plotBitmapCC: Edge-indicator bitmap plot.
In haimbar/betaMix: Detect Edges in Co-expression Graphs

plotBitmapCC

R Documentation

Edge-indicator bitmap plot.

Description

Plot a bitmap in which a black dot corresponds to a pair of highly correlated genes (an edge in the graph). The default is to show the nodes according to their order in the input. By setting orderByDegree=TRUE as below, it is possible to change the order and cluster them, and show them in increasing degree order (from left to right.)

Usage

plotBitmapCC(
  AdjMat,
  clusterInfo = NULL,
  orderByCluster = FALSE,
  showMinDegree = 0
)

Arguments

`AdjMat`	An adjacency Matrix (0/1).
`clusterInfo`	obtained from graphComponents. If not provided by the user, it will be computed on the fly.
`orderByCluster`	If false, show the bitmap is the original node order. If TRUE, show nodes by clusters, and sort by distance from the center of the cluster.
`showMinDegree`	Non-negative integer indicating the minimum degree of nodes that should be displayed. Default=0 (all nodes).

Examples

## Not run: 
   data(SIM,package = "betaMix")
   res <- betaMix(betaMix::SIM, maxalpha = 1e-6,ppr = 0.01,subsamplesize = 30000, ind=TRUE)
   adjMat <- getAdjMat(res)
   SimComp <- graphComponents(adjMat)
   plotBitmapCC(adjMat)
   plotBitmapCC(adjMat, SimComp, orderByCluster=TRUE)

## End(Not run)

haimbar/betaMix documentation built on Jan. 3, 2023, 12:54 p.m.