psSubpathway (version 0.1.0)

plotSpwNetmap: 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. The default is the KEGG node coordinates that are originally obtained from the KGML file.

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_

Examples

# NOT RUN {
# load depend package.
library(igraph)
# plot network graph of the subpathway 00982_2
plotSpwNetmap(spwid="00982_2",layout=layout_nicely)
# }