Biodiverse has always had the capacity to display a
phylogeny at the same time as one views the spatial data. In version 1 it now has the capacity to
display a tree at the same time as a spatial analysis.
Now when you run an analysis using a tree you can display
the results and more easily see which branches of the tree contributed to the
answer at that cell. If your analysis
did not use the tree then you can still see which branches occur in a cell
(group) and its neighbourhood.
The screenshot below is the example data distributed with Biodiverse,
analysed using one cell radius neighbourhood to calculate the PhyloSørenson index
of turnover between the branches in the central group (cell) and each group within
a one cell radius. Branches plotted in
blue are found only in the central group (neighbour set 1, and the blue should probably be darker), those in red are
found only in the neighbouring groups (neighbour set 2), while those in black are
found in both neighbour sets. Any branch
not found in the neighbourhood is in grey to reduce its visual impact without
hiding it.
As with the View Labels plots which have been in Biodiverse since the beginning, the branch highlighting updates as you hover the mouse over the map.
As with the View Labels plots which have been in Biodiverse since the beginning, the branch highlighting updates as you hover the mouse over the map.
The new tree plot is not restricted to the spatial
analyses. You can also visualise
matrices in the same way. The next
screenshot is the PhyloSørenson turnover surface for an index group plotted in
grey (see Laffan 2011 for more details about how this process works and is
interactive). Now the branches highlighted
are those in the index cell relative to a set in the cell that was hovered over
when the screenshot was taken (perhaps we need to highlight that in a future
version). The interpretation is otherwise
the same as the previous plot – blue branches are unique to the index group, red are unique to the neighbour group, and black are shared.
The other good news here is that you are not restricted to
using only the tree used in the analysis.
Using the chooser at the bottom of the window you can select from the
analysis tree, the currently selected project tree, or no tree at all. As of version 0.99_005 you can also hide the
panel if it gets in the way.
We don’t yet plot extra trees in the cluster plots, but if
there is sufficient need then we could be convinced to implement it.
The tree plotting is still a work-in-progress, for example
the blue could be darker, but you can try it now using the development version
of the software. https://purl.org/biodiverse/wiki/Downloads
Current users of Biodiverse will also note that the display
layout has changed. That will be the
topic of another post.
For more details about Biodiverse, see http://purl.org/biodiverse
For the full list of changes in the 0.99 series (leading to
version 1) see https://purl.org/biodiverse/wiki/ReleaseNotes
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
Shawn Laffan
24-Oct-2014
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