plotMulPhenGM function

Visualize gene association network graph for activated gene modules under multiple cell phenotypes

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.

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 cpGModule function result of a cell phenotype and the names of the lists are the corresponding cell phenotype.
• network.data: Network data constructed by the ConNetGNN function.
• 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 igraph Package. Default: layout_with_lgl.
• legend.position: This places the legend on the inside of the plot frame at the given location. See the legend() function for details.
• legend.cex: The font size of legend. Default: 1.5.
• legend.pt.cex: Expansion factor(s) for the points. Default: 3.
• 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.

Returns

A graph or list.

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.

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)