plot_ora: ORA visualization

In csbl-usp/CEMiTool: Co-expression Modules identification Tool

ORA visualization

Description

Creates a bar plot with the results of module overrepresentation analysis

Usage

plot_ora(cem, ...)

## S4 method for signature 'CEMiTool'
plot_ora(cem, n = 10, pv_cut = 0.05, ...)

Arguments

cem	Object of class CEMiTool.
...	parameters to plot_ora_single
n	number of modules to show
pv_cut	p-value significance cutoff. Default is 0.05.

Value

Object of class CEMiTool with ORA plots

Examples

# Get example CEMiTool object
data(cem)
# Read example gmt file
gmt <- read_gmt(system.file('extdata', 'pathways.gmt',
                   package='CEMiTool'))
# Run overrepresentation analysis
cem <- mod_ora(cem, gmt)
# Plot module gene expression profiles
cem <- plot_ora(cem)
# Check resulting plot
show_plot(cem, "ora")

csbl-usp/CEMiTool documentation built on March 27, 2024, 5:14 a.m.