splicePlot: Gene Splicing Plot

Description Usage Arguments Value Examples

View source: R/splicePlot.R

Description

Visualization of read coverage, splicing information and gene information in a gene region. This function is a wrapper of getDepth, getGeneinfo, spliceGene, plotBedgraph and plotGenes.

Usage

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splicePlot(bg, gene, samples, bam.dir = NA, start = NA, end = NA, 
            labels = samples, junc.type = c("score", "count"), junc.text = TRUE,
            trans.select = "rowMaxs(x)>=1", junc.select = "rowMaxs(x)>=5",
            col = SushiColors(2)(length(samples) + 1)[-1],transparency = 0.5,
            scale = "Kb", plotgenetype = "arrow", ...)

Arguments

bg

ballgown object. See ballgown.

gene

string indicating a gene ID (must be in the 'bg')

samples

names of the samples to be shown (must be in the 'bg' and have bam files in the 'bam.dir')

bam.dir

bam file directory of the samples. If NA, instead of read depth, conserved exons are drawn.

start

start position to be shown. If NA, start position of the gene will be used.

end

stop position to be shown. If NA, end position of the gene will be used.

labels

labels for samples (default: sample names). If it is NA, neigher sample names nor gene names will be labeled

junc.type

type of junction estimates to be shown ('score' for junction score; count' for junction read count)

junc.text

TRUE/FALSE indicating whether junction estimates should be labeled

trans.select

logical expression-like string, indicating transcript rows to select from a matrix of transcript coverages: NA value keeps all transcripts. See spliceGene

junc.select

logical expression-like string, indicating junction rows to select from a matrix of junction counts: NA value keeps all junctions. See spliceGene

col

a vector of length(samples) specifying colors of read depths.

transparency

value between 0 and 1 indicating the degree of transparency of read depths.

scale

scale of the labelgenome ('bp','Kb','Mb')

plotgenetype

string specifying whether the genes should resemble a 'box' or a 'arrow'. See plotGenes.

...

values to be passed to plotGenes.

Value

see plotGenes.

Examples

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data(rice.bg)
rice.bg

samples <- paste('Sample', c('027','102','237'),sep='_')
bam.dir <- system.file('extdata',package = 'VaSP')

## plot the whole gene region
splicePlot(rice.bg,samples,bam.dir,gene='MSTRG.183',bheight=0.2)

## plot the alternative splicing region
splicePlot(rice.bg,samples,bam.dir,gene='MSTRG.183',start=1179000)

VaSP documentation built on Feb. 28, 2021, 2:02 a.m.