plot_features_network: Plot features network

In ReporterScore: Generalized Reporter Score-Based Enrichment Analysis for Omics Data

Plot features network

Description

Plot features network

Usage

plot_features_network(
  ko_stat,
  map_id = "map00780",
  near_pathway = FALSE,
  modulelist = NULL,
  kos_color = c(Depleted = "seagreen", Enriched = "orange", None = "grey", Significant =
    "red2", Pathway = "#80b1d3"),
  pathway_label = TRUE,
  kos_label = TRUE,
  pathway_description = FALSE,
  kos_description = FALSE,
  str_width = 50,
  mark_module = FALSE,
  mark_color = NULL,
  return_net = FALSE,
  ...
)

Arguments

ko_stat	ko_stat result from pvalue2zs or result of 'get_reporter_score'
map_id	the pathway or module id
near_pathway	show the near_pathway if any features exist.
modulelist	NULL or customized modulelist dataframe, must contain "id","K_num","KOs","Description" columns. Take the 'KOlist' as example, use custom_modulelist.
kos_color	default, c("Depleted"="seagreen","Enriched"="orange","None"="grey","Significant"="red2")
pathway_label	show pathway_label?
kos_label	show kos_label?
pathway_description	show the pathway description?
kos_description	show the kos description?
str_width	str width
mark_module	mark the modules?
mark_color	mark colors, default, c("Depleted"="seagreen","Enriched"="orange","None"="grey","Significant"="red2")
return_net	return the network
...	additional arguments for c_net_plot

Value

network plot

Examples

if (requireNamespace("MetaNet")) {
  data("reporter_score_res")
  plot_features_network(reporter_score_res, map_id = "map05230")
  plot_features_network(reporter_score_res, map_id = "map00780", near_pathway = TRUE)
}

ReporterScore documentation built on Sept. 11, 2024, 6:44 p.m.