What value is the scatterplot component using to determine colors of the points with color encoding set to "gene expression" and Zarr format used as input?

[mukundraj]

I am using an example where I converted a Seurat object to Zarr store (via anndata format) and added the path to the config.json file. This works but I'm not sure what value is Vitessce using to modulate the colors in the scatterplot component. In case of "genes.json" rather than Zarr format as input, this was more clear since the "genes.json" file had a number explicitly associated for each cell+gene pair.

Thanks you!

[keller-mark]

For Zarr store gene expression matrices, we normalize the matrix values between 0 and 255 (code here) so that the values can be passed to the GPU with only one byte each.

We have made some related issues #893 #844, feel free to comment on those if you have thoughts as well.

[mukundraj]

Thanks! Just a quick follow up - is there a recommended way to include the gene expression value [0,255] in popover over scatterplot on hovering over a cell marker/point for a selected gene (selected using genes component) ?

On docs pages, I only found a way to show "per-observation annotations" that have been assigned a separate key in the Zarr file (http://vitessce.io/docs/data-file-types/#anndata-cellszarr). This wouldn't allow for changing the popover info based on selected gene.