What relativization is used in heatmap.bin?

Hi mothur-users,

A question about the heatmap - are the OTUs in each group relativized to the total # of OTUs in that group (a) or the maximum abundance in that group (b)?

A simplified example to make things clearer: --The group of interest has 100 sequences --OTU Z has the highest abundance with 20 sequences --All other OTUs have only 1 sequence Is the relativization for OTU Z: 20/100=0.2 (a) or 20/20=1 (b)? Is the relativization for all the other OTUs: 1/100=0.01 (a) or 1/20=0.05 (b)?

Is there any way to manipulate the relativization? If not, can that be added in the future?


Mothur finds the maximum relative abundance, in the case above 20/100 = .2.

Then scales the relative abundance for each otu, relAbund / maxRelAbund.
so OTU Z = .2 / .2 = 1.
if OTU Y’s abundance is 5, then (5/100) / .2 = .25

OTU Y would have 25% the color intensity of OTU Z.

The only thing that makes it slightly more complicated is the scale parameter. By default scale=log10, meaning log10(relAbund) / log10(maxRelAbund). You can set the scale parameter to linear, giving you relAbund / maxRelAbund, or log2 giving you log2(relAbund) / log2(maxRelAbund).

Thanks! That was very helpful.