Question: Heatmap with contour and numbers
0
gravatar for urjaswita
23 months ago by
urjaswita80
United States
urjaswita80 wrote:

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 • 1.3k views
ADD COMMENTlink modified 11 weeks ago by Biostar ♦♦ 20 • written 23 months ago by urjaswita80
1

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

ADD REPLYlink written 23 months ago by venu6.3k

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

ADD REPLYlink written 23 months ago by urjaswita80

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

ADD REPLYlink written 23 months ago by e.rempel770

How did you plot it so far? - using contourplot() in lattice? countourplot will draw the line automatically.

Take a look here, where you may be able to re-use some code: http://r.789695.n4.nabble.com/Triangular-filled-contour-plot-td1557386.html

ADD REPLYlink modified 23 months ago • written 23 months ago by Kevin Blighe48k
1

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!

ADD REPLYlink written 23 months ago by urjaswita80
1

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

ADD REPLYlink written 23 months ago by Friederike5.1k
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