VisualiseTwoIRanges: VisualiseTwoIRanges

In favorov/GenometriCorr: Genometric Correlation package

Description

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.

Usage

VisualiseTwoIRanges(
  irA,
  irB,
  start = 1,
  end = NA,
  nameA = "RangesA",
  nameB = "RangesB",
  chrom_length = NA,
  title = NA,
  pdf = NULL,
  close.device = NULL
)

Arguments

irA	First IRanges object to be vsualised.
irB	Second IRanges object to be vsualised.
start	Start of the visualisation band.
end	End of the visualisation band.
nameA	Name of irA, default is 'RangesA'
nameB	Name of irB, default is 'RangesB'
chrom_length	The length of the chromosome spanned by irA and irB
title	Title, printed at the top of the plot.
pdf	Name of a file to which the image should be written. If pdf="" the filename is constructed from nameA and nameB. The suffix ".pdf" will be appended if not included. If NULL, no pdf is opened and an x11 window is raised up as by plot.
close.device	Whether to close the plot device after writing the image. A 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 NULL that means: close an x11, do not close a pdf.

Author(s)

Alexander Favorov [e-mail], 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

GenometriCorr home

See Also

The 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')

favorov/GenometriCorr documentation built on March 30, 2021, 5:21 p.m.