plot_features_in_pathway: Plot features trend in one pathway or module

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

Plot features trend in one pathway or module

Description

Plot features trend in one pathway or module

Usage

plot_features_in_pathway(
  ko_stat,
  map_id = "map00780",
  modulelist = NULL,
  select_ko = NULL,
  box_color = reporter_color,
  show_number = TRUE,
  scale = FALSE,
  feature_type = "KOs",
  line_color = c(Depleted = "seagreen", Enriched = "orange", None = "grey", Significant =
    "red2")
)

Arguments

ko_stat	ko_stat result from pvalue2zs or result of 'get_reporter_score'
map_id	the pathway or module id
modulelist	NULL or customized modulelist dataframe, must contain "id","K_num","KOs","Description" columns. Take the 'KOlist' as example, use custom_modulelist.
select_ko	select which ko
box_color	box and point color, default: c("#e31a1c","#1f78b4")
show_number	show the numbers.
scale	scale the data by row.
feature_type	show in the title ,default: KOs
line_color	line color, default: c("Depleted"="seagreen","Enriched"="orange","None"="grey")

Value

ggplot

Examples

data("reporter_score_res")
plot_features_in_pathway(ko_stat = reporter_score_res, map_id = "map00860")

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