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PYRUS.R
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#!/usr/bin/Rscript
library(optparse)
library(dplyr)
library(seqminer)
library(data.table)
option_list<-list(make_option(c("-f", "--file"), default=NULL, type="character",help='Input an Inital Bed File'),
make_option(c("-d", "--dir"), default=NULL, type="character",help='Input Directory of Bed Files'),
make_option(c("-p", "--dirpattern"), default=".bed.gz", type="character",help='Pattern of files in Directory, defualt .bed'),
make_option(c("-a", "--annotation"), default=NULL, type="character",help='Add an Annotation File '),
make_option(c("-c", "--cordfile"), default=NULL, type="character",help='Input a Chr Coordinates Bed File'),
make_option(c("-l", "--lineColor"), default="blue,red", type="character",help='Input a Color(s) ex: blue,red'),
make_option(c("-t", "--plotTogether"), default=NULL, type="character",help='Graph Together. ex: BARX1,BARX1-DT'),
make_option(c("-r", "--HighRes"), default=NULL, type="character",help='Save Plot(s) as PNG Image, Defualt is off'),
make_option(c("-b", "--box"), default=NULL, type="character",help='Plot Box-plot Window'),
make_option(c("-s", "--singleplots"), default=NULL, type="character",help='plots each file in dirpath individually'),
make_option(c("-y", "--rename"), default=NULL, type="character",help='Rename file -f on plot'),
make_option(c("-g", "--regions"), default="1.3,2.7", type="character",help='Print only regions above 2.7 CNV or below 1.3 CNV'),
make_option(c("-v", "--minmax"), default=NULL, type="character",help='Plot outside of regions from the -g flag'),
make_option(c("-j", "--Trio"), default=NULL, type="character",help='Plot trio with files from parent:A(M) and parent:B(F) alongside the initial file -f'),
make_option(c("-k", "--subtractbynum"), default=1, type="character",help='Subtract values given in -g flag by input for only chrY and chrX if karyotype is M, Default is 1 '),
make_option(c("-u", "--topylim"), default=6, type="integer",help='change top -y lim value, defualt is 6'),
make_option(c("-x", "--sex"), default="F", type="character",help='M or F sample, if male sample, -g flag max and mins will be subtracted by 1'),
make_option(c("-w", "--isnonhuman"), default="F", type="character",help='If the initial sample is non-human, then this option will turn off kayaotyping (T or F), ex -w T'),
make_option(c("-n", "--annInput"), default=NULL, type="character",help='Input For Annotation (fill,boarder,name), ex : "red,blue,Exons'),
make_option(c("-o", "--outfile"), default=NULL, type="character",help='Outputs The Chromosome Plots Into One PDF, Defualt Is Plots Each Cordinate To Its Own PDF File'))
opt<-parse_args(OptionParser(option_list=option_list))
options(scipen = 999)
outfile=opt$outfile
addname<-''
colorofann<-"red"
bordcolofann<-"black"
nameofann<-"Exons"
max<-(as.numeric(strsplit(toString(opt$regions), ',', fixed=TRUE)[[1]][2]))
min<-(as.numeric(strsplit(toString(opt$regions), ',', fixed=TRUE)[[1]][1]))
annlen<-(-0.12)
colofline<-strsplit(toString(opt$lineColor), ',', fixed=TRUE)[[1]][1]
getcol<-strsplit(toString(opt$lineColor), ',', fixed=TRUE)[[1]][2]
isnothuman <- as.character(opt$isnonhuman)
sampleFile = opt$file
if(is.null(opt$Trio)){
inputdata<-sampleFile}
if(!is.null(opt$Trio)){
inputdata<-append(toString(opt$file),unlist(strsplit(toString(opt$Trio), ',', fixed=TRUE)))
if(is.null(opt$outfile)){
warning("PLEASE ADD (-o) OUTPUTFILE")
stop()}
if(!is.null(opt$plotTogether)){
warning("REMOVE -t FLAG")
stop()}
}
suppressWarnings({
if(inputdata==sampleFile && (isnothuman == "F")){
infile <- as.data.frame(fread(opt$file), header=F)
infile <- infile[which(infile$V1 %in% c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY")),]
chromCount <- sum(round(tapply(infile$V4, infile$V1, mean)))
chrX <- paste0(rep("X", round(tapply(infile$V4, infile$V1, mean))[names(round(tapply(infile$V4, infile$V1, mean))) == "chrX"]), collapse="")
chrY <- paste0(rep("Y", round(tapply(infile$V4, infile$V1, mean))[names(round(tapply(infile$V4, infile$V1, mean))) == "chrY"]), collapse="")
if((as.integer(round(tapply(infile$V4, infile$V1, mean))[names(round(tapply(infile$V4, infile$V1, mean))) == "chrY"])) >=1 ){
opt$sex<-'M'}
}})
if(isnothuman == "T"){
chrX<-""
chrY<-""
chromCount<-"NH"}
if(!is.null(opt$cordfile)){
coord <- read.delim(gzfile(opt$cordfile), header=F)
if(length(colnames(coord)) ==3){
coord[,4] <- paste0(strtrim(coord[,1],5),":",coord[,2],"-",coord[,3])}
if(is.null(opt$plotTogether) ){
COORD_INPUT<- list(paste0(coord[,4],",",coord[,1], ":", coord[,2], "-", coord[,3], sep=""))
}
if(!is.null(opt$plotTogether) && is.null(opt$Trio)){
getnameInitial<-strsplit(toupper(opt$plotTogether), split=',', fixed=TRUE)[[1]][1]
getnewlistname<-strsplit(toupper(opt$plotTogether), split=',', fixed=TRUE)[[1]][-1]
coord1<- coord %>% filter(coord[,4] %in% getnameInitial)
COORD_INPUT<- list(paste0(coord1[,4],",",coord1[,1], ":", coord1[,2], "-", coord1[,3], sep=""))
NEWLISTPlot <- tryCatch({
x<- lapply(getnewlistname,function(x){
coord<- coord %>% filter(coord[,4] %in% x)
NEWLISTPlot<- list(paste0(coord[,4],",",coord[,1], ":", coord[,2], "-", coord[,3], sep=""))
NEWLISTPlot<- unlist(NEWLISTPlot)
return(NEWLISTPlot)
})},
error = function(e){
y<- lapply(getnewlistname,function(x){
stop("Missing Input: Chromosome Position Bed File")}) })}
}
if(is.null(opt$highRes)){
outfilename=opt$outfile
pdf(outfilename)}
if(!is.null(opt$annInput)){
annsplit<-strsplit(opt$annInput, ',', fixed=TRUE)
colorofann<-annsplit[[1]][1]
bordcolofann<-annsplit[[1]][2]
nameofann<-toString(rbind(strtrim(annsplit[[1]][3],15)))
annlen<-(-0.2)}
if(!is.null(opt$dir)){
pattern<-toString(opt$dirpattern)
pattern1<-paste0(pattern,"$")
directory<-list.files(path=toString(opt$dir) ,pattern=pattern1, full.names=TRUE)
if(length(directory) >= 10){
opt$box="yes"}
}
if(is.null(opt$Trio)){
old.par <- par(no.readonly = TRUE)}
if(!is.null(opt$Trio)){
layout(matrix(c(2,3,1,1), 2, 2, byrow = TRUE))
old.par<-NULL}
func<-function(t){
holding<-lapply(COORD_INPUT[[1]], function(x){
par(mar=c(5.1, 4.1, 4.1, 6.1))
rangeofit<-toString(strsplit(x, ',', fixed=TRUE)[[1]][2])
chr<-strsplit(rangeofit, ':', fixed=TRUE)[[1]][1]
stsp<-strsplit(rangeofit, ':', fixed=TRUE)[[1]][2]
nameofit<-strsplit(x, ',', fixed=TRUE)[[1]][1]
startcord<-strsplit(stsp, '-', fixed=TRUE)[[1]][1]
stopcord<-strsplit(stsp, '-', fixed=TRUE)[[1]][2]
filehold<-lapply(inputdata, function(k){
inputfile<-k
filename<-toString(rbind(strtrim(strsplit(toString(basename(inputfile)), '.bed', fixed=TRUE)[[1]][1],15)))
if(!is.null(opt$Trio) && (isnothuman == "F")){
if(inputfile==opt$file ){
triomember<- "Child"
ledgendvalue<-(-0.15)}
if(inputfile!=opt$file){
triomember<-"Parent"
ledgendvalue<-(-0.5)
annlen<-(-0.5)}
infile <- as.data.frame(fread(inputfile), header=F)
infile <- infile[which(infile$V1 %in% c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY")),]
chromCount1 <- sum(round(tapply(infile$V4, infile$V1, mean)))
chrX1 <- paste0(rep("X", round(tapply(infile$V4, infile$V1, mean))[names(round(tapply(infile$V4, infile$V1, mean))) == "chrX"]), collapse="")
chrY1 <- paste0(rep("Y", round(tapply(infile$V4, infile$V1, mean))[names(round(tapply(infile$V4, infile$V1, mean))) == "chrY"]), collapse="")
triomember<-paste0(triomember,"(",chromCount1,chrX1,chrY1,")")
addname<- paste0(triomember,":")
if((as.integer(round(tapply(infile$V4, infile$V1, mean))[names(round(tapply(infile$V4, infile$V1, mean))) == "chrY"])) >=1 ){
opt$sex<-'M'
}
}
initialfile<-file.path(inputfile)
fr<-tabix.read.table(initialfile,rangeofit,col.names = TRUE,stringsAsFactors = FALSE)
if(length(fr)>=1){
par(old.par)
initialmean<-mean(fr$V4)
if(is.null(opt$outfile)){
if(!is.null(opt$HighRes) && is.null(opt$singleplots) &&is.null(opt$plotTogether)){
png(paste(nameofit, ".png", sep=""), width = 600, height = 600, units = "px", res=100) }
if(is.null(opt$HighRes) && is.null(opt$singleplots) && is.null(opt$plotTogether) ){
pdf(paste0(nameofit,".pdf")) }
if(!is.null(opt$HighRes) && !is.null(opt$singleplots) ){
png(paste(nameofit, "_",basename(t),".png", sep=""), width = 600, height = 600, units = "px", res=100) }
if(is.null(opt$HighRes) && !is.null(opt$singleplots) ){
pdf(paste0(nameofit,"-",basename(t),".pdf")) }
}
if(isnothuman == "F"){
if(chr == "chrY" ){
min<-(min-as.numeric(opt$subtractbynum))
max<-(max-as.numeric(opt$subtractbynum))}
if(opt$sex == "M" && chr == "chrX"){
max<-(max-as.numeric(opt$subtractbynum))
min<-(min-as.numeric(opt$subtractbynum))}
}
if(is.null(opt$minmax) || (!is.null(opt$minmax) && (as.numeric(initialmean)<=min || as.numeric(initialmean)>=max))){
par(mar=c(5.1, 4.1, 4.1, 6.1))
bgcolor<-function(){
par(fig=c(0.5,1,0.6,1),new=TRUE)
rect(par("usr")[1],par("usr")[3],par("usr")[2],par("usr")[4],col = "white", border="transparent")}
if(is.null(opt$plotTogether) ){
xaxisname<-paste(chr, "position")
plot(as.numeric(fr$V2), y=as.numeric(fr$V4), col=("transparent"), xlab=xaxisname ,
ylab="Estimated Copy Number", main=(bquote(paste(paste(.(addname)),italic(.(nameofit))))), pch=23,
ylim= c(0,opt$topylim), type= 'l' , cex.main=1, cex.lab=1, cex.axis=1,las=1)
abline(h=2, col="grey", lty=2)
lengthofit<-(as.numeric(stopcord)-as.numeric(startcord))
lengthofit<-lengthofit+1
mtext(paste("Length:",lengthofit), side = 3,cex=0.5)
segments(x0 = as.numeric(startcord), y0 = -0.1, x1 = as.numeric(stopcord), y1 = -0.1, col=colofline)
if(is.null(opt$Trio)){
legend("topright", inset=c(-0.2,0.5), legend=filename,pch=23,col=colofline,lty=1,xpd = TRUE,horiz = TRUE,bty = "n",cex=0.5)}
abline(h=2.7, col="grey", lty=2)
abline(h=2, col="grey", lty=1)
abline(h=1.3, col="grey", lty=2)
lines(as.numeric(fr$V2), y=as.numeric(fr$V4), type="l", col=colofline)}
if(!is.null(opt$plotTogether) && is.null(opt$Trio) ){
secondmean<-lapply(NEWLISTPlot, function(p){
plottogethernameofit<-strsplit(p, ',', fixed=TRUE)[[1]][1]
plottogetherrange<-strsplit(p, ',', fixed=TRUE)[[1]][2]
splitfromchrplot<-strsplit(plottogetherrange, ':', fixed=TRUE)
chrplot<-strsplit(rangeofit, ':', fixed=TRUE)[[1]][1]
plotlinetogether1<-tabix.read.table(initialfile,plottogetherrange,col.names = TRUE,stringsAsFactors = FALSE)
if(length(plotlinetogether1)>=1 ){
if(is.null(opt$outfile) && is.null(opt$singleplots)){
pdf(paste0(nameofit,"_and_",plottogethernameofit,".pdf"))}
xaxisname<-paste("positions",chr, "and" ,chrplot)
secmean<-mean(plotlinetogether1$V4)
plotlinetogether<-rbind(fr,plotlinetogether1)
par(mar=c(5.1, 4.1, 4.1, 6.1))
plot(as.numeric(plotlinetogether$V2), y=as.numeric(plotlinetogether$V4), xlab=xaxisname,col="transparent",
ylab="Estimated Copy Number", main=(bquote(paste(italic(.(nameofit)),paste(" and "),italic(.(plottogethernameofit))))), pch=19,
ylim= c(0,opt$topylim), type= 'l' , cex.main=1, cex.lab=1, cex.axis=1,las=1)
if(is.null(opt$Trio)){
legend("topright", inset=c(-0.2,0.5), legend=strtrim(nameofit,15),col=colofline,lty=1,xpd = TRUE,horiz = TRUE,bty = "n",cex=0.5)
legend("topright", inset=c(-0.2,0.45), legend=strtrim(plottogethernameofit,15),col=toString(getcol),lty=1,xpd = TRUE,horiz = TRUE,bty = "n",cex=0.5)}
lines(as.numeric(plotlinetogether1$V2), y=as.numeric(plotlinetogether1$V4), type="l", col=getcol)
lines(as.numeric(fr$V2), y=as.numeric(fr$V4), type="l", col=colofline)
return(secmean) }
else{ plotlinetogether<-NULL }
})
}
printline<-function(){
abline(h=2.7, col="grey", lty=2)
abline(h=2, col="grey", lty=1)
abline(h=1.3, col="grey", lty=2)
lines(as.numeric(fr$V2), y=as.numeric(fr$V4), type="l", col=colofline)}
if(!is.null(opt$annotation)){
par(mar=c(5.1, 4.1, 4.1, 6.1))
annot<-file.path(opt$annotation)
annota<-tabix.read.table(annot,rangeofit,col.names = TRUE,stringsAsFactors = FALSE)
if(length(annota)>=1){
rect(annota$V2, 0, annota$V3, 0.35, col= colorofann, border =bordcolofann)}
if(!is.null(opt$plotTogether) && is.null(opt$Trio)){
lapply(NEWLISTPlot, function(p){
plottogetherrange<-strsplit(p, ',', fixed=TRUE)[[1]][2]
annopt<-tabix.read.table(annot,plottogetherrange,col.names = TRUE,stringsAsFactors = FALSE)
if(length(annopt)>=1){
rect(annopt$V2, 0, annopt$V3, 0.35, col= colorofann, border = bordcolofann) }
else{ annopt<-NULL }
})}
legend("topright", inset=c(annlen,0.6), fill=colorofann,border=bordcolofann,legend=nameofann,xpd = TRUE,horiz = TRUE,bty = "n",cex=0.5)
}
if(!is.null(opt$dir)){
if(!is.null(opt$singleplots)){
par(mar=c(5.1, 4.1, 4.1, 6.1))
dirpass<-tabix.read.table(t,rangeofit,col.names = TRUE,stringsAsFactors = FALSE)
if(length(dirpass)>=1){
getmeans<-mean(dirpass$V4)
lines(as.numeric(dirpass$V2), y=as.numeric(dirpass$V4), type="l")
dirnames<-toString(rbind(strtrim(basename(t),15)))
legend("topright", inset=c(ledgendvalue,0.55), legend=dirnames,col="grey24",lty=1,xpd = TRUE,horiz = TRUE,bty = "n",cex=0.5)
if(!is.null(opt$plotTogether) && is.null(opt$Trio)){
meansget<-lapply(NEWLISTPlot, function(p){
plottogetherrange<-strsplit(p, ',', fixed=TRUE)[[1]][2]
listdir1<-tabix.read.table(t,plottogetherrange,col.names = TRUE,stringsAsFactors = FALSE)
plotlinetogether1<-tabix.read.table(initialfile,plottogetherrange,col.names = TRUE,stringsAsFactors = FALSE)
if(length(plotlinetogether1)>=1){
lines(as.numeric(plotlinetogether1$V2), y=as.numeric(plotlinetogether1$V4), type="l", col=getcol)}
if(length(listdir1)>=1){
par(new=TRUE)
lines(as.numeric(listdir1$V2), y=as.numeric(listdir1$V4), type="l",col="grey24")
getmeans1<-cbind(listdir1$V4)
return(getmeans1) }
else{listdir1<-NULL }
})
printlines<-printline()}
if(!is.null(opt$box) && is.null(opt$Trio)){
colobgit<-bgcolor()
if(!is.null(opt$plotTogether) && is.null(opt$Trio)){
par(mar=c(5.1, 4.1, 4.1, 6.1))
par(fig=c(0.47,0.9,0.6,1), new=TRUE)
boxplot(getmeans, col="white",ylim=c(0,opt$topylim),axes=FALSE,xpd = TRUE)
points(initialmean, col=colofline, pch=23)
par(fig=c(0.5,1,0.6,1), new=TRUE)
par(bg = "blue")
axis(side = 4,las=1,cex.axis=0.5)
abline(h=2, col="grey", lty=1)
abline(h=2.7, col="grey", lty=2)
abline(h=1.3, col="grey", lty=2)
par(fig=c(0.57,1,0.6,1), new=TRUE)
boxplot(meansget, col="white",ylim=c(0,opt$topylim),axes=FALSE,xpd = TRUE)
if(!is.null(opt$plotTogether) && is.null(opt$Trio)){
par(mar=c(5.1, 4.1, 4.1, 6.1))
par(fig=c(0.57,1,0.6,1), new=TRUE)
lapply(secondmean,function(m){
points(m, col=getcol, pch=23)})
}
par(mar=c(5.1, 4.1, 4.1, 6.1))
par(old.par) }
if(is.null(opt$plotTogether)){
par(fig=c(0.5,1,0.6,1), new=TRUE)
boxplot(getmeans, col="white",ylim=c(0,opt$topylim),axes=FALSE,xpd = TRUE)
axis(side = 4,las=1,cex.axis=0.5)
points(initialmean, col=colofline, pch=23)
abline(h=2, col="grey", lty=1)
abline(h=2.7, col="grey", lty=2)
abline(h=1.3, col="grey", lty=2)
par(old.par) }
}
}
}
if(is.null(opt$singleplots)){
x<-lapply(directory,function(y){
if(y != initialfile){
listdir<-tabix.read.table(y,rangeofit,col.names = TRUE,stringsAsFactors = FALSE)
if(length(listdir)>=1){
getmeans<-listdir$V4
lines(as.numeric(listdir$V2), y=as.numeric(listdir$V4), type="l")
printlines<-printline()
dirnames<- "Files From Directory"
par(new=TRUE)
if(is.null(opt$Trio)){legend("topright", inset=c(as.numeric(-0.225),0.55), legend=dirnames,col="grey24",lty=1,xpd = TRUE,horiz = TRUE,bty = "n",cex=0.5)}
if(!is.null(opt$plotTogether) && is.null(opt$Trio)){
y<-lapply(NEWLISTPlot, function(p){
plottogetherrange<-strsplit(p, ',', fixed=TRUE)[[1]][2]
listdir1<-tabix.read.table(y,plottogetherrange,col.names = TRUE,stringsAsFactors = FALSE)
plotlinetogether1<-tabix.read.table(initialfile,plottogetherrange,col.names = TRUE,stringsAsFactors = FALSE)
if(length(plotlinetogether1)>=1){
lines(as.numeric(plotlinetogether1$V2), y=as.numeric(plotlinetogether1$V4), type="l", col=getcol,lwd=1.0)
}
if(length(listdir1)>=1){
getmeans1<-listdir1$V4
n<-max(length(getmeans),length(getmeans1))
getmeans<-data.table(getmeans=getmeans[1:n],getmeans1=getmeans1[1:n])
par(new=TRUE)
lines(as.numeric(listdir1$V2), y=as.numeric(listdir1$V4), type="l",col="grey24")
return(getmeans) }
else{listdir1<-NULL}
})
getmeans<-do.call(rbind,y)
}
return(getmeans) }
else{getmeans<-NULL }
}
})
x<-do.call(rbind,x)
if((!is.null(opt$box) && is.null(opt$Trio)) ){
if(is.null(opt$plotTogether)){
x<-mean(x)}
else{
x<-cbind(mean(na.omit(x$getmeans)),mean(na.omit(x$getmeans1)))}
print(x)
colobgit<-bgcolor()
par(fig=c(0.5,1,0.6,1),new=TRUE)
boxplot(x, col="white",ylim=c(0,opt$topylim),axes=FALSE,xpd = TRUE)
axis(side = 4,las=1,cex.axis=0.5)
points(initialmean, col=colofline, pch=23)
abline(h=2, col="grey", lty=1)
abline(h=2.7, col="grey", lty=2)
abline(h=1.3, col="grey", lty=2)
if(is.null(opt$singleplots) && !is.null(opt$plotTogether) && is.null(opt$Trio)){
lapply(secondmean,function(m){
points(2,m, col=getcol, pch=23)})
}
}
if(!is.null(opt$Trio) && (isnothuman == "F")){
dirmean<-strtrim(toString(mean(na.omit(x))),5)
printmeans<-paste("D:",dirmean, '\n', triomember,":",strtrim(toString(initialmean),5))
legend("topright", inset=c(as.numeric(ledgendvalue),0.3), legend=printmeans,col="grey24",pch=23,xpd = TRUE,horiz = TRUE,bty = "n",cex=0.5)
legend("topright", inset=c(as.numeric(ledgendvalue),0.5), legend=filename,pch=23,col=colofline,xpd = TRUE,horiz = TRUE,bty = "n",cex=0.5)}
}
}
else{fir<-NULL}
}
if((as.numeric(initialmean)<=min || as.numeric(initialmean)>=max) ){
if(is.null(opt$Trio)){
holdthething<-paste0(chr,"\t",startcord,"\t",stopcord,"\t",nameofit,"\t",initialmean)
return(holdthething)}
if(!is.null(opt$Trio) && (isnothuman == "F")){
holdthething<-paste0(chr,"\t",startcord,"\t",stopcord,"\t",nameofit,"\t",initialmean, "\t", triomember)
return(holdthething)}
}
}
else{fir<-NULL}
})
fileholdagain<-filehold[!sapply(filehold, is.null)]
return(fileholdagain)
})
if(is.null(opt$plotTogether)){
filenameisthis<-paste0(chromCount, chrX, chrY,"_",toString(basename(opt$file)),"_chromosomal_positions_outside_of_",min,"_and_",max,".txt")
if(is.null(opt$Trio)){
header<-paste0("chrom","\t","start","\t","stop","\t","name","\t","WTC_mean","\t")
if(isnothuman == "F"){
karyotype<-paste0("The karyotype in ", inputdata, " is: ", paste0(chromCount, chrX, chrY), "\n")
header<-append(karyotype,header)}
else{header<-header}
}
if(!is.null(opt$Trio) && isnothuman == "F"){
header<-paste0("chrom","\t","start","\t","stop","\t","name","\t","WTC_mean","\t","Parent/Child")
filenameisthis<-paste0('TRIO:',filenameisthis)}
a.list<-append(header,unlist(holding[!sapply(holding, is.null)]))
lapply(a.list, write, filenameisthis, append=TRUE, ncolumns=5)}
}
if(!is.null(opt$singleplots)){
lapply(directory,func) }
if(is.null(opt$singleplots)){
lapply(1,func)}
dev.off()