cnetplot: cnetplot

In GuangchuangYu/enrichplot: Visualization of Functional Enrichment Result

Description

Gene-Concept Network

Usage

cnetplot(x, showCategory = 5, foldChange = NULL, layout = "kk", ...)

## S4 method for signature 'enrichResult'
cnetplot(x, showCategory = 5, foldChange = NULL, layout = "kk", ...)

## S4 method for signature 'list'
cnetplot(x, showCategory = 5, foldChange = NULL, layout = "kk", ...)

## S4 method for signature 'gseaResult'
cnetplot(x, showCategory = 5, foldChange = NULL, layout = "kk", ...)

## S4 method for signature 'compareClusterResult'
cnetplot(x, showCategory = 5, foldChange = NULL, layout = "kk", ...)

cnetplot.enrichResult(
  x,
  showCategory = 5,
  foldChange = NULL,
  layout = "kk",
  colorEdge = FALSE,
  circular = FALSE,
  node_label = "all",
  cex_category = 1,
  cex_gene = 1,
  cex_label_category = 1,
  cex_label_gene = 1,
  color_category = "#E5C494",
  color_gene = "#B3B3B3",
  shadowtext = "all",
  ...
)

Arguments

x	Enrichment result.
showCategory	A number or a vector of terms. If it is a number, the first n terms will be displayed. If it is a vector of terms, the selected terms will be displayed.
foldChange	Fold Change of nodes, the default value is NULL. If the user provides the Fold Change value of the nodes, it can be used to set the color of the gene node.
layout	Layout of the map, e.g. 'star', 'circle', 'gem', 'dh', 'graphopt', 'grid', 'mds', 'randomly', 'fr', 'kk', 'drl' or 'lgl'.
...	Additional parameters
colorEdge	Logical, whether coloring edge by enriched terms, the default value is FALSE.
circular	Logical, whether using circular layout, the default value is FALSE.
node_label	Select which labels to be displayed. one of 'category', 'gene', 'all'(the default) and 'none'.
cex_category	Number indicating the amount by which plotting category nodes should be scaled relative to the default, the default value is 1.
cex_gene	Number indicating the amount by which plotting gene nodes should be scaled relative to the default, the default value is 1.
cex_label_category	Scale of category node label size, the default value is 1.
cex_label_gene	Scale of gene node label size, the default value is 1.
color_category	Color of category node.
color_gene	Color of gene node.
shadowtext	select which node labels to use shadow font, one of 'category', 'gene', 'all' and 'none', default is 'all'.

Details

plot linkages of genes and enriched concepts (e.g. GO categories, KEGG pathways)

Value

ggplot object

Author(s)

Guangchuang Yu

Examples

## Not run: 
    library(DOSE)
    data(geneList)
    de <- names(geneList)[1:100]
    x <- enrichDO(de)
    x2 <- pairwise_termsim(x)
    cnetplot(x2)
    # use `layout` to change the layout of map
    cnetplot(x2, layout = "star")
    # use `showCategory` to select the displayed terms. It can be a number of a vector of terms.
    cnetplot(x2, showCategory = 10)
    categorys <- c("pre-malignant neoplasm", "intestinal disease",
                   "breast ductal carcinoma", "non-small cell lung carcinoma")
    cnetplot(x2, showCategory = categorys)
    # It can also graph compareClusterResult
    data(gcSample)
    library(clusterProfiler)
    library(DOSE)
    library(org.Hs.eg.db)
    data(gcSample)
    xx <- compareCluster(gcSample, fun="enrichGO", OrgDb="org.Hs.eg.db")
    xx2 <- pairwise_termsim(xx)
    cnetplot(xx2)

## End(Not run)

GuangchuangYu/enrichplot documentation built on Aug. 31, 2021, 7:48 p.m.