splicePlot: Gene Splicing Plot

In yuhuihui2011/vasp_test: Quantification and Visulization of Variations of Splicing in Population

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

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.depth = SushiColors(2)(length(samples) + 1)[-1],
  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.depth	a vector of length(samples) specifying colors of read depth.
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

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)

yuhuihui2011/vasp_test documentation built on March 5, 2020, 12:50 a.m.