plotModuleHeat: Plot heatmaps of the module by omics

Description Usage Arguments

Description

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

Usage

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plotModuleHeat(pathway, moduleNumber, 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

MultiOmicsModule pathway object

moduleNumber

a module number

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.