condorPlotCommunities: Plot adjacency matrix with links grouped and colored by...

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Plot adjacency matrix with links grouped and colored by community

Description

This function will generate the network link 'heatmap' with colored dots representing within-community links and black dots between-community links

Usage

condorPlotCommunities(
  condor.object,
  color_list,
  point.size = 0.01,
  xlab = "SNP",
  ylab = "Gene"
)

Arguments

condor.object	output of either condorCluster or condorModularityMax
color_list	vector of colors accepted by col inside the plot function. There must be as many colors as communities.
point.size	passed to cex in the plot
xlab	x axis label
ylab	y axis label

Value

produces a plot output.

Note

For the condor paper http://arxiv.org/abs/1509.02816, I used 35 colors from the "Tarnish" palette with "hard" clustering

References

http://tools.medialab.sciences-po.fr/iwanthue/ for a nice color generator at

Examples

r = c(1,1,1,2,2,2,3,3,3,4,4);
b = c(1,2,3,1,2,4,2,3,4,3,4);
reds <- c("Alice","Sue","Janine","Mary")
blues <- c("Bob","John","Ed","Hank")
elist <- data.frame(red=reds[r],blue=blues[b])
condor.object <- createCondorObject(elist)
condor.object <- condorCluster(condor.object)
condorPlotCommunities(condor.object,
color_list=c("darkgreen","darkorange"),point.size=2,
xlab="Women",ylab="Men")

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.