plotBitmapCC: Edge-indicator bitmap plot.

In haimbar/edgefinder: Detect Edges in Sparse Co-expression Graphs

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=T 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

   data(WT)
   WTres <- edgefinder(WT, ttl = "Wild Type")
   WTComp <- graphComponents(WTres$AdjMat)
   plotBitmapCC(WTres$AdjMat)
   plotBitmapCC(WTres$AdjMat, WTComp, orderByCluster=TRUE)
   plotBitmapCC(WTres$AdjMat, WTComp, orderByCluster=TRUE, showMinDegree = 30)

haimbar/edgefinder documentation built on Dec. 20, 2021, 2:45 p.m.