RepViz: Plot a genomic region

Description Usage Arguments Value Examples

View source: R/plotRegion.R

Description

Plot a genomic region

Usage

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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

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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.