RepViz: Plot a genomic region

In elolab/RepViz: Replicate oriented Visualization of a genomic region

Description

Plot a genomic region

Usage

RepViz(region, genome = c("hg19", "hg38", "mm10"), BAM = NULL,
  BED = NULL, avgTrack = TRUE, geneTrack = TRUE, max = NULL,
  verbose = TRUE, cex = 1)

Arguments

region	a GRange object with chr, start, end
genome	a character vector 'hg19','hg38' or 'mm10'
BAM	a path to the BAM related csv input file
BED	a path to the BED related csv input file
avgTrack	a logical indicating if the average track should be included or not
geneTrack	a logical indicating if the gene track should be included or not
max	a numerical vector containing the yaxis maximum value of each BAM track
verbose	a logical indicating whether the progress of the plotting is shown
cex	number indicating the amount by which plotting text and symbols should be scaled relative to the default.
col	vector of character user can set color of the different BED tracks.

Value

displays the region specified by the user

Examples

region <- GRanges('chr12:110938000-110940000')
setwd(tempdir())
#Copying the files to the user working directory
file.copy(from = list.files(system.file('extdata', package = 'RepViz'), full.names = TRUE),
    to = tempdir())
#Generate the visualization of the given region
RepViz::RepViz(region = region,
    genome = 'hg19',
    BAM = 'BAM_input.csv',
    BED = 'BED_input.csv',
    avgTrack = TRUE,
    geneTrack = TRUE)

elolab/RepViz documentation built on June 14, 2020, 1:21 a.m.