Tuesday 19 September 2017

Visualise spatial analysis results on the tree

Many of the indices in Biodiverse allow users to see what the relative contribution of branches on the tree are to one or more indices.  For example, one can see what the weighted branch lengths are in a phylogenetic endemism analysis, or see what the relative loss of phylogenetic diversity would be if a branch was lost from a sample.

Previously the only way to inspect these was to use a popup window by control-clicking on a cell.  This is useful, but rapidly becomes difficult when there are many cells to explore.

In version 2 of Biodiverse, users can now visualise these values on the tree as the mouse is hovered over cells.

This builds on the turnover displays that were added a while ago.

Rather than a long blog post, it is probably best to simply show a video.  In this example, a set of indices are calculated for the Acacia data set described in several publications (see the full list here and search for Acacia).

Note how the display is log scaled by default, but linear scaling can be used if preferred.  The default colour scheme uses the rainbow-ish default, as in the map display, but other schemes can also be used.  Users can also hide the legend if it gets in the way.

Shawn Laffan

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

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