DEGraph (version 1.24.0)

plotValuedGraph: Plots a graph with nodes colored according to a quantitative variable

Description

Plots a graph with nodes colored according to a quantitative variable.

Usage

plotValuedGraph(graph, values=NULL, nodeLabels=nodes(graph), qMax=0.95, colorPalette=heat.colors(10), adjustColorRange=FALSE, symmetrizeArrows=FALSE, height=1, lwd=1, cex=1, ..., verbose=FALSE)

Arguments

graph

A graph object.

values

A named vector of numeric values according to which the graph nodes should be colored.

nodeLabels

A character vector of the same length and in the same order as 'nodes(graph)': node labels to be displayed. Defaults to 'nodes(graph)'.

qMax

A numeric value, fraction of the data to be truncated in order to avoid outliers.

colorPalette

A character vector, the set of colors to be used.

adjustColorRange

A logical value. If TRUE, the color range is adjusted to the range of values of nodes actually present in the graph. Defaults to FALSE, i.e. the color range spans range(values) regardless of which nodes are present in the graph.

symmetrizeArrows

A logical value. If TRUE, arrow tails are drawn as the corresponding arrow heads. Defaults to FALSE.

height

A numeric value, the (common) size of nodes.

lwd

A numeric value, the (common) width of edges.

cex

A numeric value, the relative size of the text for gene names.

...

Further arguments to be passed to 'edgeRenderInfo' and 'nodeRenderInfo'.

verbose

If TRUE, extra information is output.

Value

A list containing the following components:

graph

The 'graph' object as plotted.

breaks

The break points in the supplied values (can be used for plotting a legend).

See Also

plotKEGGgraph plot()

Examples

library("Rgraphviz")
library("KEGGgraph")
## library("NCIgraph")

data("Loi2008_DEGraphVignette")
exprData <- exprLoi2008
classData <- classLoi2008
annData <- annLoi2008

rn <- rownames(exprData)

## Retrieve expression levels data for genes from one KEGG pathway
graph <- grListKEGG[[1]]
pname <- attr(graph, "label")
print(pname)

## DEGraph T2 test
resList <- testOneGraph(graph, exprData, classData, verbose=TRUE, prop=0.2)

## Largest connected component
res <- resList[[1]]
gr <- res$graph

## individual t statistics
shift <- apply(exprData, 1, FUN=function(x) {
  tt <- t.test(x[classData==0], x[classData==1])
  tt$statistic
})
names(shift) <- translateGeneID2KEGGID(names(shift))

## color palette
if (require(marray)) {
  pal <- maPalette(low="red", high="green", mid="black", k=100)
} else {
  pal <- heat.colors(100)
}

## plot results
dn <- getDisplayName(gr, shortLabel=TRUE)
mm <- match(translateKEGGID2GeneID(nodes(gr)), rownames(annData))
dn <- annData[mm, "NCBI.gene.symbol"]
 
pvg <- plotValuedGraph(gr, values=shift, nodeLabels=dn, qMax=0.95, colorPalette=pal, height=40, lwd=1, verbose=TRUE, cex=0.5)
title(pname)

txt1 <- sprintf("p(T2)=%s", signif(res$p.value[1], 2))
txt2 <- sprintf("p(T2F[%s])=%s", res$k, signif(res$p.value[2]))
txt <- paste(txt1, txt2, sep="\n")
stext(side=3, pos=1, txt)
if (require(fields)) {
  image.plot(legend.only=TRUE, zlim=range(pvg$breaks), col=pal, legend.shrink=0.3, legend.width=0.8, legend.lab="t-scores", legend.mar=3.3)
}