| plotMNW {GSCA} | R Documentation |
This function draws a network with multiple lines per edge, representing multiple study-specific correlations for the corresponding gene pairs. Nodes can be colored by DE information, and each line in edges can be colored based on the correlation magnitude and direction.
plotMNW(cormatrix.list, genes = NULL, mycolors = bluered(201), ncolor = "white", node.de = NULL, r = 10, nr = 2, jt = 0.1, lwd = 1, xlab1 = "", text.cex = 1, ...)
cormatrix.list |
A list of symmetric correlation matrices from multiple studies. |
genes |
Node names to be displayed in the network plot. If
NULL (default), rownames(cormatrix.list[[1]]) is used. |
mycolors |
Edge color palette. The default is bluered(201)
implemented by gplots, which sets c("blue", "white", "red")
for the correlation of c(-1, 0, 1). |
ncolor |
Node color for selected genes specified by node.de. |
node.de |
A vector of 0's and 1's. The "1" nodes are colored in
ncolor. |
r |
The radius of the big circle where nodes are placed on |
nr |
The radius of each node |
jt |
Distance between adjacent lines in an edge |
lwd |
The edge line thickness |
xlab1 |
Sub-text to be place below the network |
text.cex |
Node font size |
... |
The rest of arguments are passed to plot. |
Edge lines are sorted first and put in order separately for every edge, for effective display of study agreement.
Because edges tend to be thicker as the number of studies grow larger, including too many genes (nodes) may result in a noninformative network plot.
YounJeong Choi
Choi and Kendziorski (2009)
data(LungCancer3)
GS <- LungCancer3$info$GSdef
GSdesc <- LungCancer3$info$Name
setid <- "GO:0008033"
gid <- GS[[setid]]
ss <- c("KARS", "SARS", "AARS", "SSB", "POP1", "RPP30")
data.list <- list(Harvard = LungCancer3$data$Harvard[gid, 140:156],
Stanford = LungCancer3$data$Stanford[gid, 42:46],
Michigan = LungCancer3$data$Michigan[gid, 87:96])
cormatrix.list <- lapply(lapply(data.list, t), cor,
use = "pairwise.complete.obs")
plotMNW(cormatrix.list, genes = ss, mycolors = bluered(201), ncolor =
"yellow", node.de = c(rep(1, 3), rep(0, 3)), lwd = 5, jt = 0.3)