plotMulPhenGM {scapGNN} | R Documentation |
Visualize gene association network graph for activated gene modules under multiple cell phenotypes
Description
For multiple cell phenotypes, the plotMulPhenGM
function will display the activated gene modules for each phenotype and show the connection and status of genes in different cell phenotypes.
Usage
plotMulPhenGM(
data.list,
network.data,
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_with_lgl,
legend.position = "bottomright",
legend.cex = 1.5,
legend.pt.cex = 3,
plotgraph = TRUE
)
Arguments
data.list |
a list. Each element represents the |
network.data |
Network data constructed by the |
vertex.colors |
The fill color of the vertex. The number of colors should match the number of cell phenotypes. If |
vertex.size |
The size of the vertex. Default: |
vertex.label.cex |
The font size for vertex labels. Default: |
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: |
vertex.label.color |
The color of the labels. Default: |
edge.width |
The width of the edge. This does not affect the relative size of the edge weights. Default: |
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: |
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 |
legend.position |
This places the legend on the inside of the plot frame at the given location. See the |
legend.cex |
The font size of legend. Default: |
legend.pt.cex |
Expansion factor(s) for the points. Default: |
plotgraph |
Whether to draw the picture. Default: |
Details
plotMulPhenGM
If a gene is significantly activated in more than one cell phenotype, we call it a co-activated gene. These co-activated genes are shown on the sector diagram. Each interval of the sector diagram represents the activation strength of the gene in this cell phenotype relative to other cell phenotypes.
Value
A graph or list.
Examples
require(igraph)
require(grDevices)
# Load the result of the ConNetGNN function.
data(ConNetGNN_data)
# Obtain cpGModule results for each cell phenotype.
data(H9_0h_cpGM_data)
data(H9_24h_cpGM_data)
data(H9_36h_cpGM_data)
data.list<-list(H9_0h=H9_0h_cpGM_data,H9_24h=H9_24h_cpGM_data,H9_36h=H9_36h_cpGM_data)
plotMulPhenGM(data.list,ConNetGNN_data)