|
0
|
1 args <- commandArgs()
|
|
|
2 input <- args[4]
|
|
|
3 pngFile <- args[5]
|
|
|
4 dataTable <-read.table(file=input, header=TRUE);
|
|
|
5 chip.data<-data.frame(dataTable)
|
|
|
6 ifReg <- 0
|
|
|
7 if (length(unique(chip.data$Reg))>1) {
|
|
|
8 ifReg <- 1
|
|
|
9 }
|
|
|
10
|
|
|
11 ifPDF <- 0
|
|
|
12 bootstrap <- 1
|
|
|
13
|
|
|
14 if (length(args)>=8) {
|
|
|
15 ifPDF=args[8]
|
|
|
16 bootstrap=args[9]
|
|
|
17 }
|
|
|
18 if (length(args)==7 & args[7]==1) {
|
|
|
19 ifPDF=1
|
|
|
20 }
|
|
|
21
|
|
|
22 ifControl <- 0
|
|
|
23 if (length(args)>=7 & args[7]!=1 & args[7]!=0) {
|
|
|
24 dataTable <-read.table(file=args[7], header=TRUE);
|
|
|
25 control.data<-data.frame(dataTable)
|
|
|
26 ifControl <- 1
|
|
|
27
|
|
|
28
|
|
|
29 }
|
|
|
30
|
|
|
31 error.bar <- function(x, y, upper, lower=upper, length=0.1,...){
|
|
|
32 if(length(x) != length(y) | length(y) !=length(lower) | length(lower) != length(upper))
|
|
|
33 stop("vectors must be same length")
|
|
|
34 arrows(x,y+upper, x, y-lower, angle=90, code=3, length=length, ...)
|
|
|
35 }
|
|
|
36
|
|
|
37
|
|
|
38
|
|
|
39 logFile <- args[6]
|
|
|
40 sink(logFile, append=FALSE, split=FALSE)
|
|
|
41
|
|
|
42 if (ifReg & ifControl) {
|
|
|
43
|
|
|
44 if (ifPDF==1) {
|
|
|
45 pdf(file = pngFile, width = 14, height = 13, pointsize = 20, bg = "white")
|
|
|
46 } else {
|
|
|
47 png(filename = pngFile, width = 1140, height = 840, units = "px", pointsize = 20, bg = "white", res = NA)
|
|
|
48 plot(1:10)
|
|
|
49 }
|
|
|
50 op <- par(mfrow = c(3,1))
|
|
|
51 } else {
|
|
|
52 if (ifReg | ifControl) {
|
|
|
53
|
|
|
54 if (ifPDF==1) {
|
|
|
55 pdf(file = pngFile, width = 20, height = 17, pointsize = 20, bg = "white")
|
|
|
56 } else {
|
|
|
57 png(filename = pngFile, width = 1580, height = 1230, units = "px", pointsize = 20, bg = "white", res = NA)
|
|
|
58 plot(1:10)
|
|
|
59 }
|
|
|
60 op <- par(mfrow = c(2,1))
|
|
|
61 } else {
|
|
|
62 if (ifPDF==1) {
|
|
|
63 pdf(file = pngFile, width = 22, height = 8, pointsize = 20, bg = "white")
|
|
|
64 } else {
|
|
|
65 png(filename = pngFile, width = 1580, height = 530, units = "px", pointsize = 20, bg = "white", res = NA)
|
|
|
66 plot(1:10)
|
|
|
67 }
|
|
|
68 op <- par(mfrow = c(1,1))
|
|
|
69 }
|
|
|
70 }
|
|
|
71 myColor <- 1
|
|
|
72 myColor[1] <- colors()[131]
|
|
|
73 myColor[2] <- colors()[59]
|
|
|
74 myColor[3] <- colors()[76]
|
|
|
75 myColor[4] <- colors()[88]
|
|
|
76 myColor[5] <- colors()[17]
|
|
|
77 myColor[6] <- colors()[565]
|
|
|
78 myColor[7] <- colors()[454]
|
|
|
79 myColor[8] <- colors()[401]
|
|
|
80 myColor[9] <- colors()[99]
|
|
|
81 myColorControl <- 1
|
|
|
82 myColorControl[1] <- colors()[24]
|
|
|
83 myColorControl[2] <- colors()[278]
|
|
|
84 myColorControl[3] <- colors()[305]
|
|
|
85 myColorControl[4] <- colors()[219]
|
|
|
86 myColorControl[5] <- colors()[343]
|
|
|
87 myColorControl[6] <- colors()[245]
|
|
|
88 myLevels <- 0
|
|
|
89 nn <- colnames(chip.data)
|
|
|
90 cc <- c(1:41)
|
|
|
91 colnames(chip.data) <- cc
|
|
|
92 countTotal <- length(unique(chip.data$"1"))
|
|
|
93 tt <- which(chip.data$"16">0)
|
|
|
94 countTotalEnh <- length(unique(chip.data$"1"[tt]))
|
|
|
95 tt <- which(chip.data$"10">0)
|
|
|
96 countTotalProm <- length(unique(chip.data$"1"[tt]))
|
|
|
97 tt <- which(chip.data$"12">0)
|
|
|
98 countTotalImDown <- length(unique(chip.data$"1"[tt]))
|
|
|
99 tt <- which(chip.data$"18">0)
|
|
|
100 countTotalIntra <- length(unique(chip.data$"1"[tt]))
|
|
|
101 tt <- which(chip.data$"20">0)
|
|
|
102 countTotal5kbD <- length(unique(chip.data$"1"[tt]))
|
|
|
103 tt <- which(chip.data$"28">0)
|
|
|
104 countTotal1IntronI <- length(unique(chip.data$"1"[tt]))
|
|
|
105 tt <- which(chip.data$"32">0)
|
|
|
106 countTotalExonsI <- length(unique(chip.data$"1"[tt]))
|
|
|
107 tt <- which(chip.data$"36">0)
|
|
|
108 countTotalIntronsI <- length(unique(chip.data$"1"[tt]))
|
|
|
109 tt <- which(chip.data$"40">0)
|
|
|
110 countTotalJonctionsI <- length(unique(chip.data$"1"[tt]))
|
|
|
111
|
|
|
112 names <- c("Enh.","Prom.","Imm.Down.","Intrag.","GeneDown.","F.Intron","Exons","2,3,etc.Introns","E.I.Junctions")
|
|
|
113 yChIPTotal <- c (countTotalEnh/countTotal,countTotalProm/countTotal, countTotalImDown/countTotal,countTotalIntra/countTotal,countTotal5kbD/countTotal,countTotal1IntronI/countTotal,countTotalExonsI/countTotal,countTotalIntronsI/countTotal,countTotalJonctionsI/countTotal)
|
|
|
114 if(!ifReg&!ifControl) {
|
|
|
115 par(mar=c(5.1, 7.1, 4.1, 2.1))
|
|
|
116 barplot(yChIPTotal,xlab="",beside=TRUE, col=c(myColor), names.arg=c(names),ylab="Proportion of genes with a peak")
|
|
|
117 cat ("Proportion of genes with a peak in a given genomic region:\n")
|
|
|
118 cat (paste(c(names),sep='\t'))
|
|
|
119 cat("\n")
|
|
|
120 cat (paste(c(yChIPTotal),sep='\t'))
|
|
|
121 cat("\n\n")
|
|
|
122 }
|
|
|
123 if (ifControl) {
|
|
|
124 if (bootstrap>1) {
|
|
|
125 yControlTotalMatrix <- NULL
|
|
|
126 }
|
|
|
127 for (fileNumber in 1:bootstrap) {
|
|
|
128
|
|
|
129 if (fileNumber>=2) {
|
|
|
130 dataTable <-read.table(file=paste(args[7],fileNumber,sep=""), header=TRUE);
|
|
|
131 control.data<-data.frame(dataTable)
|
|
|
132 }
|
|
|
133
|
|
|
134 colnames(control.data) <- cc
|
|
|
135 countTotalCntr <- length(unique(control.data$"1"))
|
|
|
136 tt <- which(control.data$"16">0)
|
|
|
137 countTotalEnhCntr <- length(unique(control.data$"1"[tt]))
|
|
|
138 tt <- which(control.data$"10">0)
|
|
|
139 countTotalPromCntr <- length(unique(control.data$"1"[tt]))
|
|
|
140 tt <- which(control.data$"12">0)
|
|
|
141 countTotalImDownCntr <- length(unique(control.data$"1"[tt]))
|
|
|
142 tt <- which(control.data$"18">0)
|
|
|
143 countTotalIntraCntr <- length(unique(control.data$"1"[tt]))
|
|
|
144 tt <- which(control.data$"20">0)
|
|
|
145 countTotal5kbDCntr <- length(unique(control.data$"1"[tt]))
|
|
|
146 tt <- which(control.data$"28">0)
|
|
|
147 countTotal1IntronICntr <- length(unique(control.data$"1"[tt]))
|
|
|
148 tt <- which(control.data$"32">0)
|
|
|
149 countTotalExonsICntr <- length(unique(control.data$"1"[tt]))
|
|
|
150 tt <- which(control.data$"36">0)
|
|
|
151 countTotalIntronsICntr <- length(unique(control.data$"1"[tt]))
|
|
|
152 tt <- which(control.data$"40">0)
|
|
|
153 countTotalJonctionsICntr <- length(unique(control.data$"1"[tt]))
|
|
|
154 yControlTotal <- c (countTotalEnhCntr/countTotalCntr,countTotalPromCntr/countTotalCntr, countTotalImDownCntr/countTotalCntr,countTotalIntraCntr/countTotalCntr,countTotal5kbDCntr/countTotalCntr,countTotal1IntronICntr/countTotalCntr,countTotalExonsICntr/countTotalCntr,countTotalIntronsICntr/countTotalCntr,countTotalJonctionsICntr/countTotalCntr)
|
|
|
155 if (bootstrap>1) {
|
|
|
156 yControlTotalMatrix <- rbind(yControlTotalMatrix,yControlTotal)
|
|
|
157 }
|
|
|
158 }
|
|
|
159 if (bootstrap>1) {
|
|
|
160 yControlTotal <- colMeans(yControlTotalMatrix)
|
|
|
161 Nrows <- nrow(yControlTotalMatrix)
|
|
|
162 colVars <- Nrows/(Nrows-1) * (colMeans(yControlTotalMatrix*yControlTotalMatrix)-colMeans(yControlTotalMatrix)^2)
|
|
|
163 }
|
|
|
164 if (!ifReg) {
|
|
|
165 cum = matrix( 0, nrow=2, ncol=length(names), byrow = TRUE)
|
|
|
166 for (i in c(1:length(names))) {
|
|
|
167 cum[1,i] <- yChIPTotal[i]
|
|
|
168 cum[2,i] <- yControlTotal[i]
|
|
|
169 }
|
|
|
170 if (bootstrap>1) {
|
|
|
171 wiskers <- matrix(c(colVars-colVars,sqrt(colVars)),2,length(names),byrow=TRUE)*1.96
|
|
|
172 }
|
|
|
173 par(mar=c(5.1, 7.1, 4.1, 2.1))
|
|
|
174 barx <- barplot(cum,xlab="",beside=TRUE, col=c(myColor[6],myColor[5]), legend = c("ChIP","Control"), names.arg=c(names),ylab="Proportion of genes with a peak")
|
|
|
175 cat ("Proportion of genes with a peak from the ChIP dataset in a given genomic region:\n")
|
|
|
176 cat (paste(c(names),sep='\t'))
|
|
|
177 cat("\n")
|
|
|
178 cat (paste(c(yChIPTotal),sep='\t'))
|
|
|
179 cat("\n\n")
|
|
|
180 cat ("Proportion of genes with a peak from the Control dataset in a given genomic region:\n")
|
|
|
181 cat (paste(c(names),sep='\t'))
|
|
|
182 cat("\n")
|
|
|
183 cat (paste(c(yControlTotal),sep='\t'))
|
|
|
184 cat("\n\n")
|
|
|
185 if (bootstrap>1) {
|
|
|
186 error.bar(barx,cum,wiskers)
|
|
|
187 cat ("Standard deviation for the Control dataset in a given genomic region:\n")
|
|
|
188 cat (paste(c(names),sep='\t'))
|
|
|
189 cat("\n")
|
|
|
190 cat (paste(c(sqrt(colVars)),sep='\t'))
|
|
|
191 cat("\n\n")
|
|
|
192 }
|
|
|
193 enrich <- NULL
|
|
|
194 for (i in c(1:length(names))) {
|
|
|
195 enrich[i] <- yChIPTotal[i]/yControlTotal[i];
|
|
|
196 }
|
|
|
197 barplot(enrich-1,xlab="",beside=TRUE, col=c(myColor), names.arg=c(names),ylab="Enrichment in comparison\nwith the control dataset", yaxt="n")
|
|
|
198 minX <- min(enrich-1)
|
|
|
199 maxX <- max(enrich-1)
|
|
|
200 x = seq(length=11, from=round(minX*10)/10, by=round((maxX-minX)*10)/100)
|
|
|
201 axis(2, at=x,labels=x+1, las=2)
|
|
|
202
|
|
|
203 cat ("Enrichment of genomic regions, ChIP peaks vs Control Peaks:\n")
|
|
|
204 cat (paste(c(names),sep='\t'))
|
|
|
205 cat("\n")
|
|
|
206 cat (paste(c(yChIPTotal/yControlTotal),sep='\t'))
|
|
|
207 cat("\n\n")
|
|
|
208 if (bootstrap>1) {
|
|
|
209 z <- (yChIPTotal-yControlTotal)/sqrt(colVars)
|
|
|
210 pvalues <- 2*pnorm(-abs(z))
|
|
|
211 cat ("Two-side P-values for each genomic category:\n")
|
|
|
212 cat (paste(c(names),sep='\t'))
|
|
|
213 cat("\n")
|
|
|
214 cat (paste(c(yChIPTotal/yControlTotal),sep='\t'))
|
|
|
215 cat("\n\n")
|
|
|
216 }
|
|
|
217 }
|
|
|
218 }
|
|
|
219 if (ifReg) {
|
|
|
220 n.types <- length(levels(chip.data$"6"))
|
|
|
221 myLevels <- levels(chip.data$"6")
|
|
|
222 nlev <- length(names)
|
|
|
223
|
|
|
224 if (ifControl) {
|
|
|
225 cum = matrix( 0, nrow=length(myLevels)+1, ncol=nlev, byrow = TRUE)
|
|
|
226 cumEnrichTotal = matrix( 0, nrow=length(myLevels), ncol=nlev, byrow = TRUE)
|
|
|
227 cumEnrichControl = matrix( 0, nrow=length(myLevels), ncol=nlev, byrow = TRUE)
|
|
|
228 }else {
|
|
|
229 cum = matrix( 0, nrow=length(myLevels), ncol=nlev, byrow = TRUE)
|
|
|
230 cumEnrichTotal = matrix( 0, nrow=length(myLevels), ncol=nlev, byrow = TRUE)
|
|
|
231 }
|
|
|
232 colReg <-NULL
|
|
|
233 for (r in c(1:length(myLevels))) {
|
|
|
234 tt <- which(chip.data$"6"==myLevels[r])
|
|
|
235 subset.data <- (chip.data[tt,])
|
|
|
236 countTotalSubset <- length(unique(subset.data$"1"))
|
|
|
237 tt <- which(subset.data$"16">0)
|
|
|
238 countTotalEnhSubset <- length(unique(subset.data$"1"[tt]))
|
|
|
239 tt <- which(subset.data$"10">0)
|
|
|
240 countTotalPromSubset <- length(unique(subset.data$"1"[tt]))
|
|
|
241 tt <- which(subset.data$"12">0)
|
|
|
242 countTotalImDownSubset <- length(unique(subset.data$"1"[tt]))
|
|
|
243 tt <- which(subset.data$"18">0)
|
|
|
244 countTotalIntraSubset <- length(unique(subset.data$"1"[tt]))
|
|
|
245 tt <- which(subset.data$"20">0)
|
|
|
246 countTotal5kbDSubset <- length(unique(subset.data$"1"[tt]))
|
|
|
247 tt <- which(subset.data$"28">0)
|
|
|
248 countTotal1IntronISubset <- length(unique(subset.data$"1"[tt]))
|
|
|
249 tt <- which(subset.data$"32">0)
|
|
|
250 countTotalExonsISubset <- length(unique(subset.data$"1"[tt]))
|
|
|
251 tt <- which(subset.data$"36">0)
|
|
|
252 countTotalIntronsISubset <- length(unique(subset.data$"1"[tt]))
|
|
|
253 tt <- which(subset.data$"40">0)
|
|
|
254 countTotalJonctionsISubset <- length(unique(subset.data$"1"[tt]))
|
|
|
255 ySubsetTotal <- c (countTotalEnhSubset/countTotalSubset,countTotalPromSubset/countTotalSubset, countTotalImDownSubset/countTotalSubset,countTotalIntraSubset/countTotalSubset,countTotal5kbDSubset/countTotalSubset,countTotal1IntronISubset/countTotalSubset,countTotalExonsISubset/countTotalSubset,countTotalIntronsISubset/countTotalSubset,countTotalJonctionsISubset/countTotalSubset)
|
|
|
256 for (i in c(1:nlev)) {
|
|
|
257 cum[r,i] <- ySubsetTotal[i]
|
|
|
258 cumEnrichTotal[r,i] <- ySubsetTotal[i]/yChIPTotal[i]
|
|
|
259 if (ifControl) {
|
|
|
260 cumEnrichControl[r,i] <- ySubsetTotal[i]/yControlTotal[i]
|
|
|
261 }
|
|
|
262 }
|
|
|
263 colReg[r]<-myColor[r+3]
|
|
|
264 }
|
|
|
265 if (ifControl) {
|
|
|
266 for (i in c(1:nlev)) {
|
|
|
267 cum[4,i] <- yControlTotal[i]
|
|
|
268 }
|
|
|
269 }
|
|
|
270
|
|
|
271 cat ("Proportion of genes with a peak from the ChIP dataset in a given genomic region:\n")
|
|
|
272 for (r in c(1:length(myLevels))) {
|
|
|
273 cat (paste(myLevels[r],":\n",sep=""))
|
|
|
274 cat (paste(c(names),sep='\t'))
|
|
|
275 cat("\n")
|
|
|
276 cat (paste(c(cum[r,] ),sep='\t'))
|
|
|
277 cat("\n")
|
|
|
278 }
|
|
|
279 cat("\n")
|
|
|
280 par(mar=c(5.1, 7.1, 4.1, 2.1))
|
|
|
281 if (ifControl) {
|
|
|
282 barx <- barplot(cum,xlab="",beside=TRUE, col=c(colReg, colors()[334]), legend = c(myLevels,"Control"), names.arg=c(names),ylab="Proportion of genes with a peak")
|
|
|
283 cat ("Proportion of genes with a peak from the Control dataset in a given genomic region:\n")
|
|
|
284 cat (paste(c(names),sep='\t'))
|
|
|
285 cat("\n")
|
|
|
286 cat (paste(c(yControlTotal),sep='\t'))
|
|
|
287 cat("\n\n")
|
|
|
288 if (bootstrap>1) {
|
|
|
289 wiskers <- cum-cum
|
|
|
290 wiskers[nrow(wiskers),] <- sqrt(colVars)*1.96
|
|
|
291 error.bar(barx,cum,wiskers)
|
|
|
292 cat ("Standard deviation for the Control dataset in a given genomic region:\n")
|
|
|
293 cat (paste(c(names),sep='\t'))
|
|
|
294 cat("\n")
|
|
|
295 cat (paste(c(sqrt(colVars)),sep='\t'))
|
|
|
296 cat("\n\n")
|
|
|
297 }
|
|
|
298 } else {
|
|
|
299 barplot(cum,xlab="",beside=TRUE, col=c(colReg), legend = c(myLevels), names.arg=c(names),ylab="Proportion of genes with a peak")
|
|
|
300 }
|
|
|
301 barplot(cumEnrichTotal-1,xlab="",beside=TRUE, col=c(colReg), names.arg=c(names),ylab="Enrichment in comparison\nwith the total gene set", yaxt="n")
|
|
|
302 minX <- min(cumEnrichTotal-1)
|
|
|
303 maxX <- max(cumEnrichTotal-1)
|
|
|
304 x = seq(length=11, from=round(minX*10)/10, by=round((maxX-minX)*10)/100)
|
|
|
305 axis(2, at=x,labels=x+1, las=2)
|
|
|
306
|
|
|
307 cat ("Enrichment of genomic regions, Transcriptional categories vs All Genes:\n")
|
|
|
308 for (r in c(1:length(myLevels))) {
|
|
|
309 cat (paste(myLevels[r],":\n",sep=""))
|
|
|
310 cat (paste(c(names),sep='\t'))
|
|
|
311 cat("\n")
|
|
|
312 cat (paste(c(cumEnrichTotal[r,]),sep='\t'))
|
|
|
313 cat("\n")
|
|
|
314 }
|
|
|
315 cat("\n")
|
|
|
316
|
|
|
317 if (ifControl) {
|
|
|
318 barplot(cumEnrichControl-1,xlab="",beside=TRUE, col=c(colReg), names.arg=c(names),ylab="Enrichment in comparison\nwith control", yaxt="n")
|
|
|
319 minX <- min(cumEnrichControl-1)
|
|
|
320 maxX <- max(cumEnrichControl-1)
|
|
|
321 x = seq(length=11, from=round(minX*10)/10, by=round((maxX-minX)*10)/100)
|
|
|
322 axis(2, at=x,labels=x+1, las=2)
|
|
|
323 cat ("Enrichment of genomic regions, ChIP peaks vs Control Peaks:\n")
|
|
|
324 for (r in c(1:length(myLevels))) {
|
|
|
325 cat (paste(myLevels[r],":\n",sep=""))
|
|
|
326 cat (paste(c(names),sep='\t'))
|
|
|
327 cat("\n")
|
|
|
328 cat (paste(c(cumEnrichControl[r,]),sep='\t'))
|
|
|
329 cat("\n")
|
|
|
330 }
|
|
|
331 cat("\n")
|
|
|
332 if (bootstrap>1) {
|
|
|
333 cat ("Two-side P-values for each genomic category:\n")
|
|
|
334 for (r in c(1:length(myLevels))) {
|
|
|
335 z <- (cum[r,]-yControlTotal)/sqrt(colVars)
|
|
|
336 pvalues <- 2*pnorm(-abs(z))
|
|
|
337 cat (paste(myLevels[r],":\n",sep=""))
|
|
|
338 cat (paste(c(names),sep='\t'))
|
|
|
339 cat("\n")
|
|
|
340 cat (paste(c(pvalues),sep='\t'))
|
|
|
341 cat("\n")
|
|
|
342 }
|
|
|
343 }
|
|
|
344 }
|
|
|
345 }
|
|
|
346 sink() #stop sinking :)
|
|
|
347 dev.off()
|
|
|
348
|
