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shawnlaffan / biodiverse

A tool for the spatial analysis of diversity
http://shawnlaffan.github.io/biodiverse/
GNU General Public License v3.0
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Visualisations - add tree panel to analysis output displays #409

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
The system currently only displays the selected tree in the View Labels tab.  

It would be useful to also display the tree in the analysis outputs.  That way 
one could, for example, interrogate the tree while also visualising the PD or 
PE results from a spatial analysis.  

The system should allow the user to choose between the currently selected tree, 
the tree used in the analysis, and possibly also any trees generated by the 
indices (e.g. the PE analyses use a trimmed tree).  The latter option will need 
indices objects to be retained as currently they are destroyed.  

Ideally the system should also be able to link indices back onto the tree.  For 
example, some list indices give values for each node in the tree.  The nodes 
could be coloured based on these values.

Original issue reported on code.google.com by shawnlaffan on 30 Oct 2013 at 11:12

GoogleCodeExporter commented 9 years ago

Original comment by shawnlaffan on 13 Nov 2013 at 4:47

GoogleCodeExporter commented 9 years ago 
This issue needs to wait for issue 353 to land on the trunk as otherwise any 
branch mergers will be messy.

Original comment by shawnlaffan on 18 Apr 2014 at 11:29

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2597.

Added display of tree to spatial analysis pane.  Hover on grid highlights nodes 
in tree, and hovering on tree highlights grid, tried to copy many of the 
functions seen in cluster/label panes.  Combo in toolbar allows selection 
between tree from spatial analysis or from project tree.

Original comment by anthony....@gmail.com on 30 Jul 2014 at 7:50

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2602.

Raise the highlighted paths above the greyed out paths.  This makes them more 
visible when the tree plots are very dense.

Original comment by shawnlaffan on 1 Aug 2014 at 1:36

GoogleCodeExporter commented 9 years ago 
Need to modify some of the changes in commit r3597.  The copy-paste from the 
cluster tab has overridden the list combobox to only display tree related 
options.  Need to reinstate the spatial output lists.

Original comment by shawnlaffan on 1 Aug 2014 at 1:42

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2603.

Clean up some tabs.

Original comment by shawnlaffan on 1 Aug 2014 at 1:47

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2610.

Disable the map list combo boxes controlled by the dendrogram.  These need to 
only be controlled by the spatial plot.

Original comment by shawnlaffan on 3 Aug 2014 at 12:15

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2611.

Disable the map list combo boxes controlled by the dendrogram.  These need to 
only be controlled by the spatial plot.  
(missed one file in previous commit).

Original comment by shawnlaffan on 3 Aug 2014 at 12:17

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2612.

Dendrogram hover function clears neighbour set 2 highlights from the grid.

Original comment by shawnlaffan on 3 Aug 2014 at 12:30

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2613.

Add necessary code to SpatialMatrix.pm.  We were getting crashes. 

SpatialMatrix.pm still needs hooks to define dendrogram behaviour when cells 
are hovered on.  

Also make the tree selection combo box a bit more self-documenting.  Possibly 
should change from a toolbar to a hbox so we can add more labels.

Original comment by shawnlaffan on 3 Aug 2014 at 1:35

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2614.

Spatial plots: Make the highlighting use all labels across both neighbour sets. 
 Need to interact with the neighbour highlighting to work with subsets.  
Spatial matrix plots highlight those from the selected group as well the 
hovered group.

Original comment by shawnlaffan on 3 Aug 2014 at 2:31

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2615.

Spatial plots now highlight paths on the tree as a function of the neighbour 
sets being plotted.

Original comment by shawnlaffan on 3 Aug 2014 at 2:40

GoogleCodeExporter commented 9 years ago 
The key remaining task for this issue (that I can think of) is to add the tree 
plotting options to the display menu on the left.  This can be pilfered from 
the clustering and labels tabs as needed.

Original comment by shawnlaffan on 3 Aug 2014 at 7:27

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2617.

Refresh the dendrogram when a spatial analysis completes and is displayed.

Original comment by shawnlaffan on 4 Aug 2014 at 2:42

GoogleCodeExporter commented 9 years ago 
A rethink on the remaining task in comment #13 :

It would be useful to add a combobox to choose whether to display by length, 
depth, or rescaled by the results of a selected cell.  This would allow 
rescaling by several of the phylogenetic list functions such as the PE weights.

A second combobox could be added to control colouring of the branches based on 
some other list.  This would need more infrastructure as it would be a separate 
colour scheme from the grid and thus a legend, colour settings and scalings 
etc.  

Both these points might be best placed in their own issues as they don't really 
block issue 353.

Original comment by shawnlaffan on 4 Aug 2014 at 2:47

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2625.

SpatialMatrix dendrograms:  use colours to differentiate the branches only in 
the index group (blue), only in the hovered group (red), and in both groups 
(black).  
Add capacity in the dendrogram highlight code to handle colours as arguments.  
Also raise the line to the top of the canvas in highlight_node.

Original comment by shawnlaffan on 5 Aug 2014 at 7:05

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2626.

Click on grid background clears the node highlights, both dendrogram and grid.

Original comment by shawnlaffan on 5 Aug 2014 at 10:48

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2627.

Add the branch colouring to the spatial output plots.  
Refactor the colouring code into its own sub and fix a colouring issue with the 
internal nodes (wrong colours were being used when shared and unique).

Original comment by shawnlaffan on 5 Aug 2014 at 11:32

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2629.

SpatialMatrix.pm now uses the correct colours for the branch highlighting 
(indexing was wrong previously).

Original comment by shawnlaffan on 6 Aug 2014 at 2:07

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2733.

Use a mid-blue in the tree highlighting in the Spatial and SpatialMatrix tabs.  
This is more easily differentiated from the black when there are few branches.

Original comment by shawnlaffan on 23 Aug 2014 at 11:07

GoogleCodeExporter commented 9 years ago

Original comment by shawnlaffan on 26 Aug 2014 at 5:50

GoogleCodeExporter commented 9 years ago

Original comment by shawnlaffan on 26 Aug 2014 at 5:52

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2802.

Change the colours again.  Still need to settle on a decent option.
Possibly we need to make the lines thicker when there are few branches for the 
given space.

Original comment by shawnlaffan on 13 Sep 2014 at 3:36

GoogleCodeExporter commented 9 years ago

Original comment by shawnlaffan on 13 Sep 2014 at 10:19

GoogleCodeExporter commented 9 years ago 
Main remaining items now are to:

1.  Add a 'no tree' option to the tree selector. This saves remembering to turn 
the project tree back on.  
2.  Making the analysis tree option insensitive when there is no such tree.

Original comment by shawnlaffan on 6 Oct 2014 at 9:45

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2903.

Add a "none" option to the dendrogram chooser.

Original comment by shawnlaffan on 11 Oct 2014 at 10:06

GoogleCodeExporter commented 9 years ago 
Remaining item is to desensitise or hide the analysis tree option when one is 
not available.  

Simplest approach might be to build the options in GUI::Tabs::Spatial rather 
than get them from the glade file.

Original comment by shawnlaffan on 12 Oct 2014 at 12:45

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2904.

Only show the analysis tree as an option when one is available.  This involved 
rebuilding the combobox entries whenever the analysis is run or updated, but 
this is a cheap operation.

Original comment by shawnlaffan on 12 Oct 2014 at 1:54

GoogleCodeExporter commented 9 years ago 
Mark as fixed

Original comment by shawnlaffan on 12 Oct 2014 at 1:54

GoogleCodeExporter commented 9 years ago 
Re-open  

Need to add an option to hide the tree pane, possibly by default if there is no 
available tree at the analysis or project level.

Original comment by shawnlaffan on 19 Oct 2014 at 11:04

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2930.

Add option to hide the tree pane altogether.  
Next is to hide it by default when there are no trees to plot (i.e. the project 
and analysis have no trees).

Original comment by shawnlaffan on 19 Oct 2014 at 11:40

GoogleCodeExporter commented 9 years ago 
This issue was updated by revision r2931.

Hide the tree panel when there are no trees available at the analysis or 
project level.

Original comment by shawnlaffan on 20 Oct 2014 at 12:55

GoogleCodeExporter commented 9 years ago 
Mark as fixed (again)

Original comment by shawnlaffan on 20 Oct 2014 at 3:01