R package for plotting PSI values generated from vast-tools
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README.md

Build Status GitHub release GitHub license

psiplot

psiplot is an R package for generating plots of percent spliced-in (PSI) values of alternatively-spliced exons that were computed by vast-tools, an RNA-Seq pipeline for alternative splicing analysis. The plots are generated using ggplot2.

For a demo of psiplot, take a look at the companion Shiny app: http://kcha.shinyapps.io/psiplotter-app.

Installation

See Releases for the latest stable release or get the most up-to-date development version via devtools:

if (!require("devtools")) install.packages("devtools")
devtools::install_github("kcha/psiplot")

Getting started

Quick start

psiplot takes as input the PSI and/or cRPKM results generated by vast-tools (e.g. after running vast-tools combine or vast-tools diff). For example:

psi <- read.table("INCLUSION_LEVELS_FULL-Mmu53.tab", header = TRUE, sep = "\t",
                  stringsAsFactors = FALSE)

To plot a single splicing event, use the command plot_event. In this example, we use the provided sample dataset psi and optional sample configuration table config:

library(psiplot)
# Plot an event using provided sample dataset
plot_event(psi[1,], config=config)

Several events can be plotted together with the function plot_multievent(). This allows users to compare the inclusion patterns of small groups of events:

plot_multievent(psi[c(1,2),], config = config, event_col = c("black", "red"))

Vignette

See this vignette for more detailed usage, including how to customize psiplots using a configuration file. The vignette is also available in R using the command vignette("psiplot-usage").

Issues

Please report all bugs and issues using the issue tracker.

Related Projects

  • vast-tools
  • VastDB: A database with PSI values computed with vast-tools in many tissues and cell types of several species.
  • psiplotter-app: A companion Shiny app for visualizing PSI plots based on this package

Acknowledgements

  • Manuel Irimia
  • Nuno Barbosa-Morais
  • Tim Sterne-Weiler

Citation

Tapial, J., Ha, K.C.H., Sterne-Weiler, T., Gohr, A., Braunschweig, U., Hermoso-Pulido, A., Quesnel-Vallières, M., Permanyer, J., Sodaei, R., Marquez, Y., Cozzuto, L., Wang, X., Gómez-Velázquez, M., Rayon, T., Manzanares, M., Ponomarenko, J., Blencowe, B.J., Irimia, M. (2017). An Alternative Splicing Atlas Reveals New Regulatory Programs and Genes Simultaneously Expressing Multiple Major Isoforms in Vertebrates. Genome Res, 27(10):1759-1768. PMID: 28855263