heatmap.2 clustering slow only when rows are excluded

[CrashVector]

I have noticed a similar issue as found here: https://stackoverflow.com/questions/18551645/speeding-up-clustering-heatmap-creation

When generating a heatmap with the dendrogram argument set to "column" or "none", the process becomes extremely slow. Yet when setting dendrogram to "row" or "both", the process is very quick.

Not sure why this happens.

[talgalili]

Hey, sorry, but I'm not likely to dig into this soon. But if you find the time to write a pull request - I'll happily review it.

Cheers,
T

[cdputnam]

I've had the same problem where I don't want clustering/reordering of the input rows or columns.

I can fix it by commenting out line 231 from the file heatmap.2.R:

ddr <- as.dendrogram(hclust(dist(diag(nr))))

Having the ddr variable undefined doesn't appear to be a problem in the final output. (Runtimes improve from having to be terminated after running for > 1 hour to less than a minute.)

Hope this helps.
C.

[talgalili]

If you would like to write a PR, I'd be happy to review it. Tal

…

On Tue, Oct 7, 2025 at 10:14 PM cdputnam ***@***.***> wrote: *cdputnam* left a comment (talgalili/gplots#2) <#2 (comment)> I've had the same problem where I don't want clustering/reordering of the input rows or columns. I can fix it by commenting out line 231 from the file heatmap.2.R: ddr <- as.dendrogram(hclust(dist(diag(nr)))) Having the ddr variable undefined doesn't appear to be a problem in the final output. (Runtimes improve from having to be terminated after running for > 1 hour to less than a minute.) Hope this helps. C. — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHOJBSOAA66LP742R6XJXD3WQGHZAVCNFSM6AAAAACIRPOYO2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTGNZYGM2TONRZGE> . You are receiving this because you commented.Message ID: ***@***.***>