Plot.seed.module: Plot the DEGs modules shared by patients

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

Plot the DEGs modules shared by patients

Description

Plot the DEGs modules

Usage

## S3 method for class 'seed.module'
Plot(res.module, ann = NULL, deg = NULL,
  col.order = NULL, show.mods = NULL, overlap = NULL,
  dissimilarity = NULL, max.n = min(length(res.module), 30),
  type = c("model", "max.patients", "max.genes")[1], label.col = "blue",
  ...)

Arguments

res.module	a 'seed.module' object returned by seed.module
ann	a data.frame for the patient annotation
deg	a 'deg' to display. It is returned by bi.deg
col.order	the order of column in heatmap
show.mods	a vector, the modules to display
overlap	the similarity cutoff to display as carrying the module
dissimilarity	the similarity cutoff to display as not carrying the module
max.n	the maximum number of modules to display
type	the module type to display
label.col	the color to label
...	other setting of 'oncoPrint'

Details

This function is to display the relationship of the predicted DEG modules and the patients.

'deg' can be set to display the modules from different datasets, e.g. the modules predicted from disease A and display them in the binary DEG matrix of disease B.

The output is a heatmap Plot where the modules with maximum observations are showed.

Value

A heatmap plot

Author(s)

Guofeng Meng

Examples

Plot(seed.mod, ann.er, max.n=5)
Plot(seed.mod, ann.er, deg=deg, max.n=5)

menggf/DEComplexDisease documentation built on June 30, 2022, 1:47 p.m.