I have created a heat map using WGCNA using R. But the heat map command is not showing the plot and there is no error. I have a large number of modules and traits. I am not sure if that is the reason. But I tried making it in HPC R and it still is not showing any result plot. Thank you!
2 Answers
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The plot is probably being drawn to a device that you cannot view on a cluster. If you're using the plotNetworkHeatmap function, say, try something like this:
png("plot.png", ...) #specify height, width, etc
plotNetworkHeatmap(....) #call your function
dev.off()
Now, scp the plot.png file over to your local machine to view the plot.
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If you've copied over from some of the WGNCA tutorials you might have additionally copied the sizeGrWindow command - it's caused some of my plots to disappear.
ie:
sizeGrWindow(9,6) # delete this line
plot(...)
