bic.plot.read.distribution: Plot RSeQC read distribution stats

In bic-mskcc/bicrnaseq: MSKCC Bioinformatics Core RNASeq

Description

Plot distribution of reads across different genomic features like exons, introns, TSS, etc. for all samples in a project

Plot distribution of reads across different genomic features like exons, introns, TSS, etc. for all samples in a project

Usage

bic.plot.read.distribution(dat, file = NULL, stack = TRUE, pct = FALSE,
  col.pal = "Set3")

bic.plot.read.distribution(dat, file = NULL, stack = TRUE, pct = FALSE,
  col.pal = "Set3")

Arguments

dat	data frame containing merged output from multiple runs of RSeQC's read_distribution.py script, where rows are samples and columns are metrics; must contain "Samples" slot and may contain any other slots
file	PDF file to which plot should be saved (optional)
stack	logical indicating that bar chart should be stacked; Default: TRUE
pct	logical indicating that plot should show percentages
col.pal	name of color palette; must be from list of RColorBrewer palettes Default: "Set3"
horizontal	logical indicating that bars should be horizontal; Default: TRUE
dat	data frame containing merged output from multiple runs of RSeQC's read_distribution.py script, where rows are samples and columns are metrics; must contain "Samples" slot and may contain any other slots
pct	logical indicating that plot should show percentages
stack	logical indicating that bar chart should be stacked; Default: TRUE
col.pal	name of color palette; must be from list of RColorBrewer palettes Default: "Set3"
file	PDF file to which plot should be saved (optional)

bic-mskcc/bicrnaseq documentation built on May 24, 2019, 3:04 a.m.