Description Usage Arguments Value Author(s) See Also Examples
View source: R/renderInfo-methods.R
Extract node render information from a pePathway-class
object
1 2 3 | peNodeRenderInfo(x, y = "Pert", input.shape = "box",
default.shape = "ellipse", pos.col = "red", neg.col = "blue",
zero.col = "white")
|
x |
an object of class |
y |
a string representing the factor to be represented ( |
input.shape |
shape of nodes that have measured expression change |
default.shape |
shape of all other nodes |
pos.col |
color of nodes with a positive |
neg.col |
color of nodes with a negative |
zero.col |
color of nodes with the |
a named list as expected by nodeRenderInfo
Calin Voichita and Sorin Draghici
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | # load experiment
load(system.file("extdata/E-GEOD-21942.topTable.RData", package = "ROntoTools"))
fc <- top$logFC[top$adj.P.Val <= .01]
names(fc) <- top$entrez[top$adj.P.Val <= .01]
ref <- top$entrez
# load the set of pathways
kpg <- keggPathwayGraphs("hsa")
kpg <- setEdgeWeights(kpg)
kpg <- setNodeWeights(kpg, defaultWeight = 1)
# perform the pathway analysis
peRes <- pe(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE)
p <- peRes@pathways[[50]]
g <- layoutGraph(p@map, layoutType = "dot")
graphRenderInfo(g) <- list(fixedsize = FALSE)
edgeRenderInfo(g) <- peEdgeRenderInfo(p)
nodeRenderInfo(g) <- peNodeRenderInfo(p)
# notice the different type of nodes in the graph (box/circle)
# the color of each node represents the perturbation (red = positive, blue = negative)
# the shade represents the stregth of the perturbation
renderGraph(g)
nodeRenderInfo(g) <- peNodeRenderInfo(p, "Acc")
# now, the color of each node represents the accumulation (red = positive, blue = negative)
# notice that square nodes with no parents have no accumulation
renderGraph(g)
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