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55
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1 #!/usr/bin/env Rscript
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2
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3 #usage $0 STEP RIGHT chipPeaks outputFile.png output.txt [controlPeaks] [1 for pdf]
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4 args <- commandArgs(TRUE)
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5 #print (args)
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6 myStep <- type.convert(args[2])
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7 maxValue <- type.convert(args[3])
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8
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9 dataTable <-read.table(file=paste(args[4],".genes.ClosestPeakDist", sep=""), header=TRUE);
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10 chip.genes.ClosestPeakDist<-data.frame(dataTable)
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11 ifReg <- 0
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12 if (length(unique(chip.genes.ClosestPeakDist$Reg))>1) {
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13 ifReg <- 1
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14 }
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15 ifControl <- 0
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16
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17 #options(bitmapType='cairo')
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18 print(installed.packages())
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19
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20 ifPDF <- 0
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21 if (length(args)>=8) {
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22 ifPDF=args[8]
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23 }
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24 if (length(args)==7 & args[7]==1) {
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25 ifPDF=1
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26 }
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27
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28 suppressMessages(library(Hmisc))
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29
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30 if (length(args)>=7 & args[7]!=1 & args[7]!=0) {
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31 dataTable <-read.table(file=paste(args[7],".genes.ClosestPeakDist", sep=""), header=TRUE);
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32 control.genes.ClosestPeakDist<-data.frame(dataTable)
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33 ifControl <- 1
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34 }
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35 if (ifReg & ifControl) {
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36 if (ifPDF==1) {
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37 pdf(file = args[5], width = 19, height = 8, pointsize = 20, bg = "white")
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38 } else {
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39 png(filename = args[5], type = "cairo", width = 38.1 , height = 18, units = "cm", pointsize = 20, bg = "white")
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40 plot(1:10)
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41 }
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42 op <- par(mfrow = c(2,3))
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43 } else {
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44 if (ifPDF==1) {
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45 pdf(file = args[5], type = "cairo", width = 10, height = 13, pointsize = 20, bg = "white")
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46 } else {
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47 png(filename = args[5], width = 18, height = 23.3, units = "cm", pointsize = 20, bg = "white")
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48 plot(1:10)
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49 }
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50 # plot(1:10)
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51 op <- par(mfrow = c(2,1))
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52 }
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53 myColor <- 1
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54 myColor[1] <- colors()[131]
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55 myColor[2] <- "darkolivegreen3"
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56 myColor[3] <- "azure4"
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57 myColor[4] <- "royalblue3"
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58 myColor[5] <- colors()[17]
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59
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60 myColorControl <- 1
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61
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62 myColorControl[1] <- colors()[24]
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63 myColorControl[2] <- colors()[278]
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64 myColorControl[3] <- colors()[305]
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65 myColorControl[4] <- colors()[219]
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66 myColorControl[5] <- colors()[343]
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67
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68
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69
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70 #for cumulative:
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71 dist_real_f <- chip.genes.ClosestPeakDist
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72 if (ifControl) {
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73 dist_control_f <- control.genes.ClosestPeakDist
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74 }
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75 step <- myStep
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76 lim <- maxValue
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77 x <- 0
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78 count <- 1
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79 countL <-1
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80 n.types <- 1
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81 myLevels <- 0
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82 countTotalCont <- 0
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83 countTotal <-0
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84 countLCont <- 0
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85 cumTotalCont <- 0
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86 if (ifReg) {
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87 n.types <- length(levels(chip.genes.ClosestPeakDist$Reg))
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88 myLevels <- levels(chip.genes.ClosestPeakDist$Reg)
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89 cum = matrix( 0, nrow=lim/step +1, ncol=n.types, byrow = TRUE)
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90 for (i in c(1:n.types)) {
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91 t <- which ((dist_real_f$Reg==myLevels[i]))
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92 countL[i] <- length(t)
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93 }
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94 count <-1
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95 for (i in seq(length=lim/step +1, from=0, by=step)) {
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96 for (t in c(1:n.types)) {
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97 tt <- which ((dist_real_f$Reg==myLevels[t])&(dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
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98 cum[count,t] <- length(tt)
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99 }
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100 x[count] <- i
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101 count <- count + 1
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102 }
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103 ymax <- max(cum[,1]/countL[1], na.rm=TRUE)
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104 for (i in c(2:n.types)) {
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105 ymax <- max(ymax,max(cum[,i]/countL[i], na.rm=TRUE))
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106 }
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107 myLocCol <- myColor[2]
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108
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109 par(mar=c(5.1, 7.1, 4.1, 2.1))
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110
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111 plot (x,cum[,1]/countL[1] ,col = myColor[2],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(0, lim),xaxt="n" , ylim=c(0,ymax))
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112 for (i in c(2:n.types)) {
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113 colorr <- i+1
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114 myLocCol <- c(myLocCol,myColor[colorr])
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115 lines (x,cum[,i]/countL[i] ,col = myColor[colorr],type="l", lwd = 2)
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116 # print (myColor[colorr])
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117 }
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118
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119 gradi <- 1000
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120 if (lim>10000) {
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121 gradi <- 10000
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122 }
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123 if (lim<3000) {
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124 gradi <- 500
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125 }
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126 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
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127 axisxlab <- paste(axisx/1000,"", sep = "")
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128 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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129 ymax <- max(cum[,i]/countL[i], na.rm=TRUE)
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130
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131 minor.tick(nx=5,tick.ratio=0.5)
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132
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133 legend(lim*0.45, ymax*0.45, myLevels, cex=1, lwd = 2, bty = "n", col = myLocCol, lty = c(1), pt.bg= c(myLocCol) , merge = TRUE)
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134
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135 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
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136
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137 if (ifControl) {
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138 count <-1
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139 n.types <- length(levels(control.genes.ClosestPeakDist$Reg))
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140 myLevels <- levels(control.genes.ClosestPeakDist$Reg)
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141 cumCont = matrix( 0, nrow=lim/step +1, ncol=n.types, byrow = TRUE)
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142 for (i in c(1:n.types)) {
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143 t <- which ((dist_control_f$Reg==myLevels[i]))
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144 countLCont[i] <- length(t)
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145 }
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146 for (i in seq(length=lim/step +1, from=0, by=step)) {
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147 for (t in c(1:n.types)) {
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148 tt <- which ((dist_control_f$Reg==myLevels[t])&(dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
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149 cumCont[count,t] <- length(tt)
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150 }
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151 x[count] <- i
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152 count <- count + 1
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153 }
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154 ymax <- max(cumCont[,1]/countLCont[1], na.rm=TRUE)
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155 for (i in c(2:n.types)) {
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156 ymax <- max(ymax,max(cumCont[,i]/countLCont[i], na.rm=TRUE))
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157 }
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158 myLocColCntr <- myColorControl[2]
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159 plot (x,cumCont[,1]/countLCont[1] ,col = myLocColCntr[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(0, lim),xaxt="n" , ylim=c(0,ymax))
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160 for (i in c(2:n.types)) {
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161 colorr <- i+1
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162 myLocColCntr <- c(myLocColCntr,myColorControl[colorr])
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163 lines (x,cumCont[,i]/countLCont[i] ,col = myColorControl[colorr],type="l", lwd = 2)
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164 }
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165 if (lim>10000) {
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166 gradi <- 10000
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167 }
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168 if (lim<3000) {
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169 gradi <- 500
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170 }
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171 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
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172 axisxlab <- paste(axisx/1000, sep = "")
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173 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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174 minor.tick(nx=5,tick.ratio=0.5)
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175 legend(lim*0.45, ymax*0.45, myLevels, cex=1 , lwd = 2, bty = "n", col = myLocColCntr, lty = c(1), pt.bg= c(myLocCol) , merge = TRUE)
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176 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
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177 #real_vs_control_cumulative:
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178 count <-1
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179 countTotal <- length(dist_real_f$Reg)
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180 cumTotal <- 0
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181 for (i in seq(length=lim/step +1, from=0, by=step)) {
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182 t <- which ((dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
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183 cumTotal[count] <- length(t)
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184 x[count] <- i
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185 count <- count + 1
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186 }
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187 plot (x,cumTotal/countTotal ,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(0, lim),xaxt="n" )
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188 gradi <- 1000
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189 if (lim>10000) {
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190 gradi <- 10000
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191 }
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192 if (lim<3000) {
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193 gradi <- 500
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194 }
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195 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
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196 axisxlab <- paste(axisx/1000, sep = "")
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197 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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198 ymax <- max(cumTotal/countTotal, na.rm=TRUE)
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199 minor.tick(nx=5,tick.ratio=0.5)
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200 countTotalCont <- length(dist_control_f$Reg)
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201 cumTotalCont <- 0
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202 count <- 1
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203 for (i in seq(length=lim/step +1, from=0, by=step)) {
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204 t <- which ((dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
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205 cumTotalCont[count] <- length(t)
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206 x[count] <- i
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207 count <- count + 1
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208 }
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209 lines (x,cumTotalCont/countTotalCont ,col = colors()[328],type="l", lwd = 2)
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210 legend(lim*0.45, ymax*0.45, c("ChIP","Control"), cex=1 , lwd = 2, bty = "n", col = c(myColor[1], colors()[328]), lty = c(1), pt.bg= c(myColor[1], colors()[328]) , merge = TRUE)
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211 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
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212 }
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213 } else {
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214 countTotal <- length(dist_real_f$Reg)
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215 cumTotal <- 0
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216 count <-1
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217
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218 gradi <- 1000
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219 if (lim>10000) {
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220 gradi <- 10000
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221 }
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222 if (lim<3000) {
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223 gradi <- 500
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224 }
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225
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226 for (i in seq(length=lim/step +1, from=0, by=step)) {
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227 t <- which ((dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
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228 cumTotal[count] <- length(t)
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229 x[count] <- i
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230 count <- count + 1
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231 }
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232 par(mar=c(5.1, 7.1, 4.1, 2.1))
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233
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234 plot (x,cumTotal/countTotal ,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(0, lim),xaxt="n" )
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235 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
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236 axisxlab <- paste(axisx/1000, sep = "")
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237 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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238 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
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239 ymax <- max(cumTotal/countTotal, na.rm=TRUE)
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240 if (ifControl) {
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241 countTotalCont <- length(dist_control_f$Reg)
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242 cumTotalCont <- 0
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243 count <- 1
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244 for (i in seq(length=lim/step +1, from=0, by=step)) {
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245 t <- which ((dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
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246 cumTotalCont[count] <- length(t)
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247 x[count] <- i
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248 count <- count + 1
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249 }
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250 lines (x,cumTotalCont/countTotalCont ,col = colors()[328],type="l", lwd = 2)
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251 legend(lim*0.45, ymax*0.45, c("ChIP","Control"), cex=1 , lwd = 2, bty = "n", col = c(myColor[1], colors()[328]), lty = c(1), pt.bg= c(myColor[1], colors()[328]) , merge = TRUE)
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252 } else {
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253 legend(lim*0.45, ymax*0.45, c("ChIP"), cex=1 , lwd = 2, bty = "n", col = c(myColor[1]), lty = c(1), pt.bg= c(myColor[1]) , merge = TRUE)
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254 }
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255 }
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256
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257 sink(args[6], append=FALSE, split=FALSE)
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258 if (ifReg) {
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259 if (ifControl) {
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260 cat (paste("Dist_TSS","% genes w/ a peak in ChIP","% genes w/ a peak in control",sep='\t'))
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261 cat("\t")
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262 for (i in c(1:n.types)) {
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263 cat(paste("% ", myLevels[i]," genes w/ a peak in ChIP", sep=""))
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264 cat("\t")
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265 }
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266
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267 for (i in c(1:n.types)) {
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268 cat(paste("% ", myLevels[i]," genes w/ a peak in Control", sep=""))
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269 cat("\t")
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270 }
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271 cat("\n")
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272 for (i in c(1:length(x))) {
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273 cat(paste(x[i],cumTotal[i]/countTotal,cumTotalCont[i]/countTotalCont,sep="\t"))
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274 cat("\t")
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275 for (t in c(1:n.types)) {
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276 cat(paste(cum[i,t]/countL[t],"\t", sep=""))
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277 }
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278 for (t in c(1:n.types)) {
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279 cat(paste(cumCont[i,t]/countLCont[t],"\t", sep=""))
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280 }
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281 cat("\n")
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282 }
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283 }else {
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284 cat (paste("Dist_TSS","\t",sep=''))
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285 for (i in c(1:n.types)) {
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286 cat(paste("% ", myLevels[i]," genes w/ a peak in ChIP", "\t", sep=""))
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287 }
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288 cat("\n")
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289 for (i in c(1:length(x))) {
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290 cat(paste(x[i],"\t",sep=""))
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291 for (t in c(1:n.types)) {
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292 cat(paste(cum[i,t]/countL[t],"\t", sep=""))
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293 }
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294 cat("\n")
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295 }
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296 }
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297 } else {
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298 if (ifControl) {
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299 cat (paste("Dist_TSS","% genes w/ a peak in ChIP","% genes w/ a peak in control",sep='\t'))
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300 cat("\n")
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301 for (i in c(1:length(x))) {
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302 cat(paste(x[i],cumTotal[i]/countTotal,cumTotalCont[i]/countTotalCont,sep="\t"))
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303 cat("\n")
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304 }
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305 }else {
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306 cat (paste("Dist_TSS","% genes w/ a peak in ChIP",sep='\t'))
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307 cat("\n")
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308 for (i in c(1:length(x))) {
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309 cat(paste(x[i],cumTotal[i]/countTotal,sep="\t"))
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310 cat("\n")
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311 }
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312
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313 }
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314 }
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315
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316
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317 #stop sinking:
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318 sink()
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319
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320 #around TSS:
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321 lim <- maxValue
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322 step <- myStep
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323 my_breaks <- seq(length=lim/step*2 +1, from=-lim, by=step)
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324 chip.genes <- read.table(file=paste(args[4],".genes", sep=""), header=TRUE) ;
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325 dist_real_f <- chip.genes
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326 if (ifControl) {
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327 control.genes <- read.table(file=paste(args[4],".genes", sep=""), header=TRUE) ;
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328 dist_control_f<-data.frame(control.genes)
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329 }
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330 if (ifReg) {
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331 #n.types <- length(levels(chip.genes.ClosestPeakDist$Reg))
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332 #myLevels <- levels(dist_real_f$Reg)
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333
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334 t<- which (dist_real_f$Reg==myLevels[1])
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335 values_real <-dist_real_f$Dist[t]
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336 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
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337 ymax <- max(hTSSreal$density, na.rm=TRUE)
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338 for (i in c(2:n.types)) {
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339 t<- which (dist_real_f$Reg==myLevels[i])
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340 values_real <-dist_real_f$Dist[t]
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341 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
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342 ymax <- max(ymax,max(hTSSreal$density, na.rm=TRUE))
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343 }
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344
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345
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346 t<- which (dist_real_f$Reg==myLevels[1])
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347 values_real <-dist_real_f$Dist[t]
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348 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
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349 plot (hTSSreal$mids,hTSSreal$density,col = myLocCol[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(-lim, lim),ylim = c(0, ymax), xaxt="n" )
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350
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351 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
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352
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353 for (i in c(2:n.types)) {
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354 t<- which (dist_real_f$Reg==myLevels[i])
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355 values_real <-dist_real_f$Dist[t]
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356 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
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357 lines (hTSSreal$mids,hTSSreal$density,col = myLocCol[i],type="l", lwd = 2)
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358 }
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359 legend(lim*0.1, ymax*0.9, myLevels, cex=1 , lwd = 2, bty = "n", col = myLocCol, lty = c(1), pt.bg= c(myLocCol) , merge = TRUE)
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360
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361 gradi <- 1000
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362 if (lim>10000) {
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363 gradi <- 10000
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364 }
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365 if (lim<3000) {
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366 gradi <- 500
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367 }
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368
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369 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
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370 axisxlab <- paste(axisx/1000, sep = "")
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371 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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372
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373
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374 #minor.tick(nx=10,tick.ratio=0.5)
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375 if (ifControl) {
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376 t<- which (dist_control_f$Reg==myLevels[1])
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377 values_control <-dist_control_f$Dist[t]
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378 hTSScontrol= hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
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379 ymax <- max(hTSScontrol$density, na.rm=TRUE)
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380 for (i in c(2:n.types)) {
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381 t<- which (dist_control_f$Reg==myLevels[i])
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382 values_control <-dist_control_f$Dist[t]
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383 hTSScontrol = hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
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384 ymax <- max(ymax,max(hTSScontrol$density, na.rm=TRUE))
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385 }
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386 t<- which (dist_control_f$Reg==myLevels[1])
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387 values_control <-dist_control_f$Dist[t]
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388 hTSScontrol= hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
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389 plot (hTSScontrol$mids,hTSScontrol$density,col = myLocColCntr[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(-lim, lim),ylim = c(0, ymax),xaxt="n" )
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390 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
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391 for (i in c(2:n.types)) {
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392 t<- which (dist_control_f$Reg==myLevels[i])
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393 values_control <-dist_control_f$Dist[t]
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394 hTSScontrol = hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
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395 lines (hTSScontrol$mids,hTSScontrol$density,col = myLocColCntr[i],type="l", lwd = 2)
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396 }
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397
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398 gradi <- 1000
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399 if (lim>10000) {
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400 gradi <- 10000
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401 }
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402 if (lim<3000) {
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403 gradi <- 500
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404 }
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405
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406 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
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407 axisxlab <- paste(axisx/1000, sep = "")
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408 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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409
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410 legend(lim*0.1, ymax*0.9, myLevels, cex=1 , lwd = 2, bty = "n", col = myLocColCntr, lty = c(1), pt.bg= c(myLocCol) , merge = TRUE)
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411
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412 # minor.tick(nx=10,tick.ratio=0.5)
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413 #control vs real
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414 values_real <-dist_real_f$Dist
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415 hTSSreal = hist(values_real, plot=FALSE, breaks = c(min(values_real),my_breaks,max(values_real)) )
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416 plot (hTSSreal$mids,hTSSreal$density,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(-lim, lim),xaxt="n")
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417 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
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418 ymax <- max(hTSSreal$density, na.rm=TRUE)
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419 values_control <-dist_control_f$Dist
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420 hTSScontrol = hist(values_control, plot=FALSE, breaks = c(min(values_control),my_breaks,max(values_control)) )
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421 lines (hTSScontrol$mids,hTSScontrol$density,col = colors()[328],type="l", lwd = 2)
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422 legend(lim*0.2, ymax*0.9, c("ChIP","Control"), cex=1 , lwd = 2, bty = "n", col = c(myColor[1], colors()[328]), lty = c(1), pt.bg= c(myColor[1], colors()[328]) , merge = TRUE)
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423
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424 gradi <- 1000
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425 if (lim>10000) {
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426 gradi <- 10000
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427 }
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428 if (lim<3000) {
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429 gradi <- 500
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430 }
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431
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432 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
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433 axisxlab <- paste(axisx/1000, sep = "")
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434 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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435
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436
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437
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438 # minor.tick(nx=10,tick.ratio=0.5)
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439 }
|
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440 } else {
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441 values_real <-dist_real_f$Dist
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442 hTSSreal = hist(values_real, plot=FALSE, breaks = c(min(values_real),my_breaks,max(values_real)) )
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443 plot (hTSSreal$mids,hTSSreal$density,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(-lim, lim),xaxt="n")
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444 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
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445 ymax <- max(hTSSreal$density, na.rm=TRUE)
|
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446 if (ifControl) {
|
|
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447 values_control <-dist_control_f$Dist
|
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|
448 hTSScontrol = hist(values_control, plot=FALSE, breaks = c(min(values_control),my_breaks,max(values_control)) )
|
|
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449 lines (hTSScontrol$mids,hTSScontrol$density,col = colors()[328],type="l", lwd = 2)
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450 legend(lim*0.2, ymax*0.9, c("ChIP","Control"), cex=1 , lwd = 2, bty = "n", col = c(myColor[1], colors()[328]), lty = c(1), pt.bg= c(myColor[1], colors()[328]) , merge = TRUE)
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451 } else {
|
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452 legend(lim*0.2, ymax*0.9, c("ChIP"), cex=1 , lwd = 2, bty = "n", col = c(myColor[1]), lty = c(1), pt.bg= c(myColor[1]) , merge = TRUE)
|
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453 }
|
|
|
454
|
|
|
455 gradi <- 1000
|
|
|
456 if (lim>10000) {
|
|
|
457 gradi <- 10000
|
|
|
458 }
|
|
|
459 if (lim<3000) {
|
|
|
460 gradi <- 500
|
|
|
461 }
|
|
|
462
|
|
|
463 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
|
|
|
464 axisxlab <- paste(axisx/1000, sep = "")
|
|
|
465 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
|
|
|
466
|
|
|
467
|
|
|
468 # minor.tick(nx=10,tick.ratio=0.5)
|
|
|
469 }
|
|
|
470 suppressMessages(dev.off())
|
|
|
471 q();
|
|
|
472 cat (paste("peak height","# peaks in ChIP","# peaks in Control","#control/chip","\n",sep='\t'))
|
|
|
473 for (xval in c(minValue:maxValue)) {
|
|
|
474 for (i in (1:length(chipHist$mids))) {
|
|
|
475 if (xval==chipHist$mids[i]) {
|
|
|
476 ychip <- chipHist$counts[i]
|
|
|
477 }
|
|
|
478 }
|
|
|
479 for (i in (1:length(controlHist$mids))) {
|
|
|
480 if (xval==controlHist$mids[i]) {
|
|
|
481 ycontrol <- controlHist$counts[i]
|
|
|
482 }
|
|
|
483 }
|
|
|
484 cat (paste(xval,ychip,ycontrol,ycontrol/ychip,"\n",sep='\t'))
|
|
|
485 }
|
