940285679,797.4004224790644,977.8791425405509,2066.7189137649816))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
909 targetgene="ADCK1"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
910 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
911
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
912 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
913 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
914 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
915
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
916 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
917 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
918 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
919 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
920
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
921
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
922 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
923
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
924 targetmatvec=unlist(targetmat)+1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
925 yrange=range(targetmatvec[targetmatvec>0]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
926 # yrange[1]=1; # set the minimum value to 1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
927 for(i in 1:length(targetmat)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
928 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
929 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
930 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
931 axis(1,at=1:length(vali),labels=(collabel),las=2)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
932 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
933 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
934 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
935 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
936 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
937
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
938
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
939
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
940 # parameters
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
941 # Do not modify the variables beginning with "__"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
942 targetmat=list(c(1863.7964100146337,1585.9211075140413,1761.4442361117538,1464.211987908247),c(742.2848478370584,598.4943037315028,943.8110949939769,820.5080072920774),c(1568.3523418656262,2083.1864043829455,1810.6536381234716,1887.6261618246608),c(1018.6205931704583,513.248824268262,679.4682816233377,824.5132765048003),c(1140.6198849931827,1191.6607649965529,880.0912282864958,977.8578692204745),c(135.22813069506805,118.98848175077354,351.40560154521734,399.95473995618005),c(665.8515565746286,701.4992580829187,986.7115993118849,746.6966175147567),c(418.9132309575478,300.1351256101601,376.6411923204574,645.4205245644794),c(561.4907165816957,543.4399315781598,881.9838975946388,580.7640358448108),c(442.4311667306031,229.0972260574595,395.5678854018874,651.142337725512))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
943 targetgene="ADARB2"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
944 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
945
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
946 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
947 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
948 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
949
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
950 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
951 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
952 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
953 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
954
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
955
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
956 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
957
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
958 targetmatvec=unlist(targetmat)+1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
959 yrange=range(targetmatvec[targetmatvec>0]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
960 # yrange[1]=1; # set the minimum value to 1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
961 for(i in 1:length(targetmat)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
962 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
963 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
964 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
965 axis(1,at=1:length(vali),labels=(collabel),las=2)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
966 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
967 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
968 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
969 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
970 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
971
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
972
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
973
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
974 par(mfrow=c(1,1));
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
975 @
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
976 %
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
977
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
978
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
979 <<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>=
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
980 par(mfrow=c(2,2));
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
981
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
982 # parameters
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
983 # Do not modify the variables beginning with "__"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
984 targetmat=list(c(734.9354929079785,358.74139274113816,541.9343118982795,378.7840312603593),c(595.2977492554626,591.3905137762326,1061.787481868224,887.4532212761591),c(1655.0747300287676,943.0281165621008,1069.358159100796,2038.1098479598186),c(626.1650399575977,884.4218494311227,517.3296108924205,858.2719741548927),c(680.5502664327881,747.673892792174,533.1018551269456,1016.194017399393),c(662.9118146029966,777.8650001020718,864.9498738213518,787.3214909580882),c(880.4527205037583,621.5816210861304,671.8976043907657,1040.7978139918332),c(94.07174309222125,447.5387671820139,711.6436598617687,927.5059134033875),c(399.80490814194036,806.280159923152,1147.58849050404,1059.1076161071376),c(698.1887182625796,531.0082991564371,504.0809257354195,347.8862401907832))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
985 targetgene="ACSS2"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
986 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
987
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
988 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
989 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
990 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
991
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
992 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
993 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
994 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
995 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
996
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
997
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
998 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
999
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1000 targetmatvec=unlist(targetmat)+1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1001 yrange=range(targetmatvec[targetmatvec>0]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1002 # yrange[1]=1; # set the minimum value to 1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1003 for(i in 1:length(targetmat)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1004 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1005 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1006 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1007 axis(1,at=1:length(vali),labels=(collabel),las=2)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1008 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1009 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1010 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1011 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1012 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1013
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1014
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1015
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1016 # parameters
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1017 # Do not modify the variables beginning with "__"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1018 targetmat=list(c(408.62413405683606,523.9045092011671,483.89245311522745,701.494293542599),c(1805.0015705819953,1434.9655709645526,1712.2348341000356,2152.546111180471),c(3017.64513388016,2642.609863360463,1834.6274493599499,3573.2723190648703),c(1649.1952460855039,783.1928425685244,773.4708572611067,1332.0381038883936),c(959.82575373782,1397.6706736993847,1429.5962174173474,2811.126806015325),c(495.34652221997754,301.9110730989776,336.89513684945433,555.015876620164),c(1491.9190506031964,1331.9606166131366,2087.614246881731,1983.1804416139055),c(429.2023278582595,889.7496918975753,567.8007924429005,1132.9190058844583),c(427.7324568724435,573.6310388880576,655.4944703868597,899.4690289143276),c(690.8393633334998,767.2093151691668,1040.33722970927,993.3067647552625))
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1019 targetgene="ADNP"
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1020 collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1021
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1022 # set up color using RColorBrewer
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1023 #library(RColorBrewer)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1024 #colors <- brewer.pal(length(targetgenelist), "Set1")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1025
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1026 colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1027 "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1028 "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1029 "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1030
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1031
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1032 ## code
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1033
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1034 targetmatvec=unlist(targetmat)+1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1035 yrange=range(targetmatvec[targetmatvec>0]);
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1036 # yrange[1]=1; # set the minimum value to 1
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1037 for(i in 1:length(targetmat)){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1038 vali=targetmat[[i]]+1;
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1039 if(i==1){
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1040 plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y')
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1041 axis(1,at=1:length(vali),labels=(collabel),las=2)
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1042 # lines(0:100,rep(1,101),col='black');
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1043 }else{
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1044 lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))])
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1045 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1046 }
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1047
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1048
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1049
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1050 par(mfrow=c(1,1));
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1051 @
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1052 %__INDIVIDUAL_PAGE__
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1053
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1054
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1055
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1056
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1057
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1058
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1059
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1060
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1061
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1062 \end{document}
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
diff changeset
1063