plotValuedGraph: Plots a graph with nodes colored according to a quantitative...
In DEGraph: Two-sample tests on a graph

Description Usage Arguments Value Author(s) See Also Examples

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

1	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)

`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.

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).

Laurent Jacob, Pierre Neuvial and Sandrine Dudoit

plotKEGGgraph plot()

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)
}