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no result from heat map WGCNA

Bioinformatics Asked on April 2, 2021

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

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.

Answered by Ram RS on April 2, 2021

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(...)

Answered by Jack Gisby on April 2, 2021

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