|
23
|
1 #!/usr/bin/env Rscript
|
|
|
2
|
|
|
3 #usage $0 STEP RIGHT chipPeaks outputFile.png output.txt [controlPeaks] [1 for pdf]
|
|
|
4 args <- commandArgs(TRUE)
|
|
|
5 #print (args)
|
|
|
6 myStep <- type.convert(args[2])
|
|
|
7 maxValue <- type.convert(args[3])
|
|
|
8
|
|
|
9 dataTable <-read.table(file=paste(args[4],".genes.ClosestPeakDist", sep=""), header=TRUE);
|
|
|
10 chip.genes.ClosestPeakDist<-data.frame(dataTable)
|
|
|
11 ifReg <- 0
|
|
|
12 if (length(unique(chip.genes.ClosestPeakDist$Reg))>1) {
|
|
|
13 ifReg <- 1
|
|
|
14 }
|
|
|
15 ifControl <- 0
|
|
|
16
|
|
|
17
|
|
|
18 ifPDF <- 0
|
|
|
19 if (length(args)>=8) {
|
|
|
20 ifPDF=args[8]
|
|
|
21 }
|
|
|
22 if (length(args)==7 & args[7]==1) {
|
|
|
23 ifPDF=1
|
|
|
24 }
|
|
|
25
|
|
|
26 suppressMessages(library(Hmisc))
|
|
|
27
|
|
|
28 if (length(args)>=7 & args[7]!=1 & args[7]!=0) {
|
|
|
29 dataTable <-read.table(file=paste(args[7],".genes.ClosestPeakDist", sep=""), header=TRUE);
|
|
|
30 control.genes.ClosestPeakDist<-data.frame(dataTable)
|
|
|
31 ifControl <- 1
|
|
|
32 }
|
|
|
33 if (ifReg & ifControl) {
|
|
|
34 if (ifPDF==1) {
|
|
|
35 pdf(file = args[5], width = 19, height = 8, pointsize = 20, bg = "white")
|
|
|
36 } else {
|
|
|
37 bitmap(filename = args[5], type = "png16m", width = 1440 , height = 680, units = "px", pointsize = 20, bg = "white", res = NA)
|
|
|
38 plot(1:10)
|
|
|
39 }
|
|
|
40 op <- par(mfrow = c(2,3))
|
|
|
41 } else {
|
|
|
42 if (ifPDF==1) {
|
|
|
43 pdf(file = args[5], width = 10, height = 13, pointsize = 20, bg = "white")
|
|
|
44 } else {
|
|
|
45 bitmap(filename = args[5], type = "png16m", width = 680, height = 880, units = "px", pointsize = 20, bg = "white", res = NA)
|
|
|
46 plot(1:10)
|
|
|
47 }
|
|
|
48 # plot(1:10)
|
|
|
49 op <- par(mfrow = c(2,1))
|
|
|
50 }
|
|
|
51 myColor <- 1
|
|
|
52 myColor[1] <- colors()[131]
|
|
|
53 myColor[2] <- "darkolivegreen3"
|
|
|
54 myColor[3] <- "azure4"
|
|
|
55 myColor[4] <- "royalblue3"
|
|
|
56 myColor[5] <- colors()[17]
|
|
|
57
|
|
|
58 myColorControl <- 1
|
|
|
59
|
|
|
60 myColorControl[1] <- colors()[24]
|
|
|
61 myColorControl[2] <- colors()[278]
|
|
|
62 myColorControl[3] <- colors()[305]
|
|
|
63 myColorControl[4] <- colors()[219]
|
|
|
64 myColorControl[5] <- colors()[343]
|
|
|
65
|
|
|
66
|
|
|
67
|
|
|
68 #for cumulative:
|
|
|
69 dist_real_f <- chip.genes.ClosestPeakDist
|
|
|
70 if (ifControl) {
|
|
|
71 dist_control_f <- control.genes.ClosestPeakDist
|
|
|
72 }
|
|
|
73 step <- myStep
|
|
|
74 lim <- maxValue
|
|
|
75 x <- 0
|
|
|
76 count <- 1
|
|
|
77 countL <-1
|
|
|
78 n.types <- 1
|
|
|
79 myLevels <- 0
|
|
|
80 countTotalCont <- 0
|
|
|
81 countTotal <-0
|
|
|
82 countLCont <- 0
|
|
|
83 cumTotalCont <- 0
|
|
|
84 if (ifReg) {
|
|
|
85 n.types <- length(levels(chip.genes.ClosestPeakDist$Reg))
|
|
|
86 myLevels <- levels(chip.genes.ClosestPeakDist$Reg)
|
|
|
87 cum = matrix( 0, nrow=lim/step +1, ncol=n.types, byrow = TRUE)
|
|
|
88 for (i in c(1:n.types)) {
|
|
|
89 t <- which ((dist_real_f$Reg==myLevels[i]))
|
|
|
90 countL[i] <- length(t)
|
|
|
91 }
|
|
|
92 count <-1
|
|
|
93 for (i in seq(length=lim/step +1, from=0, by=step)) {
|
|
|
94 for (t in c(1:n.types)) {
|
|
|
95 tt <- which ((dist_real_f$Reg==myLevels[t])&(dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
|
|
|
96 cum[count,t] <- length(tt)
|
|
|
97 }
|
|
|
98 x[count] <- i
|
|
|
99 count <- count + 1
|
|
|
100 }
|
|
|
101 ymax <- max(cum[,1]/countL[1], na.rm=TRUE)
|
|
|
102 for (i in c(2:n.types)) {
|
|
|
103 ymax <- max(ymax,max(cum[,i]/countL[i], na.rm=TRUE))
|
|
|
104 }
|
|
|
105 myLocCol <- myColor[2]
|
|
|
106
|
|
|
107 par(mar=c(5.1, 7.1, 4.1, 2.1))
|
|
|
108
|
|
|
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))
|
|
|
110 for (i in c(2:n.types)) {
|
|
|
111 colorr <- i+1
|
|
|
112 myLocCol <- c(myLocCol,myColor[colorr])
|
|
|
113 lines (x,cum[,i]/countL[i] ,col = myColor[colorr],type="l", lwd = 2)
|
|
|
114 # print (myColor[colorr])
|
|
|
115 }
|
|
|
116
|
|
|
117 gradi <- 1000
|
|
|
118 if (lim>10000) {
|
|
|
119 gradi <- 10000
|
|
|
120 }
|
|
|
121 if (lim<3000) {
|
|
|
122 gradi <- 500
|
|
|
123 }
|
|
|
124 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
|
|
|
125 axisxlab <- paste(axisx/1000,"", sep = "")
|
|
|
126 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
|
|
|
127 ymax <- max(cum[,i]/countL[i], na.rm=TRUE)
|
|
|
128
|
|
|
129 minor.tick(nx=5,tick.ratio=0.5)
|
|
|
130
|
|
|
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)
|
|
|
132
|
|
|
133 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
|
|
|
134
|
|
|
135 if (ifControl) {
|
|
|
136 count <-1
|
|
|
137 n.types <- length(levels(control.genes.ClosestPeakDist$Reg))
|
|
|
138 myLevels <- levels(control.genes.ClosestPeakDist$Reg)
|
|
|
139 cumCont = matrix( 0, nrow=lim/step +1, ncol=n.types, byrow = TRUE)
|
|
|
140 for (i in c(1:n.types)) {
|
|
|
141 t <- which ((dist_control_f$Reg==myLevels[i]))
|
|
|
142 countLCont[i] <- length(t)
|
|
|
143 }
|
|
|
144 for (i in seq(length=lim/step +1, from=0, by=step)) {
|
|
|
145 for (t in c(1:n.types)) {
|
|
|
146 tt <- which ((dist_control_f$Reg==myLevels[t])&(dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
|
|
|
147 cumCont[count,t] <- length(tt)
|
|
|
148 }
|
|
|
149 x[count] <- i
|
|
|
150 count <- count + 1
|
|
|
151 }
|
|
|
152 ymax <- max(cumCont[,1]/countLCont[1], na.rm=TRUE)
|
|
|
153 for (i in c(2:n.types)) {
|
|
|
154 ymax <- max(ymax,max(cumCont[,i]/countLCont[i], na.rm=TRUE))
|
|
|
155 }
|
|
|
156 myLocColCntr <- myColorControl[2]
|
|
|
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))
|
|
|
158 for (i in c(2:n.types)) {
|
|
|
159 colorr <- i+1
|
|
|
160 myLocColCntr <- c(myLocColCntr,myColorControl[colorr])
|
|
|
161 lines (x,cumCont[,i]/countLCont[i] ,col = myColorControl[colorr],type="l", lwd = 2)
|
|
|
162 }
|
|
|
163 if (lim>10000) {
|
|
|
164 gradi <- 10000
|
|
|
165 }
|
|
|
166 if (lim<3000) {
|
|
|
167 gradi <- 500
|
|
|
168 }
|
|
|
169 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
|
|
|
170 axisxlab <- paste(axisx/1000, sep = "")
|
|
|
171 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
|
|
|
172 minor.tick(nx=5,tick.ratio=0.5)
|
|
|
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)
|
|
|
174 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
|
|
|
175 #real_vs_control_cumulative:
|
|
|
176 count <-1
|
|
|
177 countTotal <- length(dist_real_f$Reg)
|
|
|
178 cumTotal <- 0
|
|
|
179 for (i in seq(length=lim/step +1, from=0, by=step)) {
|
|
|
180 t <- which ((dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
|
|
|
181 cumTotal[count] <- length(t)
|
|
|
182 x[count] <- i
|
|
|
183 count <- count + 1
|
|
|
184 }
|
|
|
185 plot (x,cumTotal/countTotal ,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(0, lim),xaxt="n" )
|
|
|
186 gradi <- 1000
|
|
|
187 if (lim>10000) {
|
|
|
188 gradi <- 10000
|
|
|
189 }
|
|
|
190 if (lim<3000) {
|
|
|
191 gradi <- 500
|
|
|
192 }
|
|
|
193 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
|
|
|
194 axisxlab <- paste(axisx/1000, sep = "")
|
|
|
195 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
|
|
|
196 ymax <- max(cumTotal/countTotal, na.rm=TRUE)
|
|
|
197 minor.tick(nx=5,tick.ratio=0.5)
|
|
|
198 countTotalCont <- length(dist_control_f$Reg)
|
|
|
199 cumTotalCont <- 0
|
|
|
200 count <- 1
|
|
|
201 for (i in seq(length=lim/step +1, from=0, by=step)) {
|
|
|
202 t <- which ((dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
|
|
|
203 cumTotalCont[count] <- length(t)
|
|
|
204 x[count] <- i
|
|
|
205 count <- count + 1
|
|
|
206 }
|
|
|
207 lines (x,cumTotalCont/countTotalCont ,col = colors()[328],type="l", lwd = 2)
|
|
|
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)
|
|
|
209 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
|
|
|
210 }
|
|
|
211 } else {
|
|
|
212 countTotal <- length(dist_real_f$Reg)
|
|
|
213 cumTotal <- 0
|
|
|
214 count <-1
|
|
|
215
|
|
|
216 gradi <- 1000
|
|
|
217 if (lim>10000) {
|
|
|
218 gradi <- 10000
|
|
|
219 }
|
|
|
220 if (lim<3000) {
|
|
|
221 gradi <- 500
|
|
|
222 }
|
|
|
223
|
|
|
224 for (i in seq(length=lim/step +1, from=0, by=step)) {
|
|
|
225 t <- which ((dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
|
|
|
226 cumTotal[count] <- length(t)
|
|
|
227 x[count] <- i
|
|
|
228 count <- count + 1
|
|
|
229 }
|
|
|
230 par(mar=c(5.1, 7.1, 4.1, 2.1))
|
|
|
231
|
|
|
232 plot (x,cumTotal/countTotal ,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(0, lim),xaxt="n" )
|
|
|
233 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
|
|
|
234 axisxlab <- paste(axisx/1000, sep = "")
|
|
|
235 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
|
|
|
236 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
|
|
|
237 ymax <- max(cumTotal/countTotal, na.rm=TRUE)
|
|
|
238 if (ifControl) {
|
|
|
239 countTotalCont <- length(dist_control_f$Reg)
|
|
|
240 cumTotalCont <- 0
|
|
|
241 count <- 1
|
|
|
242 for (i in seq(length=lim/step +1, from=0, by=step)) {
|
|
|
243 t <- which ((dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
|
|
|
244 cumTotalCont[count] <- length(t)
|
|
|
245 x[count] <- i
|
|
|
246 count <- count + 1
|
|
|
247 }
|
|
|
248 lines (x,cumTotalCont/countTotalCont ,col = colors()[328],type="l", lwd = 2)
|
|
|
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)
|
|
|
250 } else {
|
|
|
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)
|
|
|
252 }
|
|
|
253 }
|
|
|
254
|
|
|
255 sink(args[6], append=FALSE, split=FALSE)
|
|
|
256 if (ifReg) {
|
|
|
257 if (ifControl) {
|
|
|
258 cat (paste("Dist_TSS","% genes w/ a peak in ChIP","% genes w/ a peak in control",sep='\t'))
|
|
|
259 cat("\t")
|
|
|
260 for (i in c(1:n.types)) {
|
|
|
261 cat(paste("% ", myLevels[i]," genes w/ a peak in ChIP", sep=""))
|
|
|
262 cat("\t")
|
|
|
263 }
|
|
|
264
|
|
|
265 for (i in c(1:n.types)) {
|
|
|
266 cat(paste("% ", myLevels[i]," genes w/ a peak in Control", sep=""))
|
|
|
267 cat("\t")
|
|
|
268 }
|
|
|
269 cat("\n")
|
|
|
270 for (i in c(1:length(x))) {
|
|
|
271 cat(paste(x[i],cumTotal[i]/countTotal,cumTotalCont[i]/countTotalCont,sep="\t"))
|
|
|
272 cat("\t")
|
|
|
273 for (t in c(1:n.types)) {
|
|
|
274 cat(paste(cum[i,t]/countL[t],"\t", sep=""))
|
|
|
275 }
|
|
|
276 for (t in c(1:n.types)) {
|
|
|
277 cat(paste(cumCont[i,t]/countLCont[t],"\t", sep=""))
|
|
|
278 }
|
|
|
279 cat("\n")
|
|
|
280 }
|
|
|
281 }else {
|
|
|
282 cat (paste("Dist_TSS","\t",sep=''))
|
|
|
283 for (i in c(1:n.types)) {
|
|
|
284 cat(paste("% ", myLevels[i]," genes w/ a peak in ChIP", "\t", sep=""))
|
|
|
285 }
|
|
|
286 cat("\n")
|
|
|
287 for (i in c(1:length(x))) {
|
|
|
288 cat(paste(x[i],"\t",sep=""))
|
|
|
289 for (t in c(1:n.types)) {
|
|
|
290 cat(paste(cum[i,t]/countL[t],"\t", sep=""))
|
|
|
291 }
|
|
|
292 cat("\n")
|
|
|
293 }
|
|
|
294 }
|
|
|
295 } else {
|
|
|
296 if (ifControl) {
|
|
|
297 cat (paste("Dist_TSS","% genes w/ a peak in ChIP","% genes w/ a peak in control",sep='\t'))
|
|
|
298 cat("\n")
|
|
|
299 for (i in c(1:length(x))) {
|
|
|
300 cat(paste(x[i],cumTotal[i]/countTotal,cumTotalCont[i]/countTotalCont,sep="\t"))
|
|
|
301 cat("\n")
|
|
|
302 }
|
|
|
303 }else {
|
|
|
304 cat (paste("Dist_TSS","% genes w/ a peak in ChIP",sep='\t'))
|
|
|
305 cat("\n")
|
|
|
306 for (i in c(1:length(x))) {
|
|
|
307 cat(paste(x[i],cumTotal[i]/countTotal,sep="\t"))
|
|
|
308 cat("\n")
|
|
|
309 }
|
|
|
310
|
|
|
311 }
|
|
|
312 }
|
|
|
313
|
|
|
314
|
|
|
315 #stop sinking:
|
|
|
316 sink()
|
|
|
317
|
|
|
318 #around TSS:
|
|
|
319 lim <- maxValue
|
|
|
320 step <- myStep
|
|
|
321 my_breaks <- seq(length=lim/step*2 +1, from=-lim, by=step)
|
|
|
322 chip.genes <- read.table(file=paste(args[4],".genes", sep=""), header=TRUE) ;
|
|
|
323 dist_real_f <- chip.genes
|
|
|
324 if (ifControl) {
|
|
|
325 control.genes <- read.table(file=paste(args[4],".genes", sep=""), header=TRUE) ;
|
|
|
326 dist_control_f<-data.frame(control.genes)
|
|
|
327 }
|
|
|
328 if (ifReg) {
|
|
|
329 #n.types <- length(levels(chip.genes.ClosestPeakDist$Reg))
|
|
|
330 #myLevels <- levels(dist_real_f$Reg)
|
|
|
331
|
|
|
332 t<- which (dist_real_f$Reg==myLevels[1])
|
|
|
333 values_real <-dist_real_f$Dist[t]
|
|
|
334 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
|
|
|
335 ymax <- max(hTSSreal$density, na.rm=TRUE)
|
|
|
336 for (i in c(2:n.types)) {
|
|
|
337 t<- which (dist_real_f$Reg==myLevels[i])
|
|
|
338 values_real <-dist_real_f$Dist[t]
|
|
|
339 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
|
|
|
340 ymax <- max(ymax,max(hTSSreal$density, na.rm=TRUE))
|
|
|
341 }
|
|
|
342
|
|
|
343
|
|
|
344 t<- which (dist_real_f$Reg==myLevels[1])
|
|
|
345 values_real <-dist_real_f$Dist[t]
|
|
|
346 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
|
|
|
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" )
|
|
|
348
|
|
|
349 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
|
|
|
350
|
|
|
351 for (i in c(2:n.types)) {
|
|
|
352 t<- which (dist_real_f$Reg==myLevels[i])
|
|
|
353 values_real <-dist_real_f$Dist[t]
|
|
|
354 hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real)) )
|
|
|
355 lines (hTSSreal$mids,hTSSreal$density,col = myLocCol[i],type="l", lwd = 2)
|
|
|
356 }
|
|
|
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)
|
|
|
358
|
|
|
359 gradi <- 1000
|
|
|
360 if (lim>10000) {
|
|
|
361 gradi <- 10000
|
|
|
362 }
|
|
|
363 if (lim<3000) {
|
|
|
364 gradi <- 500
|
|
|
365 }
|
|
|
366
|
|
|
367 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
|
|
|
368 axisxlab <- paste(axisx/1000, sep = "")
|
|
|
369 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
|
|
|
370
|
|
|
371
|
|
|
372 #minor.tick(nx=10,tick.ratio=0.5)
|
|
|
373 if (ifControl) {
|
|
|
374 t<- which (dist_control_f$Reg==myLevels[1])
|
|
|
375 values_control <-dist_control_f$Dist[t]
|
|
|
376 hTSScontrol= hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
|
|
|
377 ymax <- max(hTSScontrol$density, na.rm=TRUE)
|
|
|
378 for (i in c(2:n.types)) {
|
|
|
379 t<- which (dist_control_f$Reg==myLevels[i])
|
|
|
380 values_control <-dist_control_f$Dist[t]
|
|
|
381 hTSScontrol = hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
|
|
|
382 ymax <- max(ymax,max(hTSScontrol$density, na.rm=TRUE))
|
|
|
383 }
|
|
|
384 t<- which (dist_control_f$Reg==myLevels[1])
|
|
|
385 values_control <-dist_control_f$Dist[t]
|
|
|
386 hTSScontrol= hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
|
|
|
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" )
|
|
|
388 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
|
|
|
389 for (i in c(2:n.types)) {
|
|
|
390 t<- which (dist_control_f$Reg==myLevels[i])
|
|
|
391 values_control <-dist_control_f$Dist[t]
|
|
|
392 hTSScontrol = hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control)) )
|
|
|
393 lines (hTSScontrol$mids,hTSScontrol$density,col = myLocColCntr[i],type="l", lwd = 2)
|
|
|
394 }
|
|
|
395
|
|
|
396 gradi <- 1000
|
|
|
397 if (lim>10000) {
|
|
|
398 gradi <- 10000
|
|
|
399 }
|
|
|
400 if (lim<3000) {
|
|
|
401 gradi <- 500
|
|
|
402 }
|
|
|
403
|
|
|
404 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
|
|
|
405 axisxlab <- paste(axisx/1000, sep = "")
|
|
|
406 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
|
|
|
407
|
|
|
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)
|
|
|
409
|
|
|
410 # minor.tick(nx=10,tick.ratio=0.5)
|
|
|
411 #control vs real
|
|
|
412 values_real <-dist_real_f$Dist
|
|
|
413 hTSSreal = hist(values_real, plot=FALSE, breaks = c(min(values_real),my_breaks,max(values_real)) )
|
|
|
414 plot (hTSSreal$mids,hTSSreal$density,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(-lim, lim),xaxt="n")
|
|
|
415 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
|
|
|
416 ymax <- max(hTSSreal$density, na.rm=TRUE)
|
|
|
417 values_control <-dist_control_f$Dist
|
|
|
418 hTSScontrol = hist(values_control, plot=FALSE, breaks = c(min(values_control),my_breaks,max(values_control)) )
|
|
|
419 lines (hTSScontrol$mids,hTSScontrol$density,col = colors()[328],type="l", lwd = 2)
|
|
|
420 legend(lim*0.2, ymax*0.9, c("ChIP","Control"), cex=1 , lwd = 2, bty = "n", col = c(myColor[1], colors()[328]), lty = c(1), pt.bg= c(myColor[1], colors()[328]) , merge = TRUE)
|
|
|
421
|
|
|
422 gradi <- 1000
|
|
|
423 if (lim>10000) {
|
|
|
424 gradi <- 10000
|
|
|
425 }
|
|
|
426 if (lim<3000) {
|
|
|
427 gradi <- 500
|
|
|
428 }
|
|
|
429
|
|
|
430 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
|
|
|
431 axisxlab <- paste(axisx/1000, sep = "")
|
|
|
432 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
|
|
|
433
|
|
|
434
|
|
|
435
|
|
|
436 # minor.tick(nx=10,tick.ratio=0.5)
|
|
|
437 }
|
|
|
438 } else {
|
|
|
439 values_real <-dist_real_f$Dist
|
|
|
440 hTSSreal = hist(values_real, plot=FALSE, breaks = c(min(values_real),my_breaks,max(values_real)) )
|
|
|
441 plot (hTSSreal$mids,hTSSreal$density,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(-lim, lim),xaxt="n")
|
|
|
442 title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
|
|
|
443 ymax <- max(hTSSreal$density, na.rm=TRUE)
|
|
|
444 if (ifControl) {
|
|
|
445 values_control <-dist_control_f$Dist
|
|
|
446 hTSScontrol = hist(values_control, plot=FALSE, breaks = c(min(values_control),my_breaks,max(values_control)) )
|
|
|
447 lines (hTSScontrol$mids,hTSScontrol$density,col = colors()[328],type="l", lwd = 2)
|
|
|
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)
|
|
|
449 } else {
|
|
|
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)
|
|
|
451 }
|
|
|
452
|
|
|
453 gradi <- 1000
|
|
|
454 if (lim>10000) {
|
|
|
455 gradi <- 10000
|
|
|
456 }
|
|
|
457 if (lim<3000) {
|
|
|
458 gradi <- 500
|
|
|
459 }
|
|
|
460
|
|
|
461 axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
|
|
|
462 axisxlab <- paste(axisx/1000, sep = "")
|
|
|
463 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
|
|
|
464
|
|
|
465
|
|
|
466 # minor.tick(nx=10,tick.ratio=0.5)
|
|
|
467 }
|
|
|
468 suppressMessages(dev.off())
|
|
|
469 q();
|
|
|
470 cat (paste("peak height","# peaks in ChIP","# peaks in Control","#control/chip","\n",sep='\t'))
|
|
|
471 for (xval in c(minValue:maxValue)) {
|
|
|
472 for (i in (1:length(chipHist$mids))) {
|
|
|
473 if (xval==chipHist$mids[i]) {
|
|
|
474 ychip <- chipHist$counts[i]
|
|
|
475 }
|
|
|
476 }
|
|
|
477 for (i in (1:length(controlHist$mids))) {
|
|
|
478 if (xval==controlHist$mids[i]) {
|
|
|
479 ycontrol <- controlHist$counts[i]
|
|
|
480 }
|
|
|
481 }
|
|
|
482 cat (paste(xval,ychip,ycontrol,ycontrol/ychip,"\n",sep='\t'))
|
|
|
483 }
|
