R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Graphic representation of enrichment

represent_enrichment

R Documentation

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" or "identity"
`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

Examples

represent_enrichment(enrichment = list(SampleA = enrichment_test[1:10,],
SampleB = enrichment_test[3:10,]), plot = "heatmap", scale = "log")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ACSNMineR)
Loading required package: ggplot2
Loading required package: gridExtra
Loading required package: scales
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ACSNMineR/represent_enrichment.Rd_%03d_medium.png", width=480, height=480)
> ### Name: represent_enrichment
> ### Title: Graphic representation of enrichment
> ### Aliases: represent_enrichment
> 
> ### ** Examples
> 
> represent_enrichment(enrichment = list(SampleA = enrichment_test[1:10,],
+ SampleB = enrichment_test[3:10,]), plot = "heatmap", scale = "log")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>