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emapplot

emapplot


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)

enrichplot

Visualization of Functional Enrichment Result

v1.10.2
Artistic-2.0
Authors
Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>), Erqiang Hu [ctb]
Initial release

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