The Spatial and Cluster tabs have a legend option to allow you to turn it on or off.
The View Labels tab currently switches between log and linear scaling depending on the maximum value and the maximum possible value. It will use log scaling when there are more than 20 labels to highlight or the the maximum value across highlighted cells is less than 0.8 times the number of selected labels. Otherwise it will use a linear scaling (so if there are 20 selected labels, but no cell contains more than 16 then it will log scale the display).
Here is a video to demonstrate the process. The first part shows a matrix visualisation of a Region Grower analysis (a simple pair-wise complementarity analysis, in this case using richness as the index). It is much easier to see the spatial patterns when the colour stretch is log scaled. The second shows a spatial analysis. In this case the log scaling does not make too much difference. The third shows the view labels tab. Note that the log scaling makes it much easier to see an entire clade on a tree, as previously the colours would have been washed out.
For more details about Biodiverse, see http://purl.org/biodiverse
For the full list of changes in the 1.99 series (leading to version 2) see https://purl.org/biodiverse/wiki/ReleaseNotes (for all issues addressed or being targeted to fix for version 2, see https://github.com/shawnlaffan/biodiverse/milestone/4 ).
To see what else Biodiverse has been used for, see https://purl.org/biodiverse/wiki/PublicationsList
You can also join the Biodiverse-users mailing list at http://groups.google.com/group/Biodiverse-users