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3
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1 #!/usr/bin/env Rscript
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2
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3 #usage $0 STEP RIGHT chipPeaks outputFile.png output.txt [controlPeaks] [1 for pdf]
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4 args <- commandArgs(TRUE)
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5 myStep <- type.convert(args[2])
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6 maxValue <- type.convert(args[3])
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7
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8 dataTable <-read.table(file=paste(args[4],".genes.ClosestPeakDist", sep=""), header=TRUE);
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9 chip.genes.ClosestPeakDist<-data.frame(dataTable)
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10 ifReg <- 0
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11 if (length(unique(chip.genes.ClosestPeakDist$Reg))>1) {
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12 ifReg <- 1
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13 }
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14 ifControl <- 0
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15
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16 ifPDF <- 0
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17 if (length(args)>=8) {
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18 ifPDF=args[8]
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19 }
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20 if (length(args)==7 & args[7]==1) {
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21 ifPDF=1
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22 }
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23
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24 suppressMessages(library(Hmisc))
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25
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26 if (length(args)>=7 & args[7]!=1 & args[7]!=0) {
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27 dataTable <-read.table(file=paste(args[7],".genes.ClosestPeakDist", sep=""), header=TRUE);
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28 control.genes.ClosestPeakDist<-data.frame(dataTable)
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29 ifControl <- 1
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30 }
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31 if (ifReg & ifControl) {
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32 if (ifPDF==1) {
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33 pdf(file = args[5], width = 19, height = 8, pointsize = 20, bg = "white")
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34 } else {
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35 png(file = args[5], type="cairo", width = 1440 , height = 680, units = "px", pointsize = 20, bg = "white", res = NA)
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36 plot(1:10)
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37 }
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38 op <- par(mfrow = c(2,3))
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39 } else {
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40 if (ifPDF==1) {
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41 pdf(file = args[5], width = 10, height = 13, pointsize = 20, bg = "white")
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42 } else {
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43 png(file = args[5], type="cairo", width = 680, height = 880, units = "px", pointsize = 20, bg = "white", res = NA)
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44 plot(1:10)
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45 }
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46 op <- par(mfrow = c(2,1))
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47 }
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48 myColor <- 1
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49 myColor[1] <- colors()[131]
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50 myColor[2] <- "darkolivegreen3"
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51 myColor[3] <- "azure4"
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52 myColor[4] <- "royalblue3"
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53 myColor[5] <- colors()[17]
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54
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55 myColorControl <- 1
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56
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57 myColorControl[1] <- colors()[24]
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58 myColorControl[2] <- colors()[278]
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59 myColorControl[3] <- colors()[305]
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60 myColorControl[4] <- colors()[219]
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61 myColorControl[5] <- colors()[343]
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62
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63
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64
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65 #for cumulative:
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66 dist_real_f <- chip.genes.ClosestPeakDist
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67 if (ifControl) {
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68 dist_control_f <- control.genes.ClosestPeakDist
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69 }
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70 step <- myStep
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71 lim <- maxValue
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72 x <- 0
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73 count <- 1
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74 countL <-1
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75 n.types <- 1
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76 myLevels <- 0
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77 countTotalCont <- 0
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78 countTotal <-0
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79 countLCont <- 0
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80 cumTotalCont <- 0
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81 if (ifReg) {
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82 n.types <- length(levels(chip.genes.ClosestPeakDist$Reg))
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83 myLevels <- levels(chip.genes.ClosestPeakDist$Reg)
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84 cum = matrix( 0, nrow=lim/step +1, ncol=n.types, byrow = TRUE)
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85 for (i in c(1:n.types)) {
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86 t <- which ((dist_real_f$Reg==myLevels[i]))
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87 countL[i] <- length(t)
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88 }
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89 count <-1
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90 for (i in seq(length=lim/step +1, from=0, by=step)) {
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91 for (t in c(1:n.types)) {
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92 tt <- which ((dist_real_f$Reg==myLevels[t])&(dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
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93 cum[count,t] <- length(tt)
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94 }
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95 x[count] <- i
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96 count <- count + 1
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97 }
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98 ymax <- max(cum[,1]/countL[1], na.rm=TRUE)
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99 for (i in c(2:n.types)) {
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100 ymax <- max(ymax,max(cum[,i]/countL[i], na.rm=TRUE))
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101 }
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102 myLocCol <- myColor[2]
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103
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104 par(mar=c(5.1, 7.1, 4.1, 2.1))
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105
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106 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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107 for (i in c(2:n.types)) {
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108 colorr <- i+1
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109 myLocCol <- c(myLocCol,myColor[colorr])
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110 lines (x,cum[,i]/countL[i] ,col = myColor[colorr],type="l", lwd = 2)
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111 # print (myColor[colorr])
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112 }
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113
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114 gradi <- 1000
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115 if (lim>10000) {
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116 gradi <- 10000
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117 }
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118 if (lim<3000) {
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119 gradi <- 500
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120 }
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121 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
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122 axisxlab <- paste(axisx/1000,"", sep = "")
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123 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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124 ymax <- max(cum[,i]/countL[i], na.rm=TRUE)
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125
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126 minor.tick(nx=5,tick.ratio=0.5)
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127
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128 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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129
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130 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
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131
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132 if (ifControl) {
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133 count <-1
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134 n.types <- length(levels(control.genes.ClosestPeakDist$Reg))
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135 myLevels <- levels(control.genes.ClosestPeakDist$Reg)
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136 cumCont = matrix( 0, nrow=lim/step +1, ncol=n.types, byrow = TRUE)
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137 for (i in c(1:n.types)) {
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138 t <- which ((dist_control_f$Reg==myLevels[i]))
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139 countLCont[i] <- length(t)
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140 }
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141 for (i in seq(length=lim/step +1, from=0, by=step)) {
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142 for (t in c(1:n.types)) {
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143 tt <- which ((dist_control_f$Reg==myLevels[t])&(dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
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144 cumCont[count,t] <- length(tt)
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145 }
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146 x[count] <- i
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147 count <- count + 1
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148 }
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149 ymax <- max(cumCont[,1]/countLCont[1], na.rm=TRUE)
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150 for (i in c(2:n.types)) {
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151 ymax <- max(ymax,max(cumCont[,i]/countLCont[i], na.rm=TRUE))
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152 }
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153 myLocColCntr <- myColorControl[2]
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154 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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155 for (i in c(2:n.types)) {
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156 colorr <- i+1
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157 myLocColCntr <- c(myLocColCntr,myColorControl[colorr])
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158 lines (x,cumCont[,i]/countLCont[i] ,col = myColorControl[colorr],type="l", lwd = 2)
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159 }
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160 if (lim>10000) {
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161 gradi <- 10000
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162 }
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163 if (lim<3000) {
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164 gradi <- 500
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165 }
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166 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
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167 axisxlab <- paste(axisx/1000, sep = "")
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168 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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169 minor.tick(nx=5,tick.ratio=0.5)
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170 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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171 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
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172 #real_vs_control_cumulative:
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173 count <-1
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174 countTotal <- length(dist_real_f$Reg)
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175 cumTotal <- 0
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176 for (i in seq(length=lim/step +1, from=0, by=step)) {
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177 t <- which ((dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
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178 cumTotal[count] <- length(t)
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179 x[count] <- i
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180 count <- count + 1
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181 }
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182 plot (x,cumTotal/countTotal ,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(0, lim),xaxt="n" )
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183 gradi <- 1000
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184 if (lim>10000) {
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185 gradi <- 10000
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186 }
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187 if (lim<3000) {
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188 gradi <- 500
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189 }
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190 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
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191 axisxlab <- paste(axisx/1000, sep = "")
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192 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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193 ymax <- max(cumTotal/countTotal, na.rm=TRUE)
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194 minor.tick(nx=5,tick.ratio=0.5)
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195 countTotalCont <- length(dist_control_f$Reg)
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196 cumTotalCont <- 0
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197 count <- 1
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198 for (i in seq(length=lim/step +1, from=0, by=step)) {
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199 t <- which ((dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
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200 cumTotalCont[count] <- length(t)
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201 x[count] <- i
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202 count <- count + 1
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203 }
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204 lines (x,cumTotalCont/countTotalCont ,col = colors()[328],type="l", lwd = 2)
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205 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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206 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
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207 }
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208 } else {
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209 countTotal <- length(dist_real_f$Reg)
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210 cumTotal <- 0
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211 count <-1
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212
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213 gradi <- 1000
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214 if (lim>10000) {
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215 gradi <- 10000
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216 }
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217 if (lim<3000) {
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218 gradi <- 500
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219 }
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220
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221 for (i in seq(length=lim/step +1, from=0, by=step)) {
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222 t <- which ((dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
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223 cumTotal[count] <- length(t)
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224 x[count] <- i
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225 count <- count + 1
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226 }
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227 par(mar=c(5.1, 7.1, 4.1, 2.1))
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228
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229 plot (x,cumTotal/countTotal ,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(0, lim),xaxt="n" )
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230 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
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231 axisxlab <- paste(axisx/1000, sep = "")
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232 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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233 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
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234 ymax <- max(cumTotal/countTotal, na.rm=TRUE)
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235 if (ifControl) {
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236 countTotalCont <- length(dist_control_f$Reg)
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237 cumTotalCont <- 0
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238 count <- 1
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239 for (i in seq(length=lim/step +1, from=0, by=step)) {
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240 t <- which ((dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
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241 cumTotalCont[count] <- length(t)
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242 x[count] <- i
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243 count <- count + 1
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244 }
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245 lines (x,cumTotalCont/countTotalCont ,col = colors()[328],type="l", lwd = 2)
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246 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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247 } else {
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248 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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249 }
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250 }
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251
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252 sink(args[6], append=FALSE, split=FALSE)
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253 if (ifReg) {
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254 if (ifControl) {
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255 cat (paste("Dist_TSS","% genes w/ a peak in ChIP","% genes w/ a peak in control",sep='\t'))
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256 cat("\t")
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257 for (i in c(1:n.types)) {
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258 cat(paste("% ", myLevels[i]," genes w/ a peak in ChIP", sep=""))
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259 cat("\t")
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260 }
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261
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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 Control", sep=""))
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264 cat("\t")
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265 }
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266 cat("\n")
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267 for (i in c(1:length(x))) {
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268 cat(paste(x[i],cumTotal[i]/countTotal,cumTotalCont[i]/countTotalCont,sep="\t"))
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269 cat("\t")
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270 for (t in c(1:n.types)) {
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271 cat(paste(cum[i,t]/countL[t],"\t", sep=""))
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272 }
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273 for (t in c(1:n.types)) {
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274 cat(paste(cumCont[i,t]/countLCont[t],"\t", sep=""))
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275 }
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276 cat("\n")
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277 }
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278 }else {
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279 cat (paste("Dist_TSS","\t",sep=''))
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280 for (i in c(1:n.types)) {
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281 cat(paste("% ", myLevels[i]," genes w/ a peak in ChIP", "\t", sep=""))
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282 }
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283 cat("\n")
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284 for (i in c(1:length(x))) {
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285 cat(paste(x[i],"\t",sep=""))
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286 for (t in c(1:n.types)) {
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287 cat(paste(cum[i,t]/countL[t],"\t", sep=""))
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288 }
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289 cat("\n")
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290 }
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291 }
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292 } else {
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293 if (ifControl) {
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294 cat (paste("Dist_TSS","% genes w/ a peak in ChIP","% genes w/ a peak in control",sep='\t'))
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295 cat("\n")
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296 for (i in c(1:length(x))) {
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297 cat(paste(x[i],cumTotal[i]/countTotal,cumTotalCont[i]/countTotalCont,sep="\t"))
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298 cat("\n")
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299 }
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300 }else {
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301 cat (paste("Dist_TSS","% genes w/ a peak in ChIP",sep='\t'))
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302 cat("\n")
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303 for (i in c(1:length(x))) {
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304 cat(paste(x[i],cumTotal[i]/countTotal,sep="\t"))
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305 cat("\n")
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306 }
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307
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308 }
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309 }
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310
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311
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312 #stop sinking:
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313 sink()
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314
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315 #around TSS:
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316 lim <- maxValue
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317 step <- myStep
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318 my_breaks <- seq(length=lim/step*2 +1, from=-lim, by=step)
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319 chip.genes <- read.table(file=paste(args[4],".genes", sep=""), header=TRUE) ;
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320 dist_real_f <- chip.genes
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321 if (ifControl) {
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322 control.genes <- read.table(file=paste(args[4],".genes", sep=""), header=TRUE) ;
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323 dist_control_f<-data.frame(control.genes)
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324 }
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325 if (ifReg) {
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326 #n.types <- length(levels(chip.genes.ClosestPeakDist$Reg))
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327 #myLevels <- levels(dist_real_f$Reg)
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328
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329 t<- which (dist_real_f$Reg==myLevels[1])
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330 values_real <-dist_real_f$Dist[t]
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331 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
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332 ymax <- max(hTSSreal$density, na.rm=TRUE)
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333 for (i in c(2:n.types)) {
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334 t<- which (dist_real_f$Reg==myLevels[i])
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335 values_real <-dist_real_f$Dist[t]
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336 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
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337 ymax <- max(ymax,max(hTSSreal$density, na.rm=TRUE))
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338 }
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339
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340
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341 t<- which (dist_real_f$Reg==myLevels[1])
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342 values_real <-dist_real_f$Dist[t]
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343 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
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344 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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345
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346 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
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347
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348 for (i in c(2:n.types)) {
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349 t<- which (dist_real_f$Reg==myLevels[i])
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350 values_real <-dist_real_f$Dist[t]
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351 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
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352 lines (hTSSreal$mids,hTSSreal$density,col = myLocCol[i],type="l", lwd = 2)
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353 }
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354 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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355
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356 gradi <- 1000
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357 if (lim>10000) {
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358 gradi <- 10000
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359 }
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360 if (lim<3000) {
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361 gradi <- 500
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362 }
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363
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364 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
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365 axisxlab <- paste(axisx/1000, sep = "")
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366 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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367
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368
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369 #minor.tick(nx=10,tick.ratio=0.5)
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370 if (ifControl) {
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371 t<- which (dist_control_f$Reg==myLevels[1])
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372 values_control <-dist_control_f$Dist[t]
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373 hTSScontrol= hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
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374 ymax <- max(hTSScontrol$density, na.rm=TRUE)
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375 for (i in c(2:n.types)) {
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376 t<- which (dist_control_f$Reg==myLevels[i])
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377 values_control <-dist_control_f$Dist[t]
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378 hTSScontrol = hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
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379 ymax <- max(ymax,max(hTSScontrol$density, na.rm=TRUE))
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380 }
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381 t<- which (dist_control_f$Reg==myLevels[1])
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382 values_control <-dist_control_f$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 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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385 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
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386 for (i in c(2:n.types)) {
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387 t<- which (dist_control_f$Reg==myLevels[i])
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388 values_control <-dist_control_f$Dist[t]
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389 hTSScontrol = hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
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390 lines (hTSScontrol$mids,hTSScontrol$density,col = myLocColCntr[i],type="l", lwd = 2)
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391 }
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392
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393 gradi <- 1000
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394 if (lim>10000) {
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395 gradi <- 10000
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396 }
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397 if (lim<3000) {
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398 gradi <- 500
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399 }
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400
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401 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
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402 axisxlab <- paste(axisx/1000, sep = "")
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403 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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404
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405 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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406
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407 # minor.tick(nx=10,tick.ratio=0.5)
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408 #control vs real
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409 values_real <-dist_real_f$Dist
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410 hTSSreal = hist(values_real, plot=FALSE, breaks = c(min(values_real),my_breaks,max(values_real)) )
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411 plot (hTSSreal$mids,hTSSreal$density,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(-lim, lim),xaxt="n")
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412 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
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413 ymax <- max(hTSSreal$density, na.rm=TRUE)
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414 values_control <-dist_control_f$Dist
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415 hTSScontrol = hist(values_control, plot=FALSE, breaks = c(min(values_control),my_breaks,max(values_control)) )
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416 lines (hTSScontrol$mids,hTSScontrol$density,col = colors()[328],type="l", lwd = 2)
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417 legend(lim*0.2, ymax*0.9, c("ChIP","Control"), cex=1 , lwd = 2, bty = "n", col = c(myColor[1], colors()[328]), lty = c(1), pt.bg= c(myColor[1], colors()[328]) , merge = TRUE)
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418
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419 gradi <- 1000
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420 if (lim>10000) {
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421 gradi <- 10000
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422 }
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423 if (lim<3000) {
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424 gradi <- 500
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425 }
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426
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427 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
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428 axisxlab <- paste(axisx/1000, sep = "")
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429 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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430
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431
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432
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433 # minor.tick(nx=10,tick.ratio=0.5)
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434 }
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435 } else {
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436 values_real <-dist_real_f$Dist
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437 hTSSreal = hist(values_real, plot=FALSE, breaks = c(min(values_real),my_breaks,max(values_real)) )
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438 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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439 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
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440 ymax <- max(hTSSreal$density, na.rm=TRUE)
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441 if (ifControl) {
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442 values_control <-dist_control_f$Dist
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443 hTSScontrol = hist(values_control, plot=FALSE, breaks = c(min(values_control),my_breaks,max(values_control)) )
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444 lines (hTSScontrol$mids,hTSScontrol$density,col = colors()[328],type="l", lwd = 2)
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445 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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446 } else {
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447 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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448 }
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449
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450 gradi <- 1000
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451 if (lim>10000) {
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452 gradi <- 10000
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453 }
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454 if (lim<3000) {
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455 gradi <- 500
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456 }
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457
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458 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
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459 axisxlab <- paste(axisx/1000, sep = "")
|
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460 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
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461
|
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462
|
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463 # minor.tick(nx=10,tick.ratio=0.5)
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464 }
|
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465 suppressMessages(dev.off())
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466 q();
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467 cat (paste("peak height","# peaks in ChIP","# peaks in Control","#control/chip","\n",sep='\t'))
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468 for (xval in c(minValue:maxValue)) {
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469 for (i in (1:length(chipHist$mids))) {
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470 if (xval==chipHist$mids[i]) {
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471 ychip <- chipHist$counts[i]
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472 }
|
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473 }
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474 for (i in (1:length(controlHist$mids))) {
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475 if (xval==controlHist$mids[i]) {
|
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476 ycontrol <- controlHist$counts[i]
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477 }
|
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478 }
|
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|
479 cat (paste(xval,ychip,ycontrol,ycontrol/ychip,"\n",sep='\t'))
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480 }
|
