multenrich_plot: multenrich_plot

In ND91/ndlib: A list of handy functions

Description

Produces a boxplot overlayed by a heatmap-like plot for multiple enrichment analyses providing a clear overview of the enrichment scores and p-values when having performed multiple enrichment analyses (i.e. different contrasts). It is advisable to ensure that the number of pathways to be plotted is less than 100 or else the list will become very long. The concept and implementation was derived from Martin Garrido Rodriguez-Cordoba's code (https://mgrcbioinfo.github.io/my_GSEA_plot/) and was modified by me.

Usage

multenrich_plot(
  enrich_list,
  title = NULL,
  pathway_col,
  es_col,
  pval_col,
  padj_col = NULL,
  alpha = 0.05
)

Arguments

enrich_list	List of enrichment analyses, wherein each enrichment analysis requires columns containing the pathway name, the enrichment scores (make this 1 or -1 if no particular enrichment score is provided), and a p-value.
title	A title for the plot
pathway_col	The column name of the pathway columns
es_col	The column name of the enrichment scores. Make this 1 or -1 if no particular enrichment score is provided.
pval_col	The column name of the p-values columns. One could enter the adjusted p-values here as well, yet I advise not to do so as they tend to flatten out (especially Benjamini-Hochberg adjusted p-values).
padj_col	(optional) The column name of the adjusted p-values. This will be used for identifying significant hits, with the non-significant hits being plotted as transparant.
alpha	(default: 0.05) The alpha at which you define something as significant.

Value

A ggplot object containing of heatmap-like plot of the enriched pathways indicating direction, size of the enrichment and the p-value for all provided enrichment analyses.

Author(s)

Martin Garrido Rodriguez-Cordoba, modified by Andrew Y.F. Li Yim

ND91/ndlib documentation built on Aug. 10, 2020, 11:59 a.m.