plot_features_heatmap: Plot features heatmap

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

Plot features heatmap

Description

Plot features heatmap

Usage

plot_features_heatmap(
  kodf,
  group = NULL,
  metadata = NULL,
  map_id = "map00780",
  select_ko = NULL,
  only_sig = FALSE,
  columns = NULL,
  modulelist = NULL,
  KO_description = FALSE,
  str_width = 50,
  heatmap_param = list()
)

Arguments

kodf	KO_abundance table, rowname is ko id (e.g. K00001),colnames is samples. or result of 'get_reporter_score'
group	The compare group (two category) in your data, one column name of metadata when metadata exist or a vector whose length equal to columns number of kodf.
metadata	metadata
map_id	the pathway or module id
select_ko	select which ko
only_sig	only show the significant KOs
columns	change columns
modulelist	NULL or customized modulelist dataframe, must contain "id","K_num","KOs","Description" columns. Take the 'KOlist' as example, use custom_modulelist.
KO_description	show KO description rather than KO id.
str_width	str_width to wrap
heatmap_param	parameters pass to pheatmap

Value

ggplot

Examples

if (requireNamespace("pheatmap")) {
  data("reporter_score_res")
  plot_features_heatmap(reporter_score_res, map_id = "map00780")
}

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