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