plotVG: Plots a pathway with or without the comparison information,...

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

Plots a pathway with or without the comparison information, using the visNetwork library.

Description

Plots a pathway with or without the comparison information, using the visNetwork library.

Usage

plotVG(
  name,
  pathways,
  DAdata = NULL,
  colors = "hiro",
  conf = 0.05,
  adjust = TRUE,
  main = "Pathway",
  submain = "",
  no.col = "BlanchedAlmond",
  height = "800px"
)

Arguments

name	KEGG ID of the pathway to plot.
pathways	Pathways object.
DAdata	List of comparison results, returned by function DAcomp.
colors	String with the color scheme or vector of colors to be used. See define_colors for available options. Default is "hiro".
conf	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.
main	Title of the plot.
submain	Subtitle of the plot.
no.col	String with the color given to non-significant nodes.
height	Height of the plot. Default is "800px".

Value

Plot of the pathway.

Examples

pathways <- load_pathways("hsa")
plotVG("hsa04010", pathways)

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