plotgene: plotgene

In tangchao7498/ICAS:

Description

plotgene can be used to plot the gene structure and AS event

Usage

plotgene(object, SJ, flank = 200, geneModul, shrinkage = 1,
  curvature = -0.1, reduce = FALSE, highlight.region = NULL,
  highlight.color = "#0000FF80", highlight.label = NULL,
  highlight.label.size = 4, returnData = FALSE, removeTxid = FALSE,
  ...)

Arguments

object	an ICASDataSet
SJ	a charactor of SJ
flank	the distance of flanking extension
geneModul	A TxDb object made from GTF used by BAM aligner or a GRangesList object
shrinkage	the shrinkage for intron region (must be a positive >= 1). default 1 for no shrinkage
curvature	the curvature for splice junction
reduce	To collapse all gene structure annotation features or not
highlight.region	the region to highlight
highlight.color	the color of highlight.region
highlight.label	the label of highlight.region
highlight.label.size	the size of highlight region label
returnData	logical value, indicating return data or plot
removeTxid	logical value, indicating whether to remove the transcript of y axis lab

tangchao7498/ICAS documentation built on Jan. 28, 2021, 3:56 p.m.