(Oncoprint) generic assay color range from light to dark (except Treatment Response)

[dippindots]

Fix cBioPortal/cbioportal#7959

Describe changes proposed in this pull request:

• a generic assay track data color range from light to dark (except Treatment Response)

before:

after:

[pvannierop]

First, can you provide some rationale on why this is needed? Second, I remember long discussions on the colors used for treatment data (predecessor of generic assay data). If I recall well this related to another feature of generic assay data, the 'pivot threshold'. When provided, the pivot threshold represents an externally defined value that sets a color boundary. For treatment data the color would be dark red-light red-white-light blue-dark blue. So white color would represent the pivot threshold. In light of this I would recommend to expand your PR to handle this situation because there is more to it then simply changing the blue color gradient. This behavior can be activated by defining a pivot_threshold value in the meta file (see docs).

[dippindots]

Hi @pvannierop , thanks for the comment. The reason of this is because we noticed that when the pivot threshold is not specified or is not applicable, the color range is from dark to light which seems not a normal expression for low to high. And this is only affect the profile which don't specify pivot threshold. But I do noticed that for Treatment IC50 has been affected by this change, just curious that for this case (in the following screenshot), the range from 0 - 100 should use color from light to dark?

[pvannierop]

@alisman I see this has been merged. This issue is still under discussion here.