polishNetwork | R Documentation |
generate an object of grahpNEL to represent the regulation network. Each node will has three attributes: size, borderColor and fill.
polishNetwork(
cifNetwork,
nodesDefaultSize = 48,
useLogFCAsWeight = FALSE,
nodecolor = colorRampPalette(c("green", "yellow", "red"))(5),
nodeBg = "white",
nodeBorderColor = list(gene = "darkgreen", miRNA = "darkblue"),
edgelwd = 0.25,
...
)
cifNetwork |
dataframe used to draw network graph. column names of cifNetwork must contain 'from', 'to', 'logFC' and 'miRNA' |
nodesDefaultSize |
nodes default size |
useLogFCAsWeight |
how to determine the weights for each nodes. If TURE, use logFC value as weight. If FALSE, use constant 1 as weight. |
nodecolor |
a character vector of color set. The node color will be mapped to color set by log fold change. Or the column names for the colors. |
nodeBg |
background of node |
nodeBorderColor |
a list of broder node color set. nodeBorderColor's element must be gene and miRNA |
edgelwd |
the width of edge |
... |
any parameters can be passed to graph.par |
An object of graphNEL class of the network
data("ce.miRNA.map")
data("example.data")
data("ce.interactionmap")
data("ce.IDsMap")
sifNetwork<-buildNetwork(example.data$ce.bind, ce.interactionmap, level=2)
cifNetwork<-filterNetwork(rootgene=ce.IDsMap["DAF-16"], sifNetwork=sifNetwork,
exprsData=uniqueExprsData(example.data$ce.exprData, "Max", condenseName='logFC'),
mergeBy="symbols",
miRNAlist=as.character(ce.miRNA.map[ , 1]), tolerance=1)
gR<-polishNetwork(cifNetwork)
## browseNetwork(gR)
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