plotPathwayHeat: Plot heatmaps of the pathway by omics

In cavei/MOSClip: Multi Omics Survival Clip

Description

Given the pathway, it creates the heatmaps of the mostly involved genes for each omic.

Usage

plotPathwayHeat(pathway, sortBy = NULL, fileName = NULL,
  paletteNames = NULL, additionalAnnotations = NULL,
  additionalPaletteNames = NULL, withSampleNames = TRUE,
  fontsize_row = 10, fontsize_col = 1, nrowsHeatmaps = 3, h = 9,
  w = 7, discr_prop_pca = 0.15, discr_prop_events = 0.05)

Arguments

pathway	MultiOmicsPathway pathway object
sortBy	a covariate to sort by
fileName	optional filenames to save the plot
paletteNames	three palettes
additionalAnnotations	optional additional sample annotations
additionalPaletteNames	optional additional colors for annotations
withSampleNames	create also the samples names
fontsize_row	size of the fonts for rows
fontsize_col	like fontsize_row but for columns
nrowsHeatmaps	magnification respect to annotation of sample (annotations take 1 row)
h	the height of the plot
w	the width of the plot
discr_prop_pca	the minimal proportion to compute the pca classes
discr_prop_events	the minimal proportion to compute the event classes

cavei/MOSClip documentation built on May 12, 2019, 5:22 p.m.