psiplot: Produce PSI and GE plots based on output from vast-tools

In kcha/psiplot: Generate plots of PSI values generated by vast-tools

Produce PSI and GE plots based on output from vast-tools

Description

psiplot is an R package for generating plots of percent spliced-in (PSI) values of alternatively spliced exons. It requires input from VAST-TOOLS, an RNA-Seq pipeline for alternative splicing analysis.

Details

This package uses input data generated by vast-tools. A sample dataset (psi, crpkm and crpkm_counts) and sample configuration file (config) is provided.

The main functions to generate plots is plot_event and plot_expr for PSI and cRPKM values, respectively. Two other functions, plot_multievent and plot_multi, allow plotting of multiple events in scatterplots or heatmaps.

plot_multi can be used to plot multiple events in the form of a heatmap.

See vignette('psiplot-usage', package="psiplot") for usage details.

Report bugs and issues to https://github.com/kcha/psiplot/issues.

See Also

https://www.github.com/kcha/psiplot

https://www.github.com/vastgroup/vast-tools

https://www.vastdb.crg.eu

Examples

library(psiplot)
plot_event(psi[1,])
plot_event(psi[1,], config=config, subg=FALSE)
plot_expr(crpkm[1,])
plot_expr(crpkm[1,], config=config)

kcha/psiplot documentation built on March 27, 2022, 4:20 a.m.