plotSubPathway: plotSubPathway

In hanjunwei-lab/CNA2Subpathway: Identification of Dysregulated Subpathway Driven by Copy Number Alteration

Description

The function plotsubpathway can visualization of a subpathway network map.

Usage

plotSubPathway(
  subpathwayID,
  subpathwaydata,
  layout = NULL,
  margin = 0,
  vertex.label.cex = 0.8,
  vertex.label.font = 0.8,
  vertex.label.dist = 1,
  vertex.size = 12,
  edge.arrow.width = 3,
  edge.label.cex = 0.6,
  vertex.label.color = "black",
  vertex.color = "#F08080",
  vertex.frame.color = "dimgray",
  edge.color = "grey70",
  edge.label.color = "dimgray",
  sub = NULL,
  main = NULL
)

Arguments

subpathwayID	subpathway id number
subpathwaydata	The subpathwaymap data
layout	A matrix of x-y coordinates with two dims. Determine the placement of the nodes for drawing a graph.
margin	A numeric. The value is usually between -0.5 and 0.5, which is able to zoom in or out a subpathway graph. The default is 0.
vertex.label.cex	A numeric vector of node label size.
vertex.label.font	A numeric vector of label font.
vertex.label.dist	A numeric vector of label dist.
vertex.size	A numeric vector of Node size. See plot.igraph.
edge.arrow.width	Edge arrow width. The default is 3.
edge.label.cex	Edge label size.
vertex.label.color	A vector of node label colors. The default is black.
vertex.color	A vector of node colors. The default is the KEGG node color.
vertex.frame.color	A vector of node frame color. The default is dimgray.
edge.color	A vector of edge color. The default is dimgray
edge.label.color	A vector of edge label color. The default is dimgray.
sub	A character string of subtitle.
main	A character string of main title.

Value

a subpathway map

Examples

# load depend package
require(igraph)
# obtain subpathwaymap data
SubPathwaymapdata<-GetExampleData("SubPathwaymapdata")
# plot network graph of the subpathway 04915_13
plotSubPathway("04915_13",SubPathwaymapdata)

hanjunwei-lab/CNA2Subpathway documentation built on Jan. 28, 2021, 6:56 p.m.