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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
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19 ifPDF <- 0
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20 if (length(args)>=8) {
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21 ifPDF=args[8]
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22 }
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23 if (length(args)==7 & args[7]==1) {
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24 ifPDF=1
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25 }
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26
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27 suppressMessages(library(Hmisc))
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28
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29 if (length(args)>=7 & args[7]!=1 & args[7]!=0) {
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30 dataTable <-read.table(file=paste(args[7],".genes.ClosestPeakDist", sep=""), header=TRUE);
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31 control.genes.ClosestPeakDist<-data.frame(dataTable)
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32 ifControl <- 1
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33 }
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34 if (ifReg & ifControl) {
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35 if (ifPDF==1) {
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36 pdf(file = args[5], width = 19, height = 8, pointsize = 20, bg = "white")
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37 } else {
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38 png(filename = args[5], width = 1440 , height = 680, units = "px", pointsize = 20, bg = "white", res = NA)
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39 plot(1:10)
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40 }
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41 op <- par(mfrow = c(2,3))
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42 } else {
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43 if (ifPDF==1) {
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44 pdf(file = args[5], width = 10, height = 13, pointsize = 20, bg = "white")
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45 } else {
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46 png(filename = args[5], width = 680, height = 880, units = "px", pointsize = 20, bg = "white", res = NA)
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47 plot(1:10)
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48 }
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49 # plot(1:10)
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50 op <- par(mfrow = c(2,1))
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51 }
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52 myColor <- 1
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53 myColor[1] <- colors()[131]
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54 myColor[2] <- "darkolivegreen3"
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55 myColor[3] <- "azure4"
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56 myColor[4] <- "royalblue3"
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57 myColor[5] <- colors()[17]
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58
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59 myColorControl <- 1
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60
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61 myColorControl[1] <- colors()[24]
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62 myColorControl[2] <- colors()[278]
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63 myColorControl[3] <- colors()[305]
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64 myColorControl[4] <- colors()[219]
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65 myColorControl[5] <- colors()[343]
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66
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67
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68
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69 #for cumulative:
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70 dist_real_f <- chip.genes.ClosestPeakDist
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71 if (ifControl) {
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72 dist_control_f <- control.genes.ClosestPeakDist
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73 }
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74 step <- myStep
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75 lim <- maxValue
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76 x <- 0
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77 count <- 1
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78 countL <-1
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79 n.types <- 1
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80 myLevels <- 0
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81 countTotalCont <- 0
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82 countTotal <-0
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83 countLCont <- 0
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84 cumTotalCont <- 0
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85 if (ifReg) {
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86 n.types <- length(levels(chip.genes.ClosestPeakDist$Reg))
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87 myLevels <- levels(chip.genes.ClosestPeakDist$Reg)
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88 cum = matrix( 0, nrow=lim/step +1, ncol=n.types, byrow = TRUE)
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89 for (i in c(1:n.types)) {
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90 t <- which ((dist_real_f$Reg==myLevels[i]))
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91 countL[i] <- length(t)
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92 }
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93 count <-1
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94 for (i in seq(length=lim/step +1, from=0, by=step)) {
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95 for (t in c(1:n.types)) {
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96 tt <- which ((dist_real_f$Reg==myLevels[t])&(dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
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97 cum[count,t] <- length(tt)
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98 }
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99 x[count] <- i
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100 count <- count + 1
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101 }
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102 ymax <- max(cum[,1]/countL[1], na.rm=TRUE)
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103 for (i in c(2:n.types)) {
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104 ymax <- max(ymax,max(cum[,i]/countL[i], na.rm=TRUE))
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105 }
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106 myLocCol <- myColor[2]
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107
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108 par(mar=c(5.1, 7.1, 4.1, 2.1))
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109
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110 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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111 for (i in c(2:n.types)) {
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112 colorr <- i+1
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113 myLocCol <- c(myLocCol,myColor[colorr])
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114 lines (x,cum[,i]/countL[i] ,col = myColor[colorr],type="l", lwd = 2)
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115 # print (myColor[colorr])
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116 }
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117
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118 gradi <- 1000
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119 if (lim>10000) {
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120 gradi <- 10000
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121 }
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122 if (lim<3000) {
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123 gradi <- 500
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124 }
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125 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
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126 axisxlab <- paste(axisx/1000,"", sep = "")
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127 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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128 ymax <- max(cum[,i]/countL[i], na.rm=TRUE)
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129
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130 minor.tick(nx=5,tick.ratio=0.5)
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131
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132 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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133
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134 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
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135
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136 if (ifControl) {
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137 count <-1
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138 n.types <- length(levels(control.genes.ClosestPeakDist$Reg))
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139 myLevels <- levels(control.genes.ClosestPeakDist$Reg)
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140 cumCont = matrix( 0, nrow=lim/step +1, ncol=n.types, byrow = TRUE)
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141 for (i in c(1:n.types)) {
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142 t <- which ((dist_control_f$Reg==myLevels[i]))
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143 countLCont[i] <- length(t)
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144 }
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145 for (i in seq(length=lim/step +1, from=0, by=step)) {
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146 for (t in c(1:n.types)) {
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147 tt <- which ((dist_control_f$Reg==myLevels[t])&(dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
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148 cumCont[count,t] <- length(tt)
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149 }
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150 x[count] <- i
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151 count <- count + 1
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152 }
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153 ymax <- max(cumCont[,1]/countLCont[1], na.rm=TRUE)
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154 for (i in c(2:n.types)) {
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155 ymax <- max(ymax,max(cumCont[,i]/countLCont[i], na.rm=TRUE))
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156 }
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157 myLocColCntr <- myColorControl[2]
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158 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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159 for (i in c(2:n.types)) {
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160 colorr <- i+1
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161 myLocColCntr <- c(myLocColCntr,myColorControl[colorr])
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162 lines (x,cumCont[,i]/countLCont[i] ,col = myColorControl[colorr],type="l", lwd = 2)
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163 }
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164 if (lim>10000) {
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165 gradi <- 10000
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166 }
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167 if (lim<3000) {
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168 gradi <- 500
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169 }
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170 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
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171 axisxlab <- paste(axisx/1000, sep = "")
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172 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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173 minor.tick(nx=5,tick.ratio=0.5)
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174 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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175 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
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176 #real_vs_control_cumulative:
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177 count <-1
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178 countTotal <- length(dist_real_f$Reg)
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179 cumTotal <- 0
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180 for (i in seq(length=lim/step +1, from=0, by=step)) {
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181 t <- which ((dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
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182 cumTotal[count] <- length(t)
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183 x[count] <- i
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184 count <- count + 1
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185 }
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186 plot (x,cumTotal/countTotal ,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(0, lim),xaxt="n" )
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187 gradi <- 1000
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188 if (lim>10000) {
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189 gradi <- 10000
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190 }
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191 if (lim<3000) {
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192 gradi <- 500
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193 }
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194 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
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195 axisxlab <- paste(axisx/1000, sep = "")
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196 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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197 ymax <- max(cumTotal/countTotal, na.rm=TRUE)
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198 minor.tick(nx=5,tick.ratio=0.5)
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199 countTotalCont <- length(dist_control_f$Reg)
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200 cumTotalCont <- 0
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201 count <- 1
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202 for (i in seq(length=lim/step +1, from=0, by=step)) {
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203 t <- which ((dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
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204 cumTotalCont[count] <- length(t)
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205 x[count] <- i
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206 count <- count + 1
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207 }
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208 lines (x,cumTotalCont/countTotalCont ,col = colors()[328],type="l", lwd = 2)
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209 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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210 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
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211 }
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212 } else {
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213 countTotal <- length(dist_real_f$Reg)
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214 cumTotal <- 0
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215 count <-1
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216
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217 gradi <- 1000
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218 if (lim>10000) {
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219 gradi <- 10000
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220 }
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221 if (lim<3000) {
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222 gradi <- 500
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223 }
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224
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225 for (i in seq(length=lim/step +1, from=0, by=step)) {
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226 t <- which ((dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
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227 cumTotal[count] <- length(t)
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228 x[count] <- i
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229 count <- count + 1
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230 }
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231 par(mar=c(5.1, 7.1, 4.1, 2.1))
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232
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233 plot (x,cumTotal/countTotal ,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(0, lim),xaxt="n" )
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234 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
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235 axisxlab <- paste(axisx/1000, sep = "")
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236 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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237 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
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238 ymax <- max(cumTotal/countTotal, na.rm=TRUE)
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239 if (ifControl) {
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240 countTotalCont <- length(dist_control_f$Reg)
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241 cumTotalCont <- 0
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242 count <- 1
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243 for (i in seq(length=lim/step +1, from=0, by=step)) {
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244 t <- which ((dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
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245 cumTotalCont[count] <- length(t)
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246 x[count] <- i
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247 count <- count + 1
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248 }
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249 lines (x,cumTotalCont/countTotalCont ,col = colors()[328],type="l", lwd = 2)
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250 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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251 } else {
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252 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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253 }
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254 }
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255
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256 sink(args[6], append=FALSE, split=FALSE)
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257 if (ifReg) {
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258 if (ifControl) {
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259 cat (paste("Dist_TSS","% genes w/ a peak in ChIP","% genes w/ a peak in control",sep='\t'))
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260 cat("\t")
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261 for (i in c(1:n.types)) {
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262 cat(paste("% ", myLevels[i]," genes w/ a peak in ChIP", sep=""))
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263 cat("\t")
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264 }
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265
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266 for (i in c(1:n.types)) {
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267 cat(paste("% ", myLevels[i]," genes w/ a peak in Control", sep=""))
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268 cat("\t")
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269 }
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270 cat("\n")
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271 for (i in c(1:length(x))) {
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272 cat(paste(x[i],cumTotal[i]/countTotal,cumTotalCont[i]/countTotalCont,sep="\t"))
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273 cat("\t")
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274 for (t in c(1:n.types)) {
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275 cat(paste(cum[i,t]/countL[t],"\t", sep=""))
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276 }
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277 for (t in c(1:n.types)) {
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278 cat(paste(cumCont[i,t]/countLCont[t],"\t", sep=""))
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279 }
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280 cat("\n")
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281 }
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282 }else {
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283 cat (paste("Dist_TSS","\t",sep=''))
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284 for (i in c(1:n.types)) {
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285 cat(paste("% ", myLevels[i]," genes w/ a peak in ChIP", "\t", sep=""))
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286 }
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287 cat("\n")
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288 for (i in c(1:length(x))) {
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289 cat(paste(x[i],"\t",sep=""))
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290 for (t in c(1:n.types)) {
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291 cat(paste(cum[i,t]/countL[t],"\t", sep=""))
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292 }
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293 cat("\n")
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294 }
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295 }
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296 } else {
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297 if (ifControl) {
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298 cat (paste("Dist_TSS","% genes w/ a peak in ChIP","% genes w/ a peak in control",sep='\t'))
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299 cat("\n")
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300 for (i in c(1:length(x))) {
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301 cat(paste(x[i],cumTotal[i]/countTotal,cumTotalCont[i]/countTotalCont,sep="\t"))
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302 cat("\n")
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303 }
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304 }else {
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305 cat (paste("Dist_TSS","% genes w/ a peak in ChIP",sep='\t'))
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306 cat("\n")
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307 for (i in c(1:length(x))) {
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308 cat(paste(x[i],cumTotal[i]/countTotal,sep="\t"))
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309 cat("\n")
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310 }
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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 #stop sinking:
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317 sink()
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318
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319 #around TSS:
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320 lim <- maxValue
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321 step <- myStep
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322 my_breaks <- seq(length=lim/step*2 +1, from=-lim, by=step)
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323 chip.genes <- read.table(file=paste(args[4],".genes", sep=""), header=TRUE) ;
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324 dist_real_f <- chip.genes
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325 if (ifControl) {
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326 control.genes <- read.table(file=paste(args[4],".genes", sep=""), header=TRUE) ;
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327 dist_control_f<-data.frame(control.genes)
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328 }
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329 if (ifReg) {
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330 #n.types <- length(levels(chip.genes.ClosestPeakDist$Reg))
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331 #myLevels <- levels(dist_real_f$Reg)
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332
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333 t<- which (dist_real_f$Reg==myLevels[1])
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334 values_real <-dist_real_f$Dist[t]
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335 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
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336 ymax <- max(hTSSreal$density, na.rm=TRUE)
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337 for (i in c(2:n.types)) {
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338 t<- which (dist_real_f$Reg==myLevels[i])
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339 values_real <-dist_real_f$Dist[t]
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340 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
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341 ymax <- max(ymax,max(hTSSreal$density, na.rm=TRUE))
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342 }
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343
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344
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345 t<- which (dist_real_f$Reg==myLevels[1])
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346 values_real <-dist_real_f$Dist[t]
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347 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
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348 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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349
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350 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
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351
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352 for (i in c(2:n.types)) {
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353 t<- which (dist_real_f$Reg==myLevels[i])
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354 values_real <-dist_real_f$Dist[t]
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355 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
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356 lines (hTSSreal$mids,hTSSreal$density,col = myLocCol[i],type="l", lwd = 2)
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357 }
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358 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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359
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360 gradi <- 1000
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361 if (lim>10000) {
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362 gradi <- 10000
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363 }
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364 if (lim<3000) {
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365 gradi <- 500
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366 }
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367
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368 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
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369 axisxlab <- paste(axisx/1000, sep = "")
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370 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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371
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372
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373 #minor.tick(nx=10,tick.ratio=0.5)
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374 if (ifControl) {
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375 t<- which (dist_control_f$Reg==myLevels[1])
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376 values_control <-dist_control_f$Dist[t]
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377 hTSScontrol= hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
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378 ymax <- max(hTSScontrol$density, na.rm=TRUE)
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379 for (i in c(2:n.types)) {
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380 t<- which (dist_control_f$Reg==myLevels[i])
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381 values_control <-dist_control_f$Dist[t]
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382 hTSScontrol = hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
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383 ymax <- max(ymax,max(hTSScontrol$density, na.rm=TRUE))
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384 }
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385 t<- which (dist_control_f$Reg==myLevels[1])
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386 values_control <-dist_control_f$Dist[t]
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387 hTSScontrol= hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
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388 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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389 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
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390 for (i in c(2:n.types)) {
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391 t<- which (dist_control_f$Reg==myLevels[i])
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392 values_control <-dist_control_f$Dist[t]
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393 hTSScontrol = hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
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394 lines (hTSScontrol$mids,hTSScontrol$density,col = myLocColCntr[i],type="l", lwd = 2)
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395 }
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396
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397 gradi <- 1000
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398 if (lim>10000) {
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399 gradi <- 10000
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400 }
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401 if (lim<3000) {
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402 gradi <- 500
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403 }
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404
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405 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
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406 axisxlab <- paste(axisx/1000, sep = "")
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407 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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408
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409 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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410
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411 # minor.tick(nx=10,tick.ratio=0.5)
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412 #control vs real
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413 values_real <-dist_real_f$Dist
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414 hTSSreal = hist(values_real, plot=FALSE, breaks = c(min(values_real),my_breaks,max(values_real)) )
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415 plot (hTSSreal$mids,hTSSreal$density,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(-lim, lim),xaxt="n")
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416 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
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417 ymax <- max(hTSSreal$density, na.rm=TRUE)
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418 values_control <-dist_control_f$Dist
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419 hTSScontrol = hist(values_control, plot=FALSE, breaks = c(min(values_control),my_breaks,max(values_control)) )
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420 lines (hTSScontrol$mids,hTSScontrol$density,col = colors()[328],type="l", lwd = 2)
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421 legend(lim*0.2, ymax*0.9, c("ChIP","Control"), cex=1 , lwd = 2, bty = "n", col = c(myColor[1], colors()[328]), lty = c(1), pt.bg= c(myColor[1], colors()[328]) , merge = TRUE)
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422
|
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423 gradi <- 1000
|
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424 if (lim>10000) {
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425 gradi <- 10000
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426 }
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427 if (lim<3000) {
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428 gradi <- 500
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429 }
|
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430
|
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431 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
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432 axisxlab <- paste(axisx/1000, sep = "")
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433 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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434
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435
|
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436
|
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437 # minor.tick(nx=10,tick.ratio=0.5)
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438 }
|
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439 } else {
|
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440 values_real <-dist_real_f$Dist
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441 hTSSreal = hist(values_real, plot=FALSE, breaks = c(min(values_real),my_breaks,max(values_real)) )
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442 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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443 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
|
|
|
444 ymax <- max(hTSSreal$density, na.rm=TRUE)
|
|
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445 if (ifControl) {
|
|
|
446 values_control <-dist_control_f$Dist
|
|
|
447 hTSScontrol = hist(values_control, plot=FALSE, breaks = c(min(values_control),my_breaks,max(values_control)) )
|
|
|
448 lines (hTSScontrol$mids,hTSScontrol$density,col = colors()[328],type="l", lwd = 2)
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449 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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450 } else {
|
|
|
451 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)
|
|
|
452 }
|
|
|
453
|
|
|
454 gradi <- 1000
|
|
|
455 if (lim>10000) {
|
|
|
456 gradi <- 10000
|
|
|
457 }
|
|
|
458 if (lim<3000) {
|
|
|
459 gradi <- 500
|
|
|
460 }
|
|
|
461
|
|
|
462 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
|
|
|
463 axisxlab <- paste(axisx/1000, sep = "")
|
|
|
464 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
|
|
|
465
|
|
|
466
|
|
|
467 # minor.tick(nx=10,tick.ratio=0.5)
|
|
|
468 }
|
|
|
469 suppressMessages(dev.off())
|
|
|
470 q();
|
|
|
471 cat (paste("peak height","# peaks in ChIP","# peaks in Control","#control/chip","\n",sep='\t'))
|
|
|
472 for (xval in c(minValue:maxValue)) {
|
|
|
473 for (i in (1:length(chipHist$mids))) {
|
|
|
474 if (xval==chipHist$mids[i]) {
|
|
|
475 ychip <- chipHist$counts[i]
|
|
|
476 }
|
|
|
477 }
|
|
|
478 for (i in (1:length(controlHist$mids))) {
|
|
|
479 if (xval==controlHist$mids[i]) {
|
|
|
480 ycontrol <- controlHist$counts[i]
|
|
|
481 }
|
|
|
482 }
|
|
|
483 cat (paste(xval,ychip,ycontrol,ycontrol/ychip,"\n",sep='\t'))
|
|
|
484 }
|
