DAsummary: Lists and plots the top 'n' altered pathways, taking into...

In martahidalgo/hipathia: HiPathia: High-throughput Pathway Analysis

Lists and plots the top n altered pathways, taking into account the number of altered .

Description

Lists and plots the top n altered pathways, taking into account the number of altered .

Usage

DAsummary(
  DAdata,
  n = 10,
  conf.level = 0.05,
  adjust = TRUE,
  ratio = F,
  colors = "hiro",
  order.by = "number"
)

Arguments

DAdata	List of comparison results, returned by function DAcomp.
n	Number of top features to show.
conf.level	Numeric, cut off for significance. Default is 0.05.
adjust	Boolean, whether to adjust the p.value with Benjamini-Hochberg FDR method. Default is TRUE.
ratio	Boolean, whether to plot the ratio of significant paths with respect to the total paths in the pathway. Default is FALSE.
colors	String with the color scheme or vector of colors to be used. See define_colors for available options. Default is "hiro".
order.by	String, how to order table of results. Available options include ratio (default, uses the ratio of significant paths with respect to the total paths in the pathway) and number (uses the number of significant paths in the pathway).

Value

Plot and tibble including top n altered pathways.

Examples

data(DAdata)
DAsummary(DAdata)

martahidalgo/hipathia documentation built on Jan. 12, 2023, 1:44 p.m.