emapplot: emapplot

In enrichplot: Visualization of Functional Enrichment Result

Description

Enrichment Map for enrichment result of over-representation test or gene set enrichment analysis

Usage

emapplot(x, showCategory = 30, color = "p.adjust", layout = "kk", ...)

## S4 method for signature 'enrichResult'
emapplot(x, showCategory = 30, color = "p.adjust", layout = "nicely", ...)

## S4 method for signature 'gseaResult'
emapplot(x, showCategory = 30, color = "p.adjust", layout = "nicely", ...)

## S4 method for signature 'compareClusterResult'
emapplot(x, showCategory = 30, color = "p.adjust", layout = "nicely", ...)

emapplot.enrichResult(
  x,
  showCategory = 30,
  color = "p.adjust",
  layout = "nicely",
  node_scale = NULL,
  line_scale = NULL,
  min_edge = 0.2,
  node_label_size = NULL,
  cex_label_category = 1,
  cex_category = NULL,
  cex_line = NULL
)

emapplot.compareClusterResult(
  x,
  showCategory = 30,
  color = "p.adjust",
  layout = "nicely",
  split = NULL,
  pie = "equal",
  legend_n = 5,
  cex_category = NULL,
  pie_scale = NULL,
  cex_line = 1,
  min_edge = 0.2,
  cex_label_category = 1,
  node_label_size = NULL
)

Arguments

x	enrichment result.
showCategory	number of enriched terms to display
color	variable that used to color enriched terms, e.g. pvalue, p.adjust or qvalue
layout	layout of the map
...	additional parameters
node_scale	scale of node, this parameter has been changed to cex_category
line_scale	scale of line width, this parameter has been changed to cex_line
min_edge	minimum percentage of overlap genes to display the edge, should between 0 and 1, default value is 0.2
node_label_size	size of node label, this parameter has been changed to cex_label_category
cex_label_category	scale of category node label size
cex_category	number indicating the amount by which plotting category nodes should be scaled relative to the default.
cex_line	scale of line width
split	separate result by 'category' variable
pie	proportion of clusters in the pie chart, one of 'equal' (default) or 'Count'
legend_n	number of circle in legend
pie_scale	scale of pie chart or point, this parameter has been changed to "node_scale"

Details

This function visualizes gene sets as a network (i.e. enrichment map). Mutually overlapping gene sets tend to cluster together, making it easier for interpretation.

Value

ggplot object

Author(s)

Guangchuang Yu

Examples

library(DOSE)
data(geneList)
de <- names(geneList)[1:100]
x <- enrichDO(de)
x2 <- pairwise_termsim(x)
emapplot(x2)

Example output

DOSE v3.16.0  For help: https://guangchuangyu.github.io/software/DOSE

If you use DOSE in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

enrichplot documentation built on Jan. 30, 2021, 2:01 a.m.