plot.msviper: Plot msviper results

In chrischen1/viper_copy: Virtual Inference of Protein-activity by Enriched Regulon analysis

Description

This function generate a plot for msviper results showing the enrichment of the target genes for each significant master regulator on the gene expression signature

Usage

## S3 method for class 'msviper'
plot(x, mrs = 10, color = c("cornflowerblue", "salmon"),
  pval = NULL, bins = 500, cex = 0, density = 0, smooth = 0,
  sep = 0.2, hybrid = TRUE, include = c("expression", "activity"),
  gama = 2, ...)

Arguments

x	msviper object produced by msviper function
mrs	Either an integer indicating the number of master regulators to include in the plot, or a character vector containing the names of the master regulators to include in the plot
color	Vector of two components indicating the colors for the negative and positive parts of the regulon
pval	Optional matrix of p-values to include in the plot
bins	Number of bins to split the vector of scores in order to compute the density color of the bars
cex	Number indicating the text size scaling, 0 indicates automatic scaling
density	Integrer indicating the number of steps for the kernel density. Zero for not ploting it
smooth	Number indicating the proportion of point for smoothing the density distribution. Zero for not using the smoother
sep	Number indicating the separation from figure and text
hybrid	Logical, whether the 3-tail approach used for computingthe enrichment should be reflected in the plot
include	Vector indicating the information to include as heatmap to the right of the msviper plot: expression and activity
gama	Positive number indicating the exponential transformation for the activity and expression color scale
...	Given for compatibility to the plot generic function

Value

Nothing, a plot is generated in the default output device

See Also

msviper

Examples

data(bcellViper, package="bcellViper")
sig <- rowTtest(dset, "description", c("CB", "CC"), "N")$statistic
dnull <- ttestNull(dset, "description", c("CB", "CC"), "N", per=100) # Only 100 permutations to reduce computation time, but it is recommended to perform at least 1000 permutations
mra <- msviper(sig, regulon, dnull)
plot(mra, cex=.7)

chrischen1/viper_copy documentation built on May 13, 2019, 6:52 p.m.