Make a mutation score heatmap GUI

[Tom Goddard]

None of the current mutation score tools (scatter plot, histogram, color structures) give a view of all the different scores. Would be nice to have an interactive heatmap showing all the mutation scores that interacts with associated structures.

[Tom Goddard]

A basic heatmap mutation score GUI is available using command "mutationscores heatmap". There are still many features and command options to be added. Once it is more functional I plan to make opening a mutation score .csv file bring up an initial tool panel with buttons for heatmap, scatter-plot, histogram, structure coloring, and a list of currently open mutation sets.

[Tom Goddard]

I added an Options button to the heatmap gui with options to choose the colormap and to show unnormalized mutation scores.

[Tom Goddard]

Added options panel controls to choose mutation set, specify score names to include, highlight mutations with structure residues (formerly was in context menu), subtract fit. Three different colormaps are used for normalized, unnormalized, and unnormalized fit subtracted scores.

[Tom Goddard]

Made several heatmap improvements:
Added zoom factor (pixels per cell).
Made save image include all of heatmap and axes.
Allowed mouse hover to color structure residues.
Added drag box coloring of associated residues.
Added amino acid order to options panel.
Added option to group heatmap by amino acid or score name on vertical axis.

[Tom Goddard]

Here are features I plan on implementing in the next few days or week.

Show only selected residues in heatmap.
Show heatmap x-axis labels of residue amino acid and number in vertical text.
Save heatmaps in sessions.
Be able to set all heatmap options by command.

Some other possibilities are:

Allow naming heatmaps which will remember all the settings.
Show computed residue scores in heatmap instead of per-mutation scores.
Allow coloring structures based on mutation scores for selected rectangles on heatmap.

[Tom Goddard]

Added button under Options to show only selected residues in heatmap.
Also added checkbutton to show vertical residue labels on x axis for every residue.

[Tom Goddard]

Example showing boxes dragged on heatmap to color structure residues.

[Tom Goddard]

Example showing heatmap with only selected subset of residues.

[Tom Goddard]

Added session saving for heatmaps.
Fixed heatmap normalization error when there are no synonymous scores.
Made heatmap color missing scores in a distinct color, default black.
Added options to mutationscores heatmap command for all heatmap settings.
Heatmap windows have names (by default 1, 2, 3, ...) and the heatmap command can change the settings for an existing heatmap window.

[Tom Goddard]

Added options to the "mutationscores heatmap" command for all the heatmap settings.
Automatically scale axis labels so they don't overlap each other.
Made structure amino acid sequence on x-axis show in horizontal text instead of vertical text when every residue shown.
Renamed "Pixels per cell" to "Zoom factor".
Added score names Choose button that shows a panel of checkbuttons for all score names.

[Tom Goddard]

A few more suggestions from Willow today, not yet implemented.

1) Put the heatmap x and y axis labels in separate panels so they don't disappear when scrolling the heatmap.

2) Could make horizontal divider lines between groups thicker (e.g. two cells instead of 1). Maybe instead drawing the spacers as white and adding a gray 1 pixel thick line would look sharper.

3) If two or more contiguous residue ranges shown might want vertical divider lines. Not sure how one would control this. The lines are probably not wanted if showing say selected residues in a binding site. Could have a checkbutton and the user decides whether to show a vertical divider at every non-contiguous residue jump.

[Tom Goddard]

Willow suggests:

4) Potentially when selecting regions of the heatmap it would make sense for those residues to be selected in the structures not just recolored which would allow showing the residue atoms or something else.

[Tom Goddard]

Made default heatmap zoom factor 2.
Made default grouping by score instead of by amino acid if there is more than 1 score.
Made the heatmap axis labels stay not scroll out of view.