Thursday 23 August 2018

Cluster analyses - export coloured GeoTIFF of the map to match the tree branch colours

One of the features of Biodiverse that gets the most positive feedback is the ability to colour the branches of a cluster dendrogram and then have the map show the same colours.  This makes it very easy to see where a selected cluster is, and how the clusters map spatially,

Up until now, however, it has been difficult to replicate the display without resorting to screenshots and their attendant issues with resolution (and sometimes apparent JPEG compression).

While one has been able to export the colours with the tree since version 2 was released, there was no option to match the spatial data.  With the release of version 2.1, that is now an option for the Nexus tree exports - there is a new option to export a geotiff file with associated colourmaps that can be used in GIS software.

Some images will show it best.  Below are steps to export the data and then to display it in ArcMap or in QGIS.

Note that the process works for continuous as well as discrete colour schemes.  Whatever colours were last displayed are what will be used.

This is also the process used to generate Figure 6 in Link-PĂ©rez & Laffan (in press).

Exporting the data

An example cluster dendrogram with the associated spatial data.  It is easy to see the spatial distribution of the various clusters.  

The Nexus format is needed to export the coloured tree and geotiff, 

Be sure to select the geotiff option to get the spatial data.  If you want the tree colours as well then check that option too ("Export colours").

Displaying it in ArcMap

You need only add the raster to a data frame, as ArcMap looks for the colourmap automatically (as does ArcGIS Pro if you are using that).

ArcGIS will automatically see the colourmap file and display the colours as they were in Biodiverse.  

You can use FigTree to export the coloured tree to a PNG.  

...and display this tree in an ArcMap layout.  Note that the resolution can be an issue and you also have to convert the background to be white instead of transparent, but it often works well enough and images can be resampled to a higher resolution using most editing packages.  

Displaying it in QGIS

The QGIS process involves some manual loading of files via the layer properties dialogue.

In the Style section, set the Render type to be Singleband pseudocolor, then choose the folder icon to "load color map from file".  For a nexus file called example.nex, the colourmap file will be called example.nex.txt.   

And there it is, a display with the same colours as in Biodiverse.  

Shawn Laffan

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