cnetplot: cnetplot

In YuLab-SMU/enrichplot: Visualization of Functional Enrichment Result

cnetplot

Description

category-gene-network plot

Usage

## S3 method for class 'enrichResult'
cnetplot(
  x,
  layout = igraph::layout_with_kk,
  showCategory = 5,
  color_category = "#E5C494",
  size_category = 1,
  color_item = "#B3B3B3",
  size_item = 1,
  color_edge = "grey",
  size_edge = 0.5,
  node_label = "all",
  foldChange = NULL,
  hilight = "none",
  hilight_alpha = 0.3,
  ...
)

## S3 method for class 'gseaResult'
cnetplot(
  x,
  layout = igraph::layout_with_kk,
  showCategory = 5,
  color_category = "#E5C494",
  size_category = 1,
  color_item = "#B3B3B3",
  size_item = 1,
  color_edge = "grey",
  size_edge = 0.5,
  node_label = "all",
  foldChange = NULL,
  hilight = "none",
  hilight_alpha = 0.3,
  ...
)

## S3 method for class 'compareClusterResult'
cnetplot(
  x,
  layout = igraph::layout_with_kk,
  showCategory = 5,
  color_category = "#E5C494",
  size_category = 1,
  color_item = "#B3B3B3",
  size_item = 1,
  color_edge = "grey",
  size_edge = 0.5,
  node_label = "all",
  foldChange = NULL,
  hilight = "none",
  hilight_alpha = 0.3,
  pie = "equal",
  ...
)

Arguments

x	input object
layout	network layout
showCategory	selected category to be displayed
color_category	color of category node
size_category	relative size of the category
color_item	color of item node
size_item	relative size of the item (e.g., genes)
color_edge	color of edge
size_edge	relative size of edge
node_label	one of 'all', 'none', 'category', 'item', 'exclusive' or 'share'
foldChange	numeric values to color the item (e.g, foldChange of gene expression values)
hilight	selected category to be highlighted
hilight_alpha	transparent value for not selected to be highlight
...	additional parameters
pie	one of 'equal' or 'Count' to set the slice ratio of the pies

See Also

[cnetplot][ggtangle::cnetplot]

YuLab-SMU/enrichplot documentation built on Dec. 18, 2024, 11:52 p.m.