plot.msviper {viper} | R Documentation |
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
## 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, ...)
x |
msviper object produced by |
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 |
Nothing, a plot is generated in the default output device
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)