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3
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1 #usage $0 STEP RIGHT chipPeaks outputFile.png output.txt [controlPeaks]
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2 args <- commandArgs(TRUE)
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3
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4 input <- args[2]
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5 pngFile <- args[3]
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6 dataTable <-read.table(file=input, header=TRUE);
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7 chip.data<-data.frame(dataTable)
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8 ifReg <- 0
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9 if (length(unique(chip.data$Reg))>1) {
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10 ifReg <- 1
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11 }
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12
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13 ifPDF <- 0
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14 if (length(args)>=5) {
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15 ifPDF=args[5]
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16 }
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17 if (length(args)==4 & args[4]==1) {
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18 ifPDF=1
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19 }
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20
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21 ifControl <- 0
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22 if (length(args)>=4 & args[4]!=1 & args[4]!=0) {
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23 dataTable <-read.table(file=args[4], header=TRUE);
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24 control.data<-data.frame(dataTable)
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25 ifControl <- 1
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26 }
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27 if (ifReg & ifControl) {
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28
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29 if (ifPDF==1) {
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30 pdf(file = pngFile, width = 14, height = 13, pointsize = 20, bg = "white")
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31 } else {
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32 png(filename = pngFile, width = 1440, height = 1040, units = "px", pointsize = 20, bg = "white", res = NA)
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33 plot(1:10)
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34 }
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35 op <- par(mfrow = c(3,2))
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36 } else {
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37
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38 if (ifPDF==1) {
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39 pdf(file = pngFile, width = 22, height = 8, pointsize = 20, bg = "white")
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40 } else {
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41 png(filename = pngFile, width = 1580, height = 530, units = "px", pointsize = 20, bg = "white", res = NA)
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42 plot(1:10)
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43 }
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44 op <- par(mfrow = c(1,2))
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45 }
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46 myColor <- 1
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47 myColor[1] <- colors()[131]
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48 myColor[2] <- colors()[59]
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49 myColor[3] <- colors()[76]
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50 myColor[4] <- colors()[88]
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51 myColor[5] <- colors()[17]
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52 myColor[6] <- colors()[565]
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53 myColorControl <- 1
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54 myColorControl[1] <- colors()[24]
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55 myColorControl[2] <- colors()[278]
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56 myColorControl[3] <- colors()[305]
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57 myColorControl[4] <- colors()[219]
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58 myColorControl[5] <- colors()[343]
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59 myColorControl[6] <- colors()[245]
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60 myLevels <- 0
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61 if (ifReg) {
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62 if (ifControl) {
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63 #control vs real:
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64
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65 countTotal <- length(chip.data$Reg)
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66 totalChIP <- summary(chip.data$Type)/countTotal
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67 tt <- which(chip.data$Type=="intragenic")
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68 subset.chip <- chip.data[tt,]
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69 countIntra <- length(subset.chip$Reg)
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70 intraChip<- summary(subset.chip$TypeIntra)/countTotal
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71 nlev <- length(levels(chip.data$Type))
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72 countTotalCont <- length(control.data$Reg)
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73 totalContr <- summary(control.data$Type)/countTotalCont
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74 tt <- which(control.data$Type=="intragenic")
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75 subset.control <- control.data[tt,]
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76 countIntraCont <- length(subset.control$Reg)
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77 intraControl<- summary(subset.control$TypeIntra)/countTotalCont
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78 cum = matrix( 0, nrow=2, ncol=nlev, byrow = TRUE)
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79 for (i in c(1:nlev)) {
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80 cum[1,i] <- totalChIP[i]
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81 cum[2,i] <- totalContr[i]
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82 }
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83
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84 labels<-c("GeneDown.", "Enh.", "Imm.Down.", "Interg.", "Intrag.", "Prom.")
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85 if (length(labels)==length(levels(chip.data$Type))) {
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86 barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],colors()[328]), names.arg=labels,ylab="Proportion of peaks")
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87 } else {
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88 barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],colors()[328]), names.arg=c(levels(chip.data$Type)),ylab="Proportion of peaks")
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89 }
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90
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91 position <- 'topleft'
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92 inset <- c(0.1, 0)
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93 legend(position, c("ChIP","Control"), bty="n",fill=c(myColor[1],colors()[328]), inset=inset)
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94
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95 nlev <- length(levels(subset.chip$TypeIntra))
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96 cum = matrix( 0, nrow=2, ncol=nlev, byrow = TRUE)
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97 for (i in c(1:nlev)) {
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98 cum[1,i] <- intraChip[i]
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99 cum[2,i] <- intraControl[i]
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100 }
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101 barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],colors()[328]), names.arg=c(levels(subset.chip$TypeIntra)),ylab="Proportion of peaks")
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102
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103 position <- 'topleft'
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104 inset <- c(0.1, 0)
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105 legend(position, c("ChIP","Control"), bty="n",fill=c(myColor[1],colors()[328]), inset=inset)
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106 }
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107 n.types <- length(levels(chip.data$Reg))
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108 myLevels <- levels(chip.data$Reg)
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109 nlev <- length(levels(chip.data$Type))
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110 cum = matrix( 0, nrow=length(myLevels), ncol=nlev, byrow = TRUE)
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111 countTotal <- length(chip.data$Reg)
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112 colReg <-NULL
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113 for (r in c(1:length(myLevels))) {
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114 tt <- which(chip.data$Reg==myLevels[r])
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115 totalChIP <- summary(chip.data$Type[tt])/countTotal
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116 for (i in c(1:nlev)) {
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117 cum[r,i] <- totalChIP[i]
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118 }
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119 colReg[r]<-myColor[r+3]
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120 }
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121
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122 labels<-c("GeneDown.", "Enh.", "Imm.Down.", "Interg.", "Intrag.", "Prom.")
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123 if (length(labels)==length(levels(chip.data$Type))) {
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124 #barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],myColor[5]), names.arg=labels,ylab="Proportion of peaks")
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125 barplot(cum,xlab="",beside=TRUE, col=c(colReg), names.arg=labels,ylab="Proportion of peaks")
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126 } else {
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127 barplot(cum,xlab="",beside=TRUE, col=c(colReg), names.arg=c(levels(chip.data$Type)),ylab="Proportion of peaks")
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128 }
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129
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130 position <- 'topleft'
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131 inset <- c(0.1, 0)
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132 legend(position, c(myLevels), bty="n",fill=c(colReg), inset=inset)
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133
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134
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135 nlev <- length(levels(chip.data$TypeIntra))
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136 cum = matrix( 0, nrow=length(myLevels), ncol=nlev, byrow = TRUE)
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137 for (r in c(1:length(myLevels))) {
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138 tt <- which(chip.data$Reg==myLevels[r]&chip.data$Type=="intragenic")
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139 totalChIP <- summary(chip.data$TypeIntra[tt])/countTotal
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140 for (i in c(1:nlev)) {
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141 cum[r,i] <- totalChIP[i]
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142 }
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143 }
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144 barplot(cum,xlab="",beside=TRUE, col=c(colReg), names.arg=c(levels(chip.data$TypeIntra)),ylab="Proportion of peaks")
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145 position <- 'topleft'
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146 inset <- c(0.1, 0)
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147 legend(position, c(myLevels), bty="n",fill=c(colReg), inset=inset)
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148
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149
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150 if (ifControl) {
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151 nlev <- length(levels(control.data$Type))
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152 cum = matrix( 0, nrow=length(myLevels), ncol=nlev, byrow = TRUE)
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153 countTotal <- length(control.data$Reg)
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154 colReg <-NULL
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155 for (r in c(1:length(myLevels))) {
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156 tt <- which(control.data$Reg==myLevels[r])
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157 totalcontrol <- summary(control.data$Type[tt])/countTotal
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158 for (i in c(1:nlev)) {
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159 cum[r,i] <- totalcontrol[i]
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160 }
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161 colReg[r]<-myColorControl[r+3]
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162 }
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163 labels<-c("GeneDown.", "Enh.", "Imm.Down.", "Interg.", "Intrag.", "Prom.")
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164 if (length(labels)==length(levels(chip.data$Type))) {
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165 barplot(cum,xlab="",beside=TRUE, col=c(colReg), names.arg=labels,ylab="Proportion of peaks")
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166 } else {
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167 barplot(cum,xlab="",beside=TRUE, col=c(colReg), names.arg=c(levels(control.data$Type)),ylab="Proportion of peaks")
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168 }
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169 position <- 'topleft'
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170 inset <- c(0.1, 0)
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171 legend(position, c(myLevels), bty="n",fill=c(colReg), inset=inset)
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172
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173 nlev <- length(levels(control.data$TypeIntra))
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174 cum = matrix( 0, nrow=length(myLevels), ncol=nlev, byrow = TRUE)
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175 for (r in c(1:length(myLevels))) {
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176 tt <- which(control.data$Reg==myLevels[r]&control.data$Type=="intragenic")
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177 totalcontrol <- summary(control.data$TypeIntra[tt])/countTotal
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178 for (i in c(1:nlev)) {
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179 cum[r,i] <- totalcontrol[i]
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180 }
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181 }
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182 barplot(cum,xlab="",beside=TRUE, col=c(colReg), names.arg=c(levels(control.data$TypeIntra)),ylab="Proportion of peaks")
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183 position <- 'topleft'
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184 inset <- c(0.1, 0)
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185 legend(position, c(myLevels), bty="n",fill=c(colReg), inset=inset)
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186 }
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187 } else {
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188 countTotal <- length(chip.data$Reg)
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189 totalChIP <- summary(chip.data$Type)/countTotal
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190 tt <- which(chip.data$Type=="intragenic")
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191 subset.chip <- chip.data[tt,]
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192 countIntra <- length(subset.chip$Reg)
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193 intraChip<- summary(subset.chip$TypeIntra)/countTotal
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194 nlev <- length(levels(chip.data$Type))
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195 if (ifControl) {
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196 countTotalCont <- length(control.data$Reg)
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197 totalContr <- summary(control.data$Type)/countTotalCont
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198 tt <- which(control.data$Type=="intragenic")
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199 subset.control <- control.data[tt,]
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200 countIntraCont <- length(subset.control$Reg)
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201 intraControl<- summary(subset.control$TypeIntra)/countTotalCont
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202 cum = matrix( 0, nrow=2, ncol=nlev, byrow = TRUE)
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203 for (i in c(1:nlev)) {
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204 cum[1,i] <- totalChIP[i]
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205 cum[2,i] <- totalContr[i]
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206 }
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207
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208 labels<-c("GeneDown.", "Enh.", "Imm.Down.", "Interg.", "Intrag.", "Prom.")
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209 if (length(labels)==length(levels(chip.data$Type))) {
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210 #barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],myColor[5]), names.arg=labels,ylab="Proportion of peaks")
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211 barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],colors()[328]), names.arg=labels,ylab="Proportion of peaks")
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212 } else {
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213 barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],colors()[328]), names.arg=c(levels(chip.data$Type)),ylab="Proportion of peaks")
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214 }
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215
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216 position <- 'topleft'
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217 inset <- c(0.1, 0)
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218 legend(position,c("ChIP","Control"), bty="n",fill=c(myColor[1],colors()[328]), inset=inset)
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219
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220 nlev <- length(levels(subset.chip$TypeIntra))
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221 cum = matrix( 0, nrow=2, ncol=nlev, byrow = TRUE)
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222 for (i in c(1:nlev)) {
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223 cum[1,i] <- intraChip[i]
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224 cum[2,i] <- intraControl[i]
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225 }
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226 barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],colors()[328]), names.arg=c(levels(subset.chip$TypeIntra)),ylab="Proportion of peaks")
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227 position <- 'topleft'
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228 inset <- c(0.1, 0)
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229 legend(position,c("ChIP","Control"), bty="n",fill=c(myColor[1],colors()[328]), inset=inset)
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230
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231 } else {
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232 labels<-c("GeneDown.", "Enh.", "Imm.Down.", "Interg.", "Intrag.", "Prom.")
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233 if (length(labels)==length(levels(chip.data$Type))) {
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234 barplot(totalChIP,xlab="", col=myColor, names.arg=labels,ylab="Proportion of peaks")
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235 } else {
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236 barplot(totalChIP,xlab="", col=myColor,ylab="Proportion of peaks")
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237 }
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238 barplot(intraChip,xlab="", col=myColor,ylab="Proportion of peaks")
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239 }
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240 }
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241 dev.off()
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