knitr::opts_chunk$set( collapse = TRUE, warning = FALSE, comment = "#>", fig.path = "man/figures/" ) library(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.
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")
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"))
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")
.
Please report all bugs and issues using the issue tracker.
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
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