pheatmap troubles...!!
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Entering edit mode
11 weeks ago
Joori • 0

Hi there,

I'm currently analyzing my RNA-seq data.

Now that I've got my GSVA result, I want to draw a clustering heatmap with it. I'm using pheatmap.

> pathway_heatmap <- pheatmap::pheatmap(gsva_results, 
annotation_col = annot_df, # Add metadata labels!
show_colnames = FALSE, # Don't show sample labels
)

When I run this script, the function seems to run well without any error code coming out. But eventually, there is no image output.

If you know what causes this kind of problem or what I should re-check, please help.

Thank you a lot!

gsva R Rstudio pheatmap heatmap • 344 views
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Entering edit mode

Did you use silent = TRUE in your code?

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1
Entering edit mode
11 weeks ago

It should still generate the heatmap even though you are assigning it to a variable:

myheatmap <- pheatmap::pheatmap(matrix(runif(200),20,20))

ffff

Please ensure that you have no open devices by running dev.off() a few times, until it returns an error, and then retry pheatmap()

Kevin

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