plot_features_network {ReporterScore}

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,
  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?

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)
}