PlotModuleNetwork: PlotModuleNetwork

In carter-allen/IRISFGM: Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq

Description

This function will visualize co-expression gene network based on selected two biclusters. The nodes represent the gene module network from the selected bicluster. The size of the nodes indicates the degree of presence. The thickness of edges indicates the value of the correlation coefficient.

Usage

PlotModuleNetwork(object, ...)

.plotmodulenetwork(
  object = NULL,
  method = "spearman",
  node.col = "orange",
  N.bicluster = c(1, 5),
  cutoff.neg = -0.8,
  cutoff.pos = 0.8,
  layout = "circle",
  node.label = TRUE,
  node.label.cex = 1
)

## S4 method for signature 'IRISFGM'
PlotModuleNetwork(
  object = NULL,
  method = "spearman",
  node.col = "orange",
  N.bicluster = c(1, 5),
  cutoff.neg = -0.8,
  cutoff.pos = 0.8,
  layout = "circle",
  node.label = TRUE,
  node.label.cex = 1
)

Arguments

object	Input IRIS-FGM object.
...	other arguments passed to methods
method	Should be a statistical method to calculate edge weight based on expression data. It can be either "Spearman" (default) or "Pearson."
node.col	Should a color name (or color code) for nodes
N.bicluster	Should be the two numbers of biclsuters.
cutoff.neg	Should be a cutoff to show a negative correlation between two nodes (default: -0.8).
cutoff.pos	Should be a cutoff to show a positive correlation between two nodes (default: 0.8).
layout	Should be one type of layouts to show nodes' arrangement, including 'linear', 'star', 'circle'(default), 'gem', 'dh', 'graphopt', 'grid', 'mds', 'randomly', 'fr', 'kk', 'drl', 'lgl'.
node.label	Should be logic to show the nodes' label (default: TRUE).
node.label.cex	Should be a number to control the label size.

Value

It will generate co-expression network based on selected bicluster (can be one or multiple.)

Examples

## Not run: 
object <- PlotModuleNetwork(object = NULL, 
N.bicluster = c(1,5), 
Node.color = '#E8E504', 
cutoff=0.7, 
node.label.cex = 1) 

## End(Not run)

carter-allen/IRISFGM documentation built on Dec. 31, 2020, 9:54 p.m.