Tuesday 13 September 2016

New selection tool in Cluster analysis tab

A new feature just added to the Biodiverse cluster analysis tab is the ability to control the colour of branches on the tree and the cells that contain them.  This is perhaps most useful if you want to colour your Biodiverse plot to match some pre-existing map (and is the reason some users requested it).

[[ UPDATE 21-Aug-2017.  This feature has been renamed as User defined in the GUI, so wherever you see Multiselect below, you will now see User defined.  ]]

In a nutshell, users can now switch to the Multiselect mode using the combo box where the lists are selected (and the default is still Cluster).  Once there they can choose a colour or accept the system generated default, click on a branch and watch the branch and all of its descendants and the associated groups (cells) plot in that colour.

The multiselect mode is turned on by selecting it in the lower left combo box.  

Users can assign colours to any branch in the tree to colour its descendants and the associated groups. In this example the red clade has also had a sub-clade cleared of colour (note the black branches and the highlighted cells that are not coloured).

Once the branch is selected the default colour changes to the next colour in the palette (unless you turn it off using the button to the left of the brush).  Repeatedly clicking on the branch will cycle through the palette, so if you missed the colour then just keep clicking until it goes around.  The palette in use at the moment has nine colours (it is the 9-colour paired palette from http://colorbrewer2.org).

You can also uncolour branches by selecting the brush icon to change to clear mode.  When in this mode, the mouse icon will change to a brush when a branch is hovered over to remind users what will happen when they click.

There is also little need to fear mis-clicks, as users can undo and redo selections.  Simply press the "u" key on the keyboard to undo one click, and repeat to keep going back.  If you over-do it then you can press "r" to redo and reinstate a branch colour.  Note that the redo list is reset as soon as you colour a branch.

The colour selection uses the same colour selector window as for the shapefile overlays and cell outline colours.

The colour selector can be used to specify your own colours.

Unfortunately the eyedropper selector does not work well on Windows, as it can only select colours from open Biodiverse windows.  This is a limitation of the system.  The workaround is to use a colour selector tool to copy the colour specification to the clipboard and then paste it into the Color name box in the selector window.   A list of possible tools is in this superuser.com question (with the caveat that I have not tested any).

You can also type colour names into the Color name box, and the small sample I tested of the colours at these URLs worked (mostly).  DarkGoldenRod or LemonChiffon anyone?

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 

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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