plotSpwNetmap: Polt a subpathway network map

In psSubpathway: Flexible Identification of Phenotype-Specific Subpathways

Polt a subpathway network map

Description

Visualize a subpathway network map.

Usage

plotSpwNetmap(
  spwid,
  layout = NULL,
  margin = 0,
  vertex.label.cex = 0.6,
  vertex.label.font = 1,
  vertex.size = 8,
  vertex.size2 = 6,
  edge.arrow.size = 0.2,
  edge.arrow.width = 3,
  edge.label.cex = 0.6,
  vertex.label.color = "black",
  vertex.color = "#BFFFBF",
  vertex.frame.color = "dimgray",
  edge.color = "dimgray",
  edge.label.color = "dimgray",
  sub = NULL,
  main = NULL
)

Arguments

spwid	The subpathway id which the user wants to plot.
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.size	A numeric vector of Node size. See plot.igraph.
vertex.size2	A numeric vector of Node size.
edge.arrow.size	Edge arrow size.The default is 0.2.
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.

Details

plotSpwNetmap

The function plotSpwNetmap is able to display a subpathway graph. The argument layout is used to determine the placement of the nodes for drawing a graph.The layouts provided in igraph include 'layout_as_star', 'layout_as_tree', 'layout_in_circle', 'layout_nicely','layout_on_grid', 'layout_on_sphere', 'layout_randomly', 'layout_with_dh', 'layout_with_fr', 'layout_with_gem', 'layout_with_graphopt', 'layout_with_kk', 'layout_with_lgl', 'layout_with_mds'. The 'layout_as_tree' generates a tree-like layout, so it is mainly for trees. The 'layout_randomly' places the nodes randomly. The 'layout_in_circle' places the nodes on a unit circle. Detailed information on the parameters can be found in layout_

Value

a plot

Author(s)

Xudong Han, Junwei Han, Qingfei Kong

Examples

# load depend package.
library(igraph)
# plot network graph of the subpathway 00982_2
plotSpwNetmap(spwid="00982_2",layout=layout_nicely)

psSubpathway documentation built on Aug. 9, 2023, 5:09 p.m.