I just reanalyzed a dataset that I had worked on with an older mothur version, and it seems the colors of the heatmaps are swiched. Red is less similar, and black more similar, the opposite of what my old files show. I can’t really think of a way this could be user error, or is it?
Thanks for bringing this to our attention. This is a bug in version 1.20 and 1.21. In version 1.20, we changed the output of mothur’s calculators to be distance instead of similarity values. This change reversed the colors outputted by the heatmap.sim command. This will be fixed in our next release.
It’s been a while since I used heatmaps, but was this bug ever fixed (or fixed and introduced again?) The current verison (1.24.1) still produces heatmaps that are colored the opposite of what would be expected from the summary.shared command values.
I don’t know if this has been discussed/fixed already, but I do seem to have the same problem.
That, or I’m interpreting the heatmaps or diversity indices the wrong way.
When I create a heatmap based on theta-Yue-Clayton looking for similarities between 6 samples, the similarity between e.g. sample F6 and F9 is shown as bright red, being between 0.8 and 1.0
When I perform the summary.shared command, using the same input file and the same calculator, the similarity between F6 and F9 turns out to be 0.04.
So, what does the heatmap.sim show? Distances or similarities?
ps: I have been using version 1.24.1 so far. edit: I just updated to 1.27.0 and the output remains the same
The heatmap command displays similarities, but the summary.shared command outputs distances. A distance of 0.04 would mean a similarity of 0.96, which should be bright red.