plot.PCSF: Plot an interactive subnetwork

In IOR-Bioinformatics/PCSF: Network-based interpretation of highthroughput data

Description

plot.PCSF plots an interactive figure of the subnetwork obrained by the PCSF method.

Usage

## S3 method for class 'PCSF'
plot(x, style = 0, edge_width = 5, node_size = 40,
  node_label_cex = 30, Steiner_node_color = "lightblue",
  Terminal_node_color = "lightgreen", Terminal_node_legend = "Terminal",
  Steiner_node_legend = "Steiner", ...)

Arguments

x	A subnetwork obtained by the PCSF method. It is a "PCSF" object derived from igraph class and it has the edge cost and vertex prize attributes.
style	A boolean value to determine the visualization style of the network, where 0 plots the static network and 1 plots the dynamic network. The default valu is 0.
edge_width	A numeric value to emphasize a maximum edge width. A default value is 5. This value must be greater than 1.
node_size	A numeric value to emphasize a maximum node size. A default value is 40. This value must be greater than 10.
node_label_cex	A numeric value to set a node label size. A default value is 30.
Steiner_node_color	A string to set a color for Steiner nodes. A default value is "lightblue".
Terminal_node_color	A string to set a color for terminal nodes.
Terminal_node_legend	A string to set a legend for terminal nodes. A default legend is "Terminal".
Steiner_node_legend	A string to set a legend for Steiner nodes. A default legend is "Steiner".
...	Ignored.

Details

This function plots an interactive subnetwork obtained by the PCSF and PCSF_rand. The node sizes and edge widths are respectively proportional to the node prizes and edge costs while plotting the subnetwork from PCSF. In contrast, the node sizes and edge widths are proportional to the total number of abondance in randomized runs while plotting the subnetwork from PCSF_rand. The node names are displayed during the hover-over.

Author(s)

Murodzhon Akhmedov

See Also

PCSF, plot.PCSFe

Examples

## Not run: 
library("PCSF")
data("STRING")
data("Tgfb_phospho")
terminals <- Tgfb_phospho
ppi <- construct_interactome(STRING)
subnet <- PCSF(ppi, terminals, w = 2, b = 1, mu = 0.0005)
plot(subnet)
## End(Not run)

IOR-Bioinformatics/PCSF documentation built on June 2, 2019, 10:03 p.m.