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comparison my_VDM_tool.R @ 3:403a83d4b888 draft

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author xuef
date Fri, 06 Nov 2020 16:39:21 +0000
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2:dd74836c77ad 3:403a83d4b888
1 #!/usr/bin/env Rscript
2 # rm(list=ls())
3 # myfunction(inf="nor22.vcf",itype="C.elegans",qual=400,thrup=1.0,thrlow=0.0,allr="AB",snp=TRUE,lsp=0.4,pcol="black",lcol="red",xstand=TRUE,bsize=1000000,bnorm=FALSE,exclf=NULL,exclthr=0.0,exclcol="green",parn="parsed.txt",outn="output.txt",pdfn="plot.pdf")
4
5 #Rscript my_VDM_tool.R --inf "nor22.vcf" --itype "C.elegans" --qual 400 --thrup 1.0 --thrlow 0.0 --allr "AB" --snp TRUE --lsp 0.4 --pcol "black" --lcol "red" --xstand TRUE --bsize 1000000 --bnorm FALSE --exclf NULL --exclthr 0.0 --exclcol "green" --parn "parsed.txt" --outn "output.txt" --pdfn "plot.pdf"
6
7 library("getopt")
8 #input from trailing line arguments
9 args <- commandArgs(trailingOnly = TRUE)
10 #read the options from input commandArgs
11 option_specification = matrix(c(
12 'inf','i01',1,'character',
13 'itype','i02',2,'character',
14 'qual','i03',2,'double',
15 'thrup','i04',2,'double',
16 'thrlow','i05',2,'double',
17 'allr','i06',2,'character',
18 'snp','i07',2,'logical',
19 'lsp','i08',2,'double',
20 'pcol','i09',2,'character',
21 'lcol','i10',2,'character',
22 'xstand','i11',2,'logical',
23 'bsize','i12',2,'integer',
24 'bnorm','i13',2,'logical',
25 'exclf','i14',2,'character',
26 'exclthr','i15',2,'double',
27 'exclcol','i16',2,'character',
28 'parn','o1',2,'character',
29 'outn','o2',2,'character',
30 'pdfn','o3',2,'character'
31 ), byrow=TRUE, ncol=4)
32
33 # #parse options # bnorm=FALSE,exclf=NULL,exclthr=0.0,exclcol="green",parn="parsed.txt",outn="output.txt",pdfn="plot.pdf")
34 options = getopt(option_specification)
35 #
36 # #FOR DEBUGGING
37 # options<-NULL
38 # ###INPUT FILE
39 # setwd("D:/Dropbox/_galaxy/")
40 # options$inf<-"nor22.vcf"
41 # ###BASE OPTIONS
42 # #interval type
43 # options$itype<-"C.elegans"
44 # #quality filter
45 # options$qual<-200
46 # #for scaling 0-1 = upper threshold for what is considered homozygous
47 # options$thrup<-1
48 # #for scaling 0-1 = lower threshold for what is considered homozygous
49 # options$thrlow<-0
50 # #type of allelic ratio (AB/ratio)
51 # options$allr<-"AB"
52 # #include complex variants
53 # options$snp<-FALSE
54 # ###ADDITIONAL VARIANT EXCLUSION OPTIONS
55 # #files with variants to exclude
56 # options$exclf<-NULL
57 # options$exclf<-c("nor22chunk1.txt","nor22chunk5.txt")
58 # #for variants to exclude, bottom threshold for which to be used, i.e. 0=ALL, 1=HOM only, 0.8=near HOM)
59 # options$exclthr<-0
60 # #additional colour option for pre-subtraction line
61 # options$exclcol<-"green"
62 # ###PLOT OPTIONS
63 # #loess span
64 # options$lsp<-0.4
65 # #point colour
66 # options$pcol<-"black"
67 # #loess plot colour
68 # options$lcol<-"red"
69 # #standardize x-axis interval (e.g. 1Mb interval)
70 # options$xstand<-TRUE
71 # #bin size for barplot
72 # options$bsize<-1000000
73 # #normalization for barplot
74 # options$bnorm<-FALSE
75 # ###OUTPUT OPTIONS
76 # #custom files names (may not work for Galaxy)
77 # options$outn<-paste(gsub("vcf","",options$inf),"_output_q",options$qual,"-",paste(options$exclf,sep="",collapse=""),".txt",sep="")
78 # options$parn<-paste(gsub("vcf","",options$inf),"_parsed_q",options$qual,"-",paste(options$exclf,sep="",collapse=""),".txt",sep="")
79 # options$pdfn<-paste(gsub("vcf","",options$inf),"_plot_q",options$qual,"-",paste(options$exclf,sep="",collapse=""),".pdf",sep="")
80 # #fixed file names (will work in Galaxy)
81 # options$outn<-"vcf_output.txt"
82 # options$parn<-"vcf_parsedinput.txt"
83 # options$pdfn<-"vdm_mapping_plot.pdf"
84
85
86 myfunction<-function(inf,itype,qual,thrup,thrlow,allr,snp,lsp,pcol,lcol,xstand,bsize,bnorm,exclf,exclthr,exclcol,parn,outn,pdfn){
87
88 #PARAMETERS
89 # filename<-options$inf
90 # interval_type<-options$itype
91 # read_qual<-options$qual
92 # threshold_upper<-options$thrup
93 # threshold_lower<-options$thrlow
94 # allele_ratio<-options$allr
95 # snp_only<-options$snp
96 # loess_span<-options$lsp
97 # plot_color<-options$pcol
98 # loess_color<-options$lcol
99 # #transparency for selected colour (to see plot points underneath)
100 # xaxis_standard<-options$xstand
101 # bin_size<-options$bsize
102 # bfreq_norm<-options$bnorm
103 # exclusion_list<-options$exclf
104 # excl_threshold<-options$exclthr
105 # excl_loess_color<-options$exclcol
106 # vcfoutput_filename<-options$outn
107 # vcfparsed_filename<-options$parn
108 # pdf_filename<-options$pdfn
109
110 # plot_color<-rgb(c(col2rgb(plot_color)[1]),c(col2rgb(plot_color)[2]),c(col2rgb(plot_color)[3]),max=255,alpha=150)
111 # loess_color<-rgb(c(col2rgb(loess_color)[1]),c(col2rgb(loess_color)[2]),c(col2rgb(loess_color)[3]),max=255,alpha=150)
112 # excl_loess_color<-rgb(c(col2rgb(excl_loess_color)[1]),c(col2rgb(excl_loess_color)[2]),c(col2rgb(excl_loess_color)[3]),max=255,alpha=150)
113
114 filename<-inf
115 interval_type<-itype
116 read_qual<-as.numeric(qual)
117 threshold_upper<-as.numeric(thrup)
118 threshold_lower<-as.numeric(thrlow)
119 allele_ratio<-allr
120 snp_only<-snp
121 loess_span<-as.numeric(lsp)
122 plot_color<-pcol
123 loess_color<-lcol
124 xaxis_standard<-xstand
125 bin_size<-as.numeric(bsize)
126 bfreq_norm<-bnorm
127 exclusion_list<-exclf
128 excl_threshold<-as.numeric(exclthr)
129 excl_loess_color<-exclcol
130 vcfoutput_filename<-outn
131 vcfparsed_filename<-parn
132 pdf_filename<-pdfn
133
134 #transparency for selected colour (to see plot points underneath)
135 plot_color<-rgb(c(col2rgb(plot_color)[1]),c(col2rgb(plot_color)[2]),c(col2rgb(plot_color)[3]),max=255,alpha=150)
136 loess_color<-rgb(c(col2rgb(loess_color)[1]),c(col2rgb(loess_color)[2]),c(col2rgb(loess_color)[3]),max=255,alpha=150)
137 excl_loess_color<-rgb(c(col2rgb(excl_loess_color)[1]),c(col2rgb(excl_loess_color)[2]),c(col2rgb(excl_loess_color)[3]),max=255,alpha=150)
138
139 ###FIXED PARAMETERS
140 #linkage scatter plot yaxis max value=1
141 sp_yaxis<-1
142 #chromosome intervals in Mb rather than custom
143 interval_unit<-1000000
144
145
146 ######################
147 ###READ IN VCF FILE
148 #extract column names
149 vcf_readin<-readLines(filename)
150 #find header line, i.e. last line to begin with #
151 for(l in 1:length(vcf_readin)){
152 vcf_readinl<-vcf_readin[l]
153 if(substr(vcf_readinl,1,1)=="#"){next}
154 else if(substr(vcf_readinl,1,1)!="#"){rowline<-l-1;break}
155 }
156 vcf_header<-vcf_readin[rowline]
157 #e.g. CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\trgSM"
158 vcf_header<-gsub("#","",vcf_header)
159 vcf_colnames<-unlist(strsplit(vcf_header,"\t"))
160
161 #extract data (hashed vcf header skipped with read.table)
162 vcf_rtable<-read.table(filename,sep="\t",stringsAsFactors=FALSE)
163 names(vcf_rtable)<-vcf_colnames
164
165 ######################
166 ###PREPARE DATA
167
168 vcfinfo_dat<-NULL
169 vcfinfo_pdat<-NULL
170 multiallele_counter<-0
171 diviserror_counter<-0
172 for(i in c(1:nrow(vcf_rtable))){
173 vcf_line<-vcf_rtable[i,]
174 #to speed up runtime- quality filter here
175 if(vcf_line$QUAL>=read_qual){
176 #remove chrom or chr prefix from chromosome value
177 if(grepl("chrom",vcf_line$CHROM,ignore.case=TRUE)==TRUE){
178 vcf_line$CHROM<-gsub("chrom","",vcf_line$CHROM,ignore.case=TRUE)
179 }else if(grepl("chr",vcf_line$CHROM,ignore.case=TRUE)==TRUE){
180 vcf_line$CHROM<-gsub("chr","",vcf_line$CHROM,ignore.case=TRUE)
181 }
182 #PARSE INFO
183 vcfinfo_split<-strsplit(vcf_line$INFO,split=";")
184 vcfinfo_coln<-gsub("=.*","",unlist(vcfinfo_split))
185 vcfinfo_cold<-gsub(".*=","",unlist(vcfinfo_split))
186 vcfinfo_ldat<-data.frame(t(vcfinfo_cold),stringsAsFactors=FALSE)
187 names(vcfinfo_ldat)<-vcfinfo_coln
188
189 #skip if commas in values to avoid returning errors
190 if(grepl(",",vcfinfo_ldat$AO)==TRUE){
191 multiallele_counter<-multiallele_counter+1
192 next
193 }
194 #skip divide by zero errors (under "ratio" setting for ratio calculation)
195 if(as.numeric(vcfinfo_ldat$AO)+as.numeric(vcfinfo_ldat$RO)=="0"){
196 diviserror_counter<-diviserror_counter+1
197 next
198 }
199
200 #specific accounting for nonstandard categories
201 #LOF columns only present for loss-of-function variants + assign NA values to all other variants
202 if(("LOF" %in% names(vcfinfo_ldat))==TRUE){
203 LOF<-vcfinfo_ldat$LOF
204 vcfinfo_ldat<-vcfinfo_ldat[,!names(vcfinfo_ldat) %in% "LOF"]
205 vcfinfo_ldat<-cbind(vcfinfo_ldat,LOF)
206 }else{
207 LOF<-"NA"
208 vcfinfo_ldat<-cbind(vcfinfo_ldat,LOF)
209 }
210 #NMD columns only present for nonsense-mediated-decay variants + assign NA values to all other variants
211 if(("NMD" %in% names(vcfinfo_ldat))==TRUE){
212 NMD<-vcfinfo_ldat$NMD
213 vcfinfo_ldat<-vcfinfo_ldat[,!names(vcfinfo_ldat) %in% "NMD"]
214 vcfinfo_ldat<-cbind(vcfinfo_ldat,NMD)
215 }else{
216 NMD<-"NA"
217 vcfinfo_ldat<-cbind(vcfinfo_ldat,NMD)
218 }
219
220 #general accounting for nonstandard categories
221
222
223 #PARSE ANNOTATION
224 ann_rparsed<-unlist(strsplit(vcfinfo_ldat$ANN[1],split="\\|"))[1:20]
225 ann_rparsed[ann_rparsed==""]<-"novalue"
226 ann_parsed<-data.frame(t(ann_rparsed),stringsAsFactors=FALSE)
227 names(ann_parsed)<-paste("ANN",c(1:dim(ann_parsed)[2]),sep="")
228 #remove duplicate redundant INFO column (fully parsed)
229 vcf_line<-vcf_line[,names(vcf_line)!="INFO"]
230
231 #dataset keeping unparsed annotation (full)
232 vcfinfo_pldat<-cbind(vcf_line,vcfinfo_ldat)
233 vcfinfo_pdat<-rbind(vcfinfo_pdat,vcfinfo_pldat)
234
235 #dataset keeping parsed annotation (partial parsed-for relevant)
236 vcfinfo_ldat<-vcfinfo_ldat[,names(vcfinfo_ldat)!="ANN"]
237 #append copy of original data to parsed data
238 vcfinfo_lldat<-cbind(vcf_line,vcfinfo_ldat,ann_parsed)
239 vcfinfo_dat<-rbind(vcfinfo_dat,vcfinfo_lldat)
240 }
241 }
242 print(paste("rows with multiple alleles skipped: ",multiallele_counter,sep=""))
243 # print(paste("rows with AO+RO=0 (not multiple alleles) skipped: ",diviserror_counter,sep=""))
244
245 #ENSURE CORRECT DATATYPES
246 #convert dataframe columns of factor type to character type
247 vcfinfo_dat<-data.frame(lapply(vcfinfo_dat,as.character),stringsAsFactors=FALSE)
248 #convert to numeric if column is numeric and not string
249 for(n in c(1:dim(vcfinfo_dat)[2])){
250 #suppress warnings when columns with strings encountered (not converted)
251 suppressWarnings(
252 colnum_index<-!is.na(as.numeric(vcfinfo_dat[,n]))
253 )
254 if(all(colnum_index)==TRUE){
255 vcfinfo_dat[,n]<-as.numeric(vcfinfo_dat[,n])
256 }
257 }
258
259 ######################
260 #RATIO CALCULATION
261 #ratio calculation from AO and RO
262 RATIO<-c(vcfinfo_dat$AO/(vcfinfo_dat$AO+vcfinfo_dat$RO))
263 #add adj_AB for AB=0->AO=1 conversion
264 adj_AB<-replace(vcfinfo_dat$AB,vcfinfo_dat$AB==0,1)
265 vcfinfo_dat<-cbind(vcfinfo_dat,RATIO,adj_AB)
266 vcfinfo_dat<-vcfinfo_dat[with(vcfinfo_dat,order(CHROM,POS)),]
267
268 #CONSIDER ONLY SNP VARIANTS
269 if(snp_only==TRUE){
270 vcfinfo_dat<-subset(vcfinfo_dat,CIGAR=="1X")
271 }
272
273 ######################
274 #SUBTRACT VARIANTS FROM EXCLUSION LIST
275 # if(length(exclusion_list)>0){
276 # if(exclusion_list!="FALSE"){
277 if(exclusion_list!="FALSE"){
278 #keep copy of pre-subtraction data for later plotting
279 vcfinfo_origdat<-vcfinfo_dat
280
281 #identifiers for exclusion list based on CHROM/POS/REF/ALT
282 index1<-paste(vcfinfo_dat$CHROM,vcfinfo_dat$POS,sep="_")
283 index2<-paste(vcfinfo_dat$CHROM,vcfinfo_dat$POS,vcfinfo_dat$REF,sep="_")
284 index3<-paste(vcfinfo_dat$CHROM,vcfinfo_dat$POS,vcfinfo_dat$REF,vcfinfo_dat$ALT,sep="_")
285 vcfinfo_dat<-cbind(vcfinfo_dat,index1,index2,index3)
286
287 print(paste("before subtraction: ",nrow(vcfinfo_dat),sep=""))
288 #loop and subtract through exclusion lists (if multiple files)
289 for(exclusion_ind in exclusion_list){
290 exclin<-read.table(exclusion_ind,header=TRUE)
291
292 #THRESHOLD FILTER ON EXCLUSION LIST VARIANTS
293 if(allele_ratio=="AB"){
294 exclin<-subset(exclin,adj_AB>=excl_threshold)
295 }
296 if(allele_ratio=="ratio"){
297 exclin<-subset(exclin,ratio>=excl_threshold)
298 }
299
300 #identifiers for vcf data based on CHROM/POS/REF/ALT
301 index1<-paste(exclin$CHROM,exclin$POS,sep="_")
302 index2<-paste(exclin$CHROM,exclin$POS,exclin$REF,sep="_")
303 index3<-paste(exclin$CHROM,exclin$POS,exclin$REF,exclin$ALT,sep="_")
304 exclin<-cbind(exclin,index1,index2,index3)
305 #exclude based on CHROM+POS+REF+ALT
306 vcfinfo_dat<-subset(vcfinfo_dat,!(index3 %in% exclin$index3))
307 }
308 print(paste("after subtraction: ",nrow(vcfinfo_dat),sep=""))
309 }
310
311 ######################
312 #WRITE TO OUTPUT
313 #select relevant columns 2 variant type; 4 gene; !5 wormbase ID; 8 type change; 10 nucleotide change; 11 amino acid change; 16 warning message
314 vcfinfo_simp<-subset(vcfinfo_dat,select=c("CHROM","POS","QUAL","DP","REF","ALT","AB","AO","RO","RATIO","adj_AB","ANN2","ANN4","ANN8","ANN10","ANN11","ANN16"))
315 names(vcfinfo_simp)<-c("CHROM","POS","QUAL","DP","REF","ALT","AB","AO","RO","RATIO","adj_AB","VARTYPE","GENE","TYPE","NTCHANGE","PRCHANGE","WARNINGS")
316 vcfsimp_dat<-vcfinfo_simp[with(vcfinfo_simp,order(CHROM,POS)),]
317
318 #write table with quality filtered variants for VDM plotting and relevant columns
319 try(
320 write.table(vcfsimp_dat,vcfoutput_filename,sep="\t",quote=FALSE,row.names=FALSE)
321 ,silent=TRUE)
322 #write table with all unfiltered variants and all columns including parsed INFO
323 try(
324 write.table(vcfinfo_pdat,vcfparsed_filename,sep="\t",quote=FALSE,row.names=FALSE)
325 ,silent=TRUE)
326
327
328 ######################
329 ###CHROMOSOME (INTERVAL) ARRANGEMENT
330 #define chromosome and chromosome size in Mb
331 if(interval_type == 'C.elegans'){
332 chrom_n<-c('I','II','III','IV','V','X')
333 chrom_mb<-c(16,16,14,18,21,18)
334 interval_frame<-data.frame(chrom_n,chrom_mb)
335 } else if(interval_type == 'Zebrafish'){
336 chrom_n<-c('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25')
337 chrom_mb<-c(61,61,64,63,76,60,78,57,59,47,47,51,55,54,48,59,54,50,51,56,45,43,47,44,39)
338 interval_frame<-data.frame(chrom_n,chrom_mb)
339 } else if(interval_type == 'Brachypodium'){
340 chrom_n<-c('1','2','3','4','5')
341 chrom_mb<-c(75,60,60,50,30)
342 interval_frame<-data.frame(chrom_n,chrom_mb)
343 } else if(interval_type == 'Arabidopsis'){
344 chrom_n<-c('1','2','3','4','5')
345 chrom_mb<-c(31, 20,24,19,27 )
346 interval_frame<-data.frame(chrom_n,chrom_mb)
347 } else{
348 #user interval file- no headers, with chromosome in column 1 (format CHR# or CHROM#) and size in Mb (rounded up) in column 2
349 # user_interval_type<-read.table(user_interval_file)
350 user_interval_type<-read.table(interval_type)
351 if(grepl("chrom",user_interval_type[1,1],ignore.case=TRUE)==TRUE){
352 user_interval_type[,1]<-gsub("chrom","",user_interval_type[,1],ignore.case=TRUE)
353 }else if(grep("chr",user_interval_type[1,1],ignore.case=TRUE)==TRUE){
354 user_interval_type[,1]<-gsub("chr","",user_interval_type[,1],ignore.case=TRUE)
355 }
356 chrom_n<-user_interval_type[,1]
357 chrom_mb<-user_interval_type[,2]
358 interval_frame<-data.frame(chrom_n,chrom_mb)
359 }
360 names(interval_frame)<-c("CHROM","INTERVAL")
361
362
363 ######################
364 ###PLOTTING
365 #VDM SCATTER PLOT
366 #save to pdf
367 pdf(file=pdf_filename,width=9,height=8)
368 #par(mfrow=c(2,3))
369 for(chromind in interval_frame$CHROM){
370 #subset by data by chromosome for plotting
371 intervalind<-interval_frame$INTERVAL[interval_frame$CHROM==chromind]
372 chr_dat<-subset(vcfsimp_dat,CHROM==chromind,silent=TRUE)
373
374 #same subsetting by chromosome for pre-subtraction data
375 # if(length(exclusion_list)>0){
376 if(exclusion_list!="FALSE"){
377 chr_origdat<-subset(vcfinfo_origdat,CHROM==chromind,silent=TRUE)
378 }
379
380 #define x-axis upper limit
381 if(xaxis_standard==TRUE){
382 #for standardized x-axis (max x-axis chromosome length)
383 scupper_xaxis<-max(interval_frame$INTERVAL)
384 scupper_xval<-scupper_xaxis*interval_unit
385 } else if(xaxis_standard==FALSE){
386 scupper_xaxis<-intervalind
387 scupper_xval<-intervalind*interval_unit
388 }
389
390 if(allele_ratio=="AB"){
391 plot(chr_dat$POS,chr_dat$adj_AB,cex=0.60,xlim=c(0,scupper_xval),ylim=c(0,sp_yaxis),main=paste("Chr",chromind," Variant Discovery Mapping",sep=""),xlab="Position along Chromosome (in Mb)",ylab='Ratio of Variant Reads/Total Reads [AB]',pch=10, col=plot_color,xaxt='n')
392 try(lines(loess.smooth(chr_dat$POS,chr_dat$adj_AB,span=loess_span),lwd=5,col=loess_color))
393 #plot loess curve for data without subtraction of exclusion variants
394 # if(length(exclusion_list)>0){
395 if(exclusion_list!="FALSE"){
396 try(lines(loess.smooth(chr_origdat$POS,chr_origdat$adj_AB,span=loess_span),lty="longdash",lwd=4,col=excl_loess_color))
397 }
398
399 axis(1,at=seq(0,scupper_xval,by=interval_unit),labels=c(0:scupper_xaxis))
400 abline(h=seq(0,sp_yaxis,by=0.1),v=c(1:scupper_xaxis)*interval_unit,col="gray")
401 } else if(allele_ratio=="ratio"){
402 plot(chr_dat$POS,chr_dat$RATIO,cex=0.60,xlim=c(0,scupper_xval),ylim=c(0,sp_yaxis),main=paste("Chr",chromind," Variant Discovery Mapping",sep=""),xlab="Position along Chromosome (in Mb)",ylab='Ratio of Variant Reads/Total Reads [ratio]',pch=10, col=plot_color,xaxt='n')
403 try(lines(loess.smooth(chr_dat$POS,chr_dat$RATIO,span=loess_span),lwd=5,col=loess_color))
404 #plot loess curve for data without subtraction of exclusion variants
405 # if(length(exclusion_list)>0){
406 if(exclusion_list!="FALSE"){
407 try(lines(loess.smooth(chr_origdat$POS,chr_origdat$adj_AB,span=loess_span),lty="longdash",lwd=4,col=excl_loess_color))
408 }
409 axis(1,at=seq(0,scupper_xval,by=interval_unit),labels=c(0:scupper_xaxis))
410 abline(h=seq(0,sp_yaxis,by=0.1),v=c(1:scupper_xaxis)*interval_unit,col="gray")
411 }
412 }
413
414 ######################
415 #graph barplots
416 location_index<-NULL
417 meanSNP_dat<-NULL
418 # prepare table of counts and calculations
419 for(chromind in interval_frame$CHROM){
420 #for standardized x-axis
421 if(xaxis_standard==TRUE){
422 intervalind<-max(interval_frame$INTERVAL)*1000000/bin_size
423 } else if(xaxis_standard==FALSE){
424 intervalind<-interval_frame$INTERVAL[interval_frame$CHROM==chromind]*1000000/bin_size
425 }
426 #start intervals with **1 and end with **0
427 interval_begin<-c(((0:(intervalind-1))*bin_size)+1)
428 interval_end<-c((1:intervalind)*bin_size)
429
430 #define x-axis upper limit
431 if(xaxis_standard==TRUE){
432 upper_xaxis<-max(interval_frame$INTERVAL)
433 } else if(xaxis_standard==FALSE){
434 upper_xaxis<-interval_frame$INTERVAL[interval_frame$CHROM==chromind]
435 }
436 #prepare columns
437 snp_counter<-0
438 purealt_counter<-0
439 pureref_counter<-0
440 het_counter<-0
441 chr_mean<-0
442 normed_freq<-0
443 ratio<-0
444
445 interval_index<-data.frame(chromind,interval_begin,interval_end,snp_counter,purealt_counter,pureref_counter,het_counter,chr_mean,normed_freq)
446 chr_dat<-subset(vcfinfo_dat,CHROM==chromind)
447 #ratio calculation
448 ratio<-chr_dat$AO/(chr_dat$AO+chr_dat$RO)
449
450 #if counter based on adj_AB or ratio
451 if(allele_ratio=="ratio"){
452 chr_purealtdat<-subset(chr_dat,ratio>=threshold_upper)#;chr_purealtdat
453 chr_purerefdat<-subset(chr_dat,ratio<=threshold_lower)#;chr_purerefdat
454 chr_hetdat<-subset(chr_dat,ratio>threshold_lower & ratio<threshold_upper)#;chr_hetdat
455 } else if(allele_ratio=="AB"){
456 chr_purealtdat<-subset(chr_dat,adj_AB>=threshold_upper)#;chr_purealtdat
457 chr_purerefdat<-subset(chr_dat,adj_AB<=threshold_lower)#;chr_purerefdat
458 chr_hetdat<-subset(chr_dat,adj_AB>threshold_lower & adj_AB<threshold_upper)#;chr_hetdat
459 }
460 #if chromosome with data, count number of snps within each bin (positions rounded up to nearest bin), else skip to next chromosome
461 if(dim(chr_dat)[1]>0){
462 for(i in 1:dim(chr_dat)[1]){
463 chr_datind<-chr_dat[i,]
464 #round up to nearest bin-size interval
465 chr_datind_upper<-ceiling(chr_datind$POS/bin_size)*bin_size
466 interval_coln<-NULL;interval_rown<-NULL
467 #identify row and and counter column to increment
468 interval_coln<-which(names(interval_index)=="snp_counter")
469 interval_rown<-match(chr_datind_upper,interval_index$interval_end)
470 interval_index[interval_rown,interval_coln]<-c(interval_index$snp_counter[interval_rown]+1)
471 }
472 }else{
473 next
474 }
475 ##if chromosome with pure AO, count number of snps with each bin (positions rounded up to nearest bin)
476 if(dim(chr_purealtdat)[1]>0){
477 for(i in 1:dim(chr_purealtdat)[1]){
478 chr_purealtind<-chr_purealtdat[i,]
479 chr_purealtind_upper<-ceiling(chr_purealtind$POS/bin_size)*bin_size
480 interval_coln<-NULL;interval_rown<-NULL
481 interval_coln<-which(names(interval_index)=="purealt_counter")
482 interval_rown<-match(chr_purealtind_upper,interval_index$interval_end)
483 interval_index[interval_rown,interval_coln]<-c(interval_index$purealt_counter[interval_rown]+1)
484 }
485 }
486 #if chromosome with pure RO, count number of snps with each bin (positions rounded up to nearest bin)
487 if(dim(chr_purerefdat)[1]>0){
488 for(i in 1:dim(chr_purerefdat)[1]){
489 chr_purerefind<-chr_purerefdat[i,]
490 chr_purerefind_upper<-ceiling(chr_purerefind$POS/bin_size)*bin_size
491 interval_coln<-NULL;interval_rown<-NULL
492 interval_coln<-which(names(interval_index)=="pureref_counter")
493 interval_rown<-match(chr_purerefind_upper,interval_index$interval_end)
494 interval_index[interval_rown,interval_coln]<-c(interval_index$pureref_counter[interval_rown]+1)
495 }
496 }
497 #if chromosome with hets, count number of snps with each bin (positions rounded up to nearest bin)
498 if(dim(chr_hetdat)[1]>0){
499 for(i in 1:dim(chr_hetdat)[1]){
500 chr_hetind<-chr_hetdat[i,]
501 chr_hetind_upper<-ceiling(chr_hetind$POS/bin_size)*bin_size
502 interval_coln<-NULL;interval_rown<-NULL
503 interval_coln<-which(names(interval_index)=="het_counter")
504 interval_rown<-match(chr_hetind_upper,interval_index$interval_end)
505 interval_index[interval_rown,interval_coln]<-c(interval_index$het_counter[interval_rown]+1)
506 }
507 }
508 #irrespective of standardized x-axis, mean should be calculated from actual interval range of chromosome
509 chr_mean<-sum(interval_index$purealt_counter)/(interval_frame$INTERVAL[interval_frame$CHROM==chromind]*1000000/bin_size)
510 interval_index$chr_mean<-chr_mean
511 meanSNP_dat<-rbind(meanSNP_dat,data.frame(chromind,chr_mean))
512 #normalization treatment for if SNPs are AO=0, AO=total SNPs, or AO and RO in bin
513 for(i in 1:dim(interval_index)[1]){
514 chr_intind<-interval_index[i,]
515 #hom definition based on specified upper and lower thresholds
516 if(chr_intind$purealt_counter<=threshold_lower){
517 interval_coln<-NULL
518 interval_coln<-which(names(interval_index)=="normed_freq")
519 interval_index[i,interval_coln]=0
520 } else if (chr_intind$purealt_counter==chr_intind$snp_counter){
521 interval_coln<-NULL
522 interval_coln<-which(names(interval_index)=="normed_freq")
523 interval_index[i,interval_coln]=(chr_intind$purealt_counter)^2/chr_mean
524 } else {
525 interval_coln<-NULL
526 interval_coln<-which(names(interval_index)=="normed_freq")
527 interval_index[i,interval_coln]=chr_mean*(chr_intind$purealt_counter)^2/(chr_intind$snp_counter-chr_intind$purealt_counter)
528 }
529 }
530 location_index<-rbind(location_index,interval_index)
531 }
532
533 for(chromind in interval_frame$CHROM){
534 interval_index<-location_index[location_index$chromind==chromind,]
535 #assign 0 values to avoid empty datatable error
536 if(dim(interval_index)[1]==0){
537 interval_index[1,]<-rep(0,dim(interval_index)[2])
538 }
539 # }
540 #set up x_axis
541 if(xaxis_standard==TRUE){
542 #for standardized x-axis (max x-axis chromosome length)
543 bpupper_xaxis<-max(interval_frame$INTERVAL)
544 bpupper_xval<-bpupper_xaxis*interval_unit
545 }else if(xaxis_standard==FALSE){
546 bpupper_xaxis<-intervalind
547 bpupper_xval<-intervalind*interval_unit
548 }
549 #set up y_axis range for barplots
550 if(bfreq_norm==TRUE){
551 bp_yaxis<-5*ceiling(max(location_index$normed_freq)/5)
552 #assign non-0 value to yaxis to avoid error
553 if(bp_yaxis==0){
554 bp_yaxis<-10
555 }
556 if(xaxis_standard==TRUE){
557 bplot<-barplot(interval_index$normed_freq,space=0,ylim=c(0,bp_yaxis),main=paste("Chr",chromind," Variant Only",sep=""),xlab="Position along Chromosome (in Mb)",ylab='Normalised Frequency')
558 }else if(xaxis_standard==FALSE){
559 bplot<-barplot(interval_index$normed_freq,space=0,xlim=c(0,bpupper_xaxis),ylim=c(0,bp_yaxis),main=paste("Chr",chromind," Variant Only",sep=""),xlab="Position along Chromosome (in Mb)",ylab='Normalised Frequency')
560 }
561
562 }else if(bfreq_norm==FALSE){
563 bp_yaxis<-5*ceiling(max(location_index$purealt_counter)/5)
564 #assign non-0 value to yaxis to avoid error
565 if(bp_yaxis==0){
566 bp_yaxis<-10
567 }
568 if(xaxis_standard==TRUE){
569 bplot<-barplot(interval_index$purealt_counter,space=0,ylim=c(0,bp_yaxis),main=paste("Chr",chromind," Variant Only",sep=""),xlab="Position along Chromosome (in Mb)",ylab='Frequency')
570 }else if(xaxis_standard==FALSE){
571 bplot<-barplot(interval_index$purealt_counter,space=0,xlim=c(0,bpupper_xaxis),ylim=c(0,bp_yaxis),main=paste("Chr",chromind," Variant Only",sep=""),xlab="Position along Chromosome (in Mb)",ylab='Frequency')
572 }
573 }
574 bp_xaxis1<-as.numeric(bplot)
575 bp_xaxis2<-c(bp_xaxis1,tail(bp_xaxis1,1)+bp_xaxis1[2]-bp_xaxis1[1])
576 bp_xaxis<-bp_xaxis2-bp_xaxis1[1]
577
578 axis(1,at=bp_xaxis,labels=seq(0,bpupper_xaxis,by=c(bin_size/1000000)))
579
580 }
581 dev.off()
582 }
583
584
585 # myfunction(options$inf,options$itype,options$qual,options$thrup,options$thrlow,options$allr,options$snp,options$lsp,options$pcol,options$lcol,options$xstand,
586 # options$bsize,options$bnorm,options$exclf,options$exclthr,options$exclcol,options$parn,options$outn,options$pdfn)
587
588
589 myfunction(inf=options$inf,itype=options$itype,qual=options$qual,thrup=options$thrup,thrlow=options$thrlow,
590 allr=options$allr,snp=options$snp,lsp=options$lsp,pcol=options$pcol,lcol=options$lcol,xstand=options$xstand,bsize=options$bsize,
591 bnorm=options$bnorm,exclf=options$exclf,exclthr=options$exclthr,exclcol=options$exclcol,parn=options$parn,outn=options$outn,pdfn=options$pdfn)
592