module.compare: Compare and plot the overlap among predicted modules

In menggf/decd: A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis

Description

Plot the overlap among predicted DEG modules

Usage

module.compare(res.module1, res.module2, used.mods1 = NULL,
  used.mods2 = NULL, type = c("model", "max.patients", "max.genes")[1],
  max.n1 = 30, max.n2 = max.n1, show.overlap = TRUE, cex = 10)

Arguments

res.module1	a 'seed.module' or 'cluster.module' object returned by seed.module or cluster.module
res.module2	a 'seed.module' or 'cluster.module' object returned by seed.module or cluster.module
used.mods1	the modules to display
used.mods2	the modules to display
type	the module type to display
max.n1	the maximum number of modules to display. If "used.mods1" is set, this option will be ignored.
max.n2	the maximum number of modules to display. If "used.mods2" is set, this option will be ignored.
show.overlap	boolean, display the overlap number
cex	the font cex to display the overlap number

Details

This function is to compare the modules from different studies, e.g. the different diseases or the different data for the same disease.

Value

The heatmap plot for gene overlaps.

Author(s)

Guofeng Meng

References

Gu Z, Eils R and Schlesner M (2016). Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics.

Examples

## Not run: 
module.compare(res.mod1,res.mod2, type="model", max.n=20)

## End(Not run)

menggf/decd documentation built on Jan. 2, 2020, 12:53 a.m.