This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Heatmap with contour and numbers

I'm not sure if this is a good fit on this forum, but I guess graphics is an integral part of bioinformatics, so here goes. I wish to create a heatmap like the one in panel D in this figure. I could plot the heatmap easily, but I couldn't find how to put the contour lines and numbers on it. Is there a package/command in R/Python or maybe they wrote a custom script. Any help is much appreciated. Thanks!

Image panel D from Villar et al.

heatmap r
• 3,962 views • link
updated by Biostar Biostar • written by urjaswita urjaswita

If I remember correct, there is an option trace in heatmap.2 function. May be you can play with it to get it done.

• 0 views • link
written by venu venu

I tried trace. It only traces across rows or columns, but not the pattern in the heatmap. I will dig deeper though. Thank you!

• 0 views • link
written by urjaswita urjaswita

Honestly, I don't really understand the plot, much less explain how you could do something similar in R/Python.

• 0 views • link
written by e.rempel e.rempel

I tried heatmap.2 and pheatmap in R. Both created a nice heatmap, but I couldn't find an option to get contour lines and numbers.

I'll check the lattice. Thanks!

• 0 views • link
written by urjaswita urjaswita

did you try asking the author for information on how this was done?

• 0 views • link
written by Friederike Friederike

0 answers

No answers yet.

Log in to answer this question.

More posts like this