ACSNMineR (version 0.16.8.25)

represent_enrichment: Graphic representation of enrichment

Description

Graphic representation of enrichment

Usage

represent_enrichment(enrichment, plot = "heatmap", scale = "log", low = "steelblue", high = "white", nrow = 1, sample_name = "Sample", na.value = "grey")

Arguments

enrichment

Data frame or list of dataframes with p-values or corrected p-values (whenever available) and module names for representation. The name of the dataframe will be used as sample name.

plot

Any of "heatmap" or "bar"

scale

Any of "log", "identity" or "reverselog" (i.e. -log10(p-value))

low

Color to be used in heatmap mode corresponding to lowest value

high

Color to be used in heatmap mode corresponding to highest value

nrow

Number of rows of the grid for display in bar mode.

sample_name

used only is enrichment is a dataframe

na.value

color for the missing values in the heatmap

Value

Function returns a ggplot2 object if input is a dataframe or a gridExtra object if the output is a list.

Examples

represent_enrichment(enrichment = enrichment_test,scale = "reverselog",
                    sample_name = "test",plot = "bar")

represent_enrichment(enrichment = list(SampleA = enrichment_test, 
                                     SampleB = enrichment_test[1:3,]), 
                     plot = "heatmap", scale = "log")