How to modify colormaps or use custom colormaps?

[mukundraj]

Is there a way to modify a colormap available in Vitessce or add custom colormaps? E.g. to always map zero value to a predefined color. Thanks!

[ilan-gold]

Currently, no, unfortunately not - the 6 (or 8, can't remember) colors for imaging channels are fixed and the additive colormaps are from a shader library. What did you have in mind that we don't have?

[mukundraj]

This was for having the zero value mapped to a shade of gray for all colormaps.

[ilan-gold]

Sorry, the answer is the same. The maps are fixed, certainly how the colors scale to zero are for now - we could implement a color picker in theory but that would only provide a linear scale, not one in which the zero value is fixed to a non-black color like you are asking for.

[qu4drupole]

Is it still impossible to add custom colormaps?

Can use custom colors for cell sets?

[keller-mark]

It is possible to define custom colors for cell/observation sets.

For cell sets, the obsSetColor coordination type can be set to an array:

 [
  {
    "path": ["Cell Type", "B cell"],
    "color": [255, 0, 0]
  },
  {
    "path": ["Cell Type", "T cell"],
    "color": [0, 255, 0]
  },
  {
    "path": ["Cell Type", "Neuron"],
    "color": [128, 255, 0]
  }
]

[qu4drupole]

Ah, I was so close, but didn't think to specify the path like that. Thank you!