R/visualiseTwoIRanges.R
In favorov/GenometriCorr: Genometric Correlation package
Defines functions
VisualiseTwoGRanges
VisualiseTwoIRanges
Documented in
VisualiseTwoGRanges
VisualiseTwoIRanges
# GenometriCorrelation project evaluating two interval markups genomewide independence.
# (c) 2010-2020 Alexander Favorov, Loris Mularoni,
# Yulia Medvedeva, Harris A. Jaffee,
# Ekaterina V. Zhuravleva, Veronica Busa,
# Leslie M. Cope, Andrey A. Mironov,
# Vsevolod J. Makeev, Sarah J. Wheelan.
# VisualiseTwoIRanges is a function that visualise a pair of IRanges on a chromosome in two colors
# HJ -- pdf and close.device arguments
#'VisualiseTwoIRanges
#'
#'VisualiseTwoIRanges is a function that displays the intervals of two IRanges, one above the other, in different colors, along a chromosome or subset of a chromosome. The intent is to show large-scale relationships between the two IRanges.
#'
#' @param irA First \code{IRanges} object to be vsualised.
#' @param irB Second \code{IRanges} object to be vsualised.
#' @param start Start of the visualisation band.
#' @param end End of the visualisation band.
#' @param nameA Name of \code{irA}, default is 'RangesA'
#' @param nameB Name of \code{irB}, default is 'RangesB'
#' @param chrom_length The length of the chromosome spanned by \code{irA} and \code{irB}
#' @param title Title, printed at the top of the plot.
#' @param pdf Name of a file to which the image should be written. If \code{pdf=""} the filename is constructed from \code{nameA} and \code{nameB}. The suffix ".pdf" will be appended if not included. If \code{NULL}, no pdf is opened and an x11 window is raised up as by \code{plot}.
#' @param close.device Whether to close the plot device after writing the image. A \code{FALSE} setting allows multiple images to be written to the same pdf file, but then eventually closing the device is up to the user. Default is \code{NULL} that means: close an x11, do not close a pdf.
#' @author Alexander Favorov \email{favorov@@sensi.org}, Loris Mularoni, Yulia Medvedeva, Harris A. Jaffee, Ekaterina V. Zhuravleva, Veronica Busa, Leslie M. Cope, Andrey A. Mironov, Vsevolod J. Makeev, Sarah J. Wheelan.
#' @references \href{http://genometricorr.sourceforge.net/}{GenometriCorr home}
#' @seealso The \code{\link{GenometriCorr}} documentation and vignette.
#' @examples
#'
#' library('rtracklayer')
#' library('plyranges')
#' library('GenometriCorr')
#'
#' cpgis<-import(system.file("extdata", "UCSCcpgis_hg19.bed", package = "GenometriCorr"));
#'
#' refseq<-import(system.file("extdata", "UCSCrefseqgenes_hg19.bed", package = "GenometriCorr"));
#'
#'
#' human.chrom.length<-c(249250621,243199373,198022430,191154276,180915260,171115067,159138663,146364022,141213431,135534747,135006516,133851895,115169878,107349540,102531392,90354753,81195210,78077248,59128983,63025520,48129895,51304566,59373566,155270560)
#'
#'
#' names(human.chrom.length)<-c('chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chrY','chrX')
#'
#' VisualiseTwoIRanges(
#' (cpgis %>% filter(seqnqmes=='chr1')@ranges,
#' (refseq %>% filter(seqnqmes=='chr1')@ranges,
#' nameA='CpG Islands', nameB='RefSeq Genes',
#' chrom_length=human.chrom.length[['chr1']],
#' title="CpGIslands and RefGenes on chr1, hg19",
#' pdf='CpGi_vs_RefSeq_genes_chr1_hg19')
#'
#' @family GenometriCorr 2-range visualisation
#' @keywords hplot
#' @export
VisualiseTwoIRanges<-function(irA, irB, start=1, end=NA, nameA='RangesA', nameB='RangesB',
chrom_length=NA, title=NA, pdf=NULL, close.device=NULL)
{
pixelizeIRanges<-function(iranges,start,end,max.pixels=10000)
{
len=end-start+1
if (len>max.pixels)
{
#less than max_pixels*bin are to cover len
bin <- len %/% max.pixels
if ((len %% max.pixels) > 0) bin<-bin+1
test.ranges<-IRanges(start=seq.int(from=1,by=bin,length.out=max.pixels),width=bin)
overrle<-findOverlaps(test.ranges,iranges)
masker<-tapply(width(iranges[S4Vectors::subjectHits(overrle)]),S4Vectors::queryHits(overrle),sum)
mask<-rep(0,max.pixels)
mask[as.integer(names(masker))]<-as.integer(masker)
} else
{
mask<-as.vector(coverage(iranges,shift=1-start,width=len))
bin<-1
}
return(mask)
}
#require(grDevices)
if (!inherits(irA,"IRanges"))
stop("The first parameter for TwoIRangesIndependence is to be IRanges.")
if (!inherits(irB,"IRanges"))
stop("The second parameter for TwoIRangesIndependence is to be IRanges.")
if (is.na(chrom_length))
{
if (is.na(end))
{
chrom_length<-chromosomes.length.eval(irA,irB)
end<-chrom_length
warning("Chromosome length and the right margin of picture are evaluated rather than pre-given")
}
else
chrom_length<-chromosomes.length.eval(irA,irB)
}
if (is.na(end))
end<-chrom_length
if (end<=start)
stop("End is less or equal than start.")
len<-end-start+1
# pdf
if (!is.null(pdf)) {
if (length(grep("\\.pdf$", pdf)) == 0)
pdf <- paste(pdf, ".pdf", sep="")
if(pdf==".pdf")
pdf<-paste0(nameA,"_",nameB,pdf)
pdf(pdf)
if (is.null(close.device)) close.device=TRUE
} else
{
if (is.null(close.device)) close.device=FALSE
}
par(yaxt='n')
plot(c(start,end), c(-1, 1), type = "n", xlab="", ylab="", bty='n')
#find intersection for IRanges
intersectionC<-intersect(irA, irB)
#we are ready to think about what to plot.. \
#let's get the length of the raster we are to prepare
pixels<-as.integer(dev.size('px')[1]*(end-start+1)/xinch(dev.size('in')[1]))
#dev.size('px')[1] is how many pixels the thing will provide us with
#end+start-1 is real (in bp) length of our plot
#xinch is how many bp are there in argument inches
#so, xinch(dev.size('in')[1])/dev.size('px')[1]
#is how many nucleotides are there in a pixel
maskA<-pixelizeIRanges(irA,start,end,max.pixels=pixels)
maskB<-pixelizeIRanges(irB,start,end,max.pixels=pixels)
maskC<-pixelizeIRanges(intersectionC,start,end,max.pixels=pixels)
#to debug
#maskA=sample(c(0,100,10000),pixels,replace=T,c(8/10,1/10,1/10))
#maskB=sample(c(0,100,10000),pixels,replace=T,c(8/10,1/10,1/10))
#
#when we convert the data to pixels, we inversely regulate the coplementary colors.
#So, (e.g. red channel) zero gives maximal level of the complement (see as.raster call below)
#and the color will be white.
#And, the maximal level of mask give zero to G and B channels, so we have pure red
#For blue, we regulate G and R;
#For purple, only green is under regulation (Katya? is it correct?)
maxA<-max(maskA)
if(maxA==0)
{
maxintenseA<-0
} else
{
maskA <- 1-(maskA/maxA)
#too sharp: maskA <- exp(-maskA)
maxintenseA<-max(maskA)
}
maxB<-max(maskB)
if(maxB==0)
{
maxintenseB<-0
} else
{
maskB <- 1-(maskB/maxB)
#too sharp: maskB <- exp(-maskB)
maxintenseB<-max(maskB)
}
#maxC<-max(maskC)
maxC<-min(c(maxA,maxB))
if(maxC==0)
{
maxintenseC<-0
} else
{
maskC <- 1-(maskC/maxC)
maxintenseC<-max(maskC)
}
img_len<-length(maskA)
if (img_len != length(maskB))
{
stop("Image lengths are different, something went wrong.");
}
if (maxintenseA==0) #not to divide by 0 in as.raster
image_red<-
as.raster(array(c(rep(1,img_len),rep(1,img_len),rep(1,img_len)),c(1,img_len,3)),max=1)
else
image_red<-
as.raster(array(c(rep(maxintenseA,img_len),maskA,maskA),c(1,img_len,3)),max=maxintenseA)
if (maxB==0) #not to divide by 0 in as.raster
image_blue<-
as.raster(array(c(rep(1,img_len),rep(1,img_len),rep(1,img_len)),c(1,img_len,3)),max=1)
else
image_blue<-
as.raster(array(c(maskB,maskB,rep(maxintenseB,img_len)),c(1,img_len,3)),max=maxintenseB)
if (maxC==0) #not to divide by 0 in as.raster
image_purple<-
as.raster(array(c(rep(1,img_len),rep(1,img_len),rep(1,img_len)),c(1,img_len,3)),max=1)
else
image_purple<-
as.raster(array(c(rep(1,img_len),maskC,rep(1,img_len)),c(1,img_len,3)),max=maxintenseC)
#rasterImage(image_red, start, .05,end,.75)
#rasterImage(image_blue, start, -.75,end,-.05)
rasterImage(image_red, start, 0.20,end,0.75)
rasterImage(image_blue, start, -0.75,end,-0.20)
rasterImage(image_purple, start, 0.15,end,-0.15)
text(c(start+len/2,start+len/2),c(.9,-.9),c(nameA,nameB))
text(c(start-len/50),c(0,0),c('intersection'),srt=90)
text(c(start+len+len/50),c(0.5),c(maxA),srt=90)
text(c(start+len+len/50),c(0),c(maxC),srt=90)
text(c(start+len+len/50),c(-0.5),c(maxB),srt=90)
text(c(start+len/2),c(-1),c(paste0('Chromosome position: ',as.integer(xinch(dev.size('in')[1])/dev.size('px')[1]),' nucleotides per pixel')))
if (!is.na(title))
{
title(main=title)
}
title(sub=paste0("On the right: covered nucleotides that yields full color intensity of a pixel"))
if (close.device)
invisible(dev.off())
}
#'VisualiseTwoGRanges
#'
#'VisualiseTwoGRanges is a function that displays the markups that are contatined two GRanges, in a multi-page pdf, page per chromosome, by \code{\link{VisualiseTwoIRanges}} for aech chromosome. The intent is to show large-scale relationships between the two markups. All the chromosome lenght data is provided by the GRanges.
#'
#' @param grA First \code{GRanges} object to be vsualised.
#' @param grB Second \code{GRanges} object to be vsualised.
#' @param nameA Name of \code{grA}, default is 'RangesA'
#' @param nameB Name of \code{grB}, default is 'RangesB'
#' @param title Title, printed at the top of the plot.
#' @param pdf Name of a file to which the image should be written. If \code{pdf=""} the filename is constructed from \code{nameA} and \code{nameB}. The suffix ".pdf" will be appended if not included. If \code{NULL}, no pdf is opened and an x11 window is raised up as by \code{plot}.
#' @param close.device Whether to close the plot device after writing the image. A \code{FALSE} setting allows multiple images to be written to the same pdf file, but then eventually closing the device is up to the user. Default is \code{NULL} that means: close an x11, do not close a pdf.
#' @author Alexander Favorov \email{favorov@@sensi.org}, Loris Mularoni, Yulia Medvedeva, Harris A. Jaffee, Ekaterina V. Zhuravleva, Leslie M. Cope, Andrey A. Mironov, Vsevolod J. Makeev, Sarah J. Wheelan.
#' @references \href{http://genometricorr.sourceforge.net/}{GenometriCorr home}
#' @seealso The \code{\link{GenometriCorr}} documentation and vignette.
#' @family GenometriCorr 2-range visualisations
#' @keywords hplot
#' @export
VisualiseTwoGRanges<-function(grA, grB, nameA='RangesA', nameB='RangesB', title=NA, pdf=NULL, close.device=NULL)
{
if (!inherits(grA,"GRanges"))
stop("The first parameter for TwoGRangesIndependence is to be GRanges.")
if (!inherits(grB,"GRanges"))
stop("The second parameter for TwoGRangesIndependence is to be GRanges.")
sqinf<-seqinfo(grA)
if(!all.equal(seqinfo(grB),sqinf))
stop("The seqinfo() grA and grB is supposed to return exactly the same.")
# pdf
if (!is.null(pdf)) {
if (length(grep("\\.pdf$", pdf)) == 0)
pdf <- paste(pdf, ".pdf", sep="")
if(pdf==".pdf")
pdf<-paste0(nameA,"_",nameB,pdf)
pdf(pdf)
if (is.null(close.device)) close.device=TRUE
} else
{
if (is.null(close.device)) close.device=FALSE
}
for (chn in 1:length(sqinf))
VisualiseTwoIRanges(
ranges(grA[start(seqnames(grA))[chn]:end(seqnames(grA))[chn]]),
ranges(grB[start(seqnames(grB))[chn]:end(seqnames(grB))[chn]]),
chrom_length = seqlengths(sqinf)[chn],
nameA=nameA,
nameB=nameB,
pdf=NULL,
title=ifelse(is.na(title),seqnames(sqinf)[chn],paste0(title,", ",seqnames(sqinf)[chn]))
)
if (close.device)
invisible(dev.off())
}
favorov/GenometriCorr documentation built on March 30, 2021, 5:21 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions VisualiseTwoGRanges VisualiseTwoIRanges
Documented in VisualiseTwoGRanges VisualiseTwoIRanges
# GenometriCorrelation project evaluating two interval markups genomewide independence.
# (c) 2010-2020 Alexander Favorov, Loris Mularoni,
# Yulia Medvedeva, Harris A. Jaffee,
# Ekaterina V. Zhuravleva, Veronica Busa,
# Leslie M. Cope, Andrey A. Mironov,
# Vsevolod J. Makeev, Sarah J. Wheelan.
# VisualiseTwoIRanges is a function that visualise a pair of IRanges on a chromosome in two colors
# HJ -- pdf and close.device arguments
#'VisualiseTwoIRanges
#'
#'VisualiseTwoIRanges is a function that displays the intervals of two IRanges, one above the other, in different colors, along a chromosome or subset of a chromosome. The intent is to show large-scale relationships between the two IRanges.
#'
#' @param irA First \code{IRanges} object to be vsualised.
#' @param irB Second \code{IRanges} object to be vsualised.
#' @param start Start of the visualisation band.
#' @param end End of the visualisation band.
#' @param nameA Name of \code{irA}, default is 'RangesA'
#' @param nameB Name of \code{irB}, default is 'RangesB'
#' @param chrom_length The length of the chromosome spanned by \code{irA} and \code{irB}
#' @param title Title, printed at the top of the plot.
#' @param pdf Name of a file to which the image should be written. If \code{pdf=""} the filename is constructed from \code{nameA} and \code{nameB}. The suffix ".pdf" will be appended if not included. If \code{NULL}, no pdf is opened and an x11 window is raised up as by \code{plot}.
#' @param close.device Whether to close the plot device after writing the image. A \code{FALSE} setting allows multiple images to be written to the same pdf file, but then eventually closing the device is up to the user. Default is \code{NULL} that means: close an x11, do not close a pdf.
#' @author Alexander Favorov \email{favorov@@sensi.org}, Loris Mularoni, Yulia Medvedeva, Harris A. Jaffee, Ekaterina V. Zhuravleva, Veronica Busa, Leslie M. Cope, Andrey A. Mironov, Vsevolod J. Makeev, Sarah J. Wheelan.
#' @references \href{http://genometricorr.sourceforge.net/}{GenometriCorr home}
#' @seealso The \code{\link{GenometriCorr}} documentation and vignette.
#' @examples
#'
#' library('rtracklayer')
#' library('plyranges')
#' library('GenometriCorr')
#'
#' cpgis<-import(system.file("extdata", "UCSCcpgis_hg19.bed", package = "GenometriCorr"));
#'
#' refseq<-import(system.file("extdata", "UCSCrefseqgenes_hg19.bed", package = "GenometriCorr"));
#'
#'
#' human.chrom.length<-c(249250621,243199373,198022430,191154276,180915260,171115067,159138663,146364022,141213431,135534747,135006516,133851895,115169878,107349540,102531392,90354753,81195210,78077248,59128983,63025520,48129895,51304566,59373566,155270560)
#'
#'
#' names(human.chrom.length)<-c('chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chrY','chrX')
#'
#' VisualiseTwoIRanges(
#' (cpgis %>% filter(seqnqmes=='chr1')@ranges,
#' (refseq %>% filter(seqnqmes=='chr1')@ranges,
#' nameA='CpG Islands', nameB='RefSeq Genes',
#' chrom_length=human.chrom.length[['chr1']],
#' title="CpGIslands and RefGenes on chr1, hg19",
#' pdf='CpGi_vs_RefSeq_genes_chr1_hg19')
#'
#' @family GenometriCorr 2-range visualisation
#' @keywords hplot
#' @export
VisualiseTwoIRanges<-function(irA, irB, start=1, end=NA, nameA='RangesA', nameB='RangesB',
chrom_length=NA, title=NA, pdf=NULL, close.device=NULL)
{
pixelizeIRanges<-function(iranges,start,end,max.pixels=10000)
{
len=end-start+1
if (len>max.pixels)
{
#less than max_pixels*bin are to cover len
bin <- len %/% max.pixels
if ((len %% max.pixels) > 0) bin<-bin+1
test.ranges<-IRanges(start=seq.int(from=1,by=bin,length.out=max.pixels),width=bin)
overrle<-findOverlaps(test.ranges,iranges)
masker<-tapply(width(iranges[S4Vectors::subjectHits(overrle)]),S4Vectors::queryHits(overrle),sum)
mask<-rep(0,max.pixels)
mask[as.integer(names(masker))]<-as.integer(masker)
} else
{
mask<-as.vector(coverage(iranges,shift=1-start,width=len))
bin<-1
}
return(mask)
}
#require(grDevices)
if (!inherits(irA,"IRanges"))
stop("The first parameter for TwoIRangesIndependence is to be IRanges.")
if (!inherits(irB,"IRanges"))
stop("The second parameter for TwoIRangesIndependence is to be IRanges.")
if (is.na(chrom_length))
{
if (is.na(end))
{
chrom_length<-chromosomes.length.eval(irA,irB)
end<-chrom_length
warning("Chromosome length and the right margin of picture are evaluated rather than pre-given")
}
else
chrom_length<-chromosomes.length.eval(irA,irB)
}
if (is.na(end))
end<-chrom_length
if (end<=start)
stop("End is less or equal than start.")
len<-end-start+1
# pdf
if (!is.null(pdf)) {
if (length(grep("\\.pdf$", pdf)) == 0)
pdf <- paste(pdf, ".pdf", sep="")
if(pdf==".pdf")
pdf<-paste0(nameA,"_",nameB,pdf)
pdf(pdf)
if (is.null(close.device)) close.device=TRUE
} else
{
if (is.null(close.device)) close.device=FALSE
}
par(yaxt='n')
plot(c(start,end), c(-1, 1), type = "n", xlab="", ylab="", bty='n')
#find intersection for IRanges
intersectionC<-intersect(irA, irB)
#we are ready to think about what to plot.. \
#let's get the length of the raster we are to prepare
pixels<-as.integer(dev.size('px')[1]*(end-start+1)/xinch(dev.size('in')[1]))
#dev.size('px')[1] is how many pixels the thing will provide us with
#end+start-1 is real (in bp) length of our plot
#xinch is how many bp are there in argument inches
#so, xinch(dev.size('in')[1])/dev.size('px')[1]
#is how many nucleotides are there in a pixel
maskA<-pixelizeIRanges(irA,start,end,max.pixels=pixels)
maskB<-pixelizeIRanges(irB,start,end,max.pixels=pixels)
maskC<-pixelizeIRanges(intersectionC,start,end,max.pixels=pixels)
#to debug
#maskA=sample(c(0,100,10000),pixels,replace=T,c(8/10,1/10,1/10))
#maskB=sample(c(0,100,10000),pixels,replace=T,c(8/10,1/10,1/10))
#
#when we convert the data to pixels, we inversely regulate the coplementary colors.
#So, (e.g. red channel) zero gives maximal level of the complement (see as.raster call below)
#and the color will be white.
#And, the maximal level of mask give zero to G and B channels, so we have pure red
#For blue, we regulate G and R;
#For purple, only green is under regulation (Katya? is it correct?)
maxA<-max(maskA)
if(maxA==0)
{
maxintenseA<-0
} else
{
maskA <- 1-(maskA/maxA)
#too sharp: maskA <- exp(-maskA)
maxintenseA<-max(maskA)
}
maxB<-max(maskB)
if(maxB==0)
{
maxintenseB<-0
} else
{
maskB <- 1-(maskB/maxB)
#too sharp: maskB <- exp(-maskB)
maxintenseB<-max(maskB)
}
#maxC<-max(maskC)
maxC<-min(c(maxA,maxB))
if(maxC==0)
{
maxintenseC<-0
} else
{
maskC <- 1-(maskC/maxC)
maxintenseC<-max(maskC)
}
img_len<-length(maskA)
if (img_len != length(maskB))
{
stop("Image lengths are different, something went wrong.");
}
if (maxintenseA==0) #not to divide by 0 in as.raster
image_red<-
as.raster(array(c(rep(1,img_len),rep(1,img_len),rep(1,img_len)),c(1,img_len,3)),max=1)
else
image_red<-
as.raster(array(c(rep(maxintenseA,img_len),maskA,maskA),c(1,img_len,3)),max=maxintenseA)
if (maxB==0) #not to divide by 0 in as.raster
image_blue<-
as.raster(array(c(rep(1,img_len),rep(1,img_len),rep(1,img_len)),c(1,img_len,3)),max=1)
else
image_blue<-
as.raster(array(c(maskB,maskB,rep(maxintenseB,img_len)),c(1,img_len,3)),max=maxintenseB)
if (maxC==0) #not to divide by 0 in as.raster
image_purple<-
as.raster(array(c(rep(1,img_len),rep(1,img_len),rep(1,img_len)),c(1,img_len,3)),max=1)
else
image_purple<-
as.raster(array(c(rep(1,img_len),maskC,rep(1,img_len)),c(1,img_len,3)),max=maxintenseC)
#rasterImage(image_red, start, .05,end,.75)
#rasterImage(image_blue, start, -.75,end,-.05)
rasterImage(image_red, start, 0.20,end,0.75)
rasterImage(image_blue, start, -0.75,end,-0.20)
rasterImage(image_purple, start, 0.15,end,-0.15)
text(c(start+len/2,start+len/2),c(.9,-.9),c(nameA,nameB))
text(c(start-len/50),c(0,0),c('intersection'),srt=90)
text(c(start+len+len/50),c(0.5),c(maxA),srt=90)
text(c(start+len+len/50),c(0),c(maxC),srt=90)
text(c(start+len+len/50),c(-0.5),c(maxB),srt=90)
text(c(start+len/2),c(-1),c(paste0('Chromosome position: ',as.integer(xinch(dev.size('in')[1])/dev.size('px')[1]),' nucleotides per pixel')))
if (!is.na(title))
{
title(main=title)
}
title(sub=paste0("On the right: covered nucleotides that yields full color intensity of a pixel"))
if (close.device)
invisible(dev.off())
}
#'VisualiseTwoGRanges
#'
#'VisualiseTwoGRanges is a function that displays the markups that are contatined two GRanges, in a multi-page pdf, page per chromosome, by \code{\link{VisualiseTwoIRanges}} for aech chromosome. The intent is to show large-scale relationships between the two markups. All the chromosome lenght data is provided by the GRanges.
#'
#' @param grA First \code{GRanges} object to be vsualised.
#' @param grB Second \code{GRanges} object to be vsualised.
#' @param nameA Name of \code{grA}, default is 'RangesA'
#' @param nameB Name of \code{grB}, default is 'RangesB'
#' @param title Title, printed at the top of the plot.
#' @param pdf Name of a file to which the image should be written. If \code{pdf=""} the filename is constructed from \code{nameA} and \code{nameB}. The suffix ".pdf" will be appended if not included. If \code{NULL}, no pdf is opened and an x11 window is raised up as by \code{plot}.
#' @param close.device Whether to close the plot device after writing the image. A \code{FALSE} setting allows multiple images to be written to the same pdf file, but then eventually closing the device is up to the user. Default is \code{NULL} that means: close an x11, do not close a pdf.
#' @author Alexander Favorov \email{favorov@@sensi.org}, Loris Mularoni, Yulia Medvedeva, Harris A. Jaffee, Ekaterina V. Zhuravleva, Leslie M. Cope, Andrey A. Mironov, Vsevolod J. Makeev, Sarah J. Wheelan.
#' @references \href{http://genometricorr.sourceforge.net/}{GenometriCorr home}
#' @seealso The \code{\link{GenometriCorr}} documentation and vignette.
#' @family GenometriCorr 2-range visualisations
#' @keywords hplot
#' @export
VisualiseTwoGRanges<-function(grA, grB, nameA='RangesA', nameB='RangesB', title=NA, pdf=NULL, close.device=NULL)
{
if (!inherits(grA,"GRanges"))
stop("The first parameter for TwoGRangesIndependence is to be GRanges.")
if (!inherits(grB,"GRanges"))
stop("The second parameter for TwoGRangesIndependence is to be GRanges.")
sqinf<-seqinfo(grA)
if(!all.equal(seqinfo(grB),sqinf))
stop("The seqinfo() grA and grB is supposed to return exactly the same.")
# pdf
if (!is.null(pdf)) {
if (length(grep("\\.pdf$", pdf)) == 0)
pdf <- paste(pdf, ".pdf", sep="")
if(pdf==".pdf")
pdf<-paste0(nameA,"_",nameB,pdf)
pdf(pdf)
if (is.null(close.device)) close.device=TRUE
} else
{
if (is.null(close.device)) close.device=FALSE
}
for (chn in 1:length(sqinf))
VisualiseTwoIRanges(
ranges(grA[start(seqnames(grA))[chn]:end(seqnames(grA))[chn]]),
ranges(grB[start(seqnames(grB))[chn]:end(seqnames(grB))[chn]]),
chrom_length = seqlengths(sqinf)[chn],
nameA=nameA,
nameB=nameB,
pdf=NULL,
title=ifelse(is.na(title),seqnames(sqinf)[chn],paste0(title,", ",seqnames(sqinf)[chn]))
)
if (close.device)
invisible(dev.off())
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.