heatmap function

[tram-nguyen-n]

Convert the ComplexHeatmap code to a function in the package. Allow users to select their given assay, and the start and end positions of the protein for plotting.

[lgeistlinger]

consider clustering of rows / amino acids by default to work out patterns of amino acid groups based on biochemical properties. this can be turned off by the user through the ... argument.

[lgeistlinger]

the interpretation of the heatmap / dms score needs some revisiting. higher dms score = higher dms fitness. ie lower dms score more likely to be pathogenic.

[tram-nguyen-n]

Additional modifications to heatmap function:

• Have function omit multiple mutations
• Reorder rows according to this: DEKRHNQSTPGAVILMCFYW

[tram-nguyen-n]

Write test cases for plot_dms_heatmap()

[tram-nguyen-n]

Allow user-specified DMS assay_name parameter and DMS list rather than ProteinGym default

[tram-nguyen-n]

• Update message on start / end position.
• More details about starting/end data points in function documentation
• exact_coordinates TRUE/FALSE

[tram-nguyen-n]

Color scale (maybe flip)

• Red = low DMS
• Blue = high DMS

[tram-nguyen-n]

Include reference AA on the x-axis. Following: https://pop.evemodel.org/protein/NP_570602-2

[tram-nguyen-n]

Allow side-by-side model prediction + DMS score heatmaps

[lgeistlinger]

Reference for DMS vs prediction heatmaps --> Fig3 in EVE paper: https://www.nature.com/articles/s41586-021-04043-8
We could do a side-by-side heatmap comparison (or top vs bottom)