set.heat: Plot a heatmap of NEA/GSEA output

In NEArender: Network Enrichment Analysis

Description

Plots a heatmap where width and height of each element reflect respective sizes of input FGS and AGS.

Usage

set.heat(List1, List2, Z, Log = TRUE)

Arguments

List1	AGS or FGS object that lists members of each individual AGS/FGS.
List2	FGS or AGS object that lists members of each individual FGS/AGS.
Z	matrix (output of nea.render with Z-scores that will define coloring of the heatmap.
Log	If TRUE, then the Z values will be log-transformed (the default).

See Also

nea.render

Examples

ags.list <- samples2ags(fantom5.43samples, Ntop=20, method="topnorm")
data(can.sig.go)
fpath <- can.sig.go
fgs.list <- import.gs(fpath)
data(net.kegg)
netpath <- net.kegg
net <- import.net(netpath)
n1 <- nea.render(AGS=ags.list, FGS=fgs.list, NET=net, graph=TRUE)
set.heat(ags.list, fgs.list, n1$z, Log=FALSE)

Example output

[1] "Network of 42491 edges between 4064 nodes..."
[1] "Preparing input datasets:"
[1] "Network: 4064 genes/proteins."
[1] "FGS: 1293 genes in 34 groups."
[1] "AGS: 854 genes in 43 groups..."
[1] "Calculating N links expected by chance..."
[1] "Rendering integer IDs..."
   user  system elapsed 
  0.463   0.012   0.476 
[1] "Counting actual links..."
   user  system elapsed 
  0.052   0.000   0.051 
[1] "Calculating statistics..."
[1] "Done."
NULL

NEArender documentation built on May 2, 2019, 8:30 a.m.