plot_biotextgraph: plot_biotextgraph

In noriakis/wcGeneSummary: visualization and interpretation of textual information from omics summary data through network analysis

plot_biotextgraph

Description

Plot biotextgraph after processing graph

Usage

plot_biotextgraph(
  ret,
  edge_link = TRUE,
  edge_label = FALSE,
  show_legend = FALSE,
  cat_colors = NULL,
  query_color = "grey",
  font_family = "sans",
  colorize = FALSE,
  color_by_tag = FALSE,
  color_by_community = FALSE,
  tag_colors = NULL,
  color_text = TRUE,
  scale_range = c(5, 10),
  pal = c("blue", "red"),
  layout = "nicely",
  na_edge_color = "grey",
  add_pseudo_freq = FALSE,
  discrete_color_word = FALSE,
  use_seed = 42
)

Arguments

ret	biotext object
edge_link	whether to use edge link or edge diagonal
edge_label	whether to show edge label
show_legend	whether to show legend
cat_colors	named vector specifying color for each category of node
query_color	color for queried nodes
font_family	font family
colorize	colorize the word frequency and query separately if FALSE, no node is plotted for query nodes. it overrides color_by_tag.
color_by_tag	color by tagging information (color scale will be discrete)
color_by_community	color by community information in graph
tag_colors	palette for node color in discrete mode
color_text	whether to color the text
scale_range	scale range for node and text size
pal	palette for node color specified as (low, high)
layout	graph layout
na_edge_color	edge color for NA value
add_pseudo_freq	add pseudo value for nodes other than words
discrete_color_word	colorize words by "Words" category, not frequency.
use_seed	seed value for ggrepel

Details

Plot the network stored in biotextgraph object after processing the graph.

Value

biotext class object

See Also

plotwc plotnet

Examples

testgenes <- c("IRF3","PNKP","DDX41","ERCC1","ERCC2","XRCC1")
refseq(testgenes) |> plot_biotextgraph()

noriakis/wcGeneSummary documentation built on May 31, 2024, 4:42 p.m.