plotGANetwork: Visualize gene association network graph of a gene module or...

In scapGNN: Graph Neural Network-Based Framework for Single Cell Active Pathways and Gene Modules Analysis

Visualize gene association network graph of a gene module or pathway at the specified cell phenotype

Description

Based on the gene set input by the user, plotGANetwork functional draws the gene association network in the specified cell phenotype. The node size in the network reflects the activation strength of the gene. The thickness of the edge indicates the strength of interaction between genes.

Usage

plotGANetwork(
  network.data,
  cellset,
  geneset,
  rwr.gamma = 0.7,
  vertex.colors = NULL,
  vertex.size = 10,
  vertex.label.cex = 0.8,
  vertex.label.dist = 1,
  vertex.label.color = "black",
  edge.width = 5,
  margin = 0,
  layout = layout_as_star,
  main = NULL,
  plotgraph = TRUE
)

Arguments

network.data	Network data constructed by the ConNetGNN function.
cellset	A vector of cell id. A cell set corresponding to the specified cell phenotype.
geneset	A vector of gene id. A gene module or pathway.
rwr.gamma	Restart parameter. Default: 0.7.
vertex.colors	The fill color of the vertex. The number of colors should match the number of cell phenotypes. If NULL (default), the system will automatically assign colors.
vertex.size	The size of the vertex. Default: 10.
vertex.label.cex	The font size for vertex labels. Default: 0.8.
vertex.label.dist	The distance of the label from the center of the vertex. If it is 0 then the label is centered on the vertex. Default: 1.
vertex.label.color	The color of the labels. Default: black.
edge.width	The width of the edge. This does not affect the relative size of the edge weights. Default: 5.
margin	The amount of empty space below, over, at the left and right of the plot, it is a numeric vector of length four. Usually values between 0 and 0.5 are meaningful, but negative values are also possible, that will make the plot zoom in to a part of the graph. If it is shorter than four then it is recycled. Default: 0.
layout	Either a function or a numeric matrix. It specifies how the vertices will be placed on the plot. For details, please refer to the igraphPackage. Default: layout_as_star.
main	A main title for the plot.
plotgraph	Whether to draw the picture. Default: TRUE. If FALSE, the image will not be displayed but the network data will be returned in the igraph data format.

Details

plotGANetwork

Value

A graph or list.

Examples

require(igraph)

# Load the result of the ConNetGNN function.
data(ConNetGNN_data)

data("Hv_exp")
index<-grep("0h",colnames(Hv_exp))
cellset<-colnames(Hv_exp)[index]
pathways<-load_path_data(system.file("extdata", "KEGG_human.gmt", package = "scapGNN"))
geneset<-pathways[[which(names(pathways)=="Tight junction [PATH:hsa04530]")]]
plotGANetwork(ConNetGNN_data,cellset,geneset,main = "Tight junction [PATH:hsa04530]")

scapGNN documentation built on Aug. 8, 2023, 9:06 a.m.