plotEnrichAdv: Advanced Plot for gene enrichment analysis of ORA method

In genekitr: Gene Analysis Toolkit

Advanced Plot for gene enrichment analysis of ORA method

Description

Over-representation analysis (ORA) is a simple method for objectively deciding whether a set of variables of known or suspected biological relevance, such as a gene set or pathway, is more prevalent in a set of variables of interest than we expect by chance.

Usage

plotEnrichAdv(
  up_enrich_df,
  down_enrich_df,
  plot_type = c("one", "two"),
  term_metric = c("FoldEnrich", "GeneRatio", "Count", "RichFactor"),
  stats_metric = c("p.adjust", "pvalue", "qvalue"),
  wrap_length = NULL,
  xlim_left = NULL,
  xlim_right = NULL,
  color,
  ...
)

Arguments

up_enrich_df	Enrichment analysis 'data.frame' for up-regulated genes.
down_enrich_df	Enrichment analysis 'data.frame' for down-regulated genes.
plot_type	Choose from "one" and "two". "One" represents both up and down pathways are plotted together; "two" represents up and down are plotted seperately.
term_metric	Pathway term metric from one of 'GeneRatio','Count','FoldEnrich' and 'RichFactor'.
stats_metric	Statistic metric from one of "pvalue", "p.adjust", "qvalue".
wrap_length	Numeric, wrap text if longer than this length. Default is NULL.
xlim_left	X-axis left limit
xlim_right	X-axis right limit
color	Plot colors.
...	other arguments from 'plot_theme' function

Details

Both up and down regulated pathways could be plotted in one figure as two-side barplot

Value

A ggplot object

genekitr documentation built on Sept. 8, 2023, 6:06 p.m.