cnetplot
Gene-Concept Network
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 '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, node_label_size = NULL, cex_label_category = 1, cex_label_gene = 1, ... )
x |
enrichment result |
showCategory |
number of enriched terms to display |
foldChange |
fold Change |
layout |
layout of the network |
... |
additional parameters |
colorEdge |
whether coloring edge by enriched terms |
circular |
whether using circular layout |
node_label |
select which labels to be displayed. one of 'category', 'gene', 'all' and 'none', default is "all". |
cex_category |
number indicating the amount by which plotting category nodes should be scaled relative to the default. |
cex_gene |
number indicating the amount by which plotting gene nodes should be scaled relative to the default. |
node_label_size |
size of node label, this parameter has been changed to cex_label_category and cex_label_gene |
cex_label_category |
scale of category node label size |
cex_label_gene |
scale of gene node label size |
plot linkages of genes and enriched concepts (e.g. GO categories, KEGG pathways)
ggplot object
Guangchuang Yu
library(DOSE) data(geneList) de <- names(geneList)[1:100] x <- enrichDO(de) cnetplot(x)
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