Color customization in static tSNE/UMAP scatter plots

[carlocolantuoni]

Currently the display curator automatically chooses a dot size for static scatter plots based on the number of dots being plotted. this works well in most situations, but causes issues in some cases - the dots are so big they go off the plot when the number of dots is very small (10 or 20). On the other end of the things, when there are very many dots in a large scRNA-seq dataset, and with some of the new large spatial datasets, having the option to set or control the dot size would be very helpful.

similarly, the color scale is set automatically to the yellow-orange scale. could we incorporate the black-centered diverging color scale @adkinsrs developed for PCA projection as an option here? possibly along with other preset color scales from scanpy?

[carlocolantuoni]

sorry - looks like this can be combined with: https://github.com/IGS/gEAR/issues/618

[adkinsrs]

This will be done in the "ui-v2" branch

[adkinsrs]

I think the first step will be to add predefined color scales as choices. Then after that, I will focus on adding the special PCA color scale as an all-around option, though I'd rather not force two-way diverging colorscales on everything that chooses that option. Rather, I would make a "two-way" checkbox to let the user choose.

[carlocolantuoni]

Sounds good 👍

On Mon, Mar 11, 2024, 11:12 Shaun Adkins @.***> wrote:

I think the first step will be to add predefined color scales as choices. Then after that, I will focus on adding the special PCA color scale as an all-around option, though I'd rather not force two-way diverging colorscales on everything that chooses that option. Rather, I would make a "two-way" checkbox to let the user choose.

— Reply to this email directly, view it on GitHub https://github.com/IGS/gEAR/issues/668#issuecomment-1988675746, or unsubscribe https://github.com/notifications/unsubscribe-auth/AH7KC7TZLVOPBPAO4FOCJ5DYXXJWXAVCNFSM6AAAAABEPUVMD6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBYGY3TKNZUGY . You are receiving this because you authored the thread.Message ID: @.***>

[carlocolantuoni]

Ok

On Mon, Mar 11, 2024, 09:05 Shaun Adkins @.***> wrote:

This will be done in the "ui-v2" branch

— Reply to this email directly, view it on GitHub https://github.com/IGS/gEAR/issues/668#issuecomment-1988397590, or unsubscribe https://github.com/notifications/unsubscribe-auth/AH7KC7XMTZTFNAPNRTWK2Z3YXW23BAVCNFSM6AAAAABEPUVMD6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBYGM4TONJZGA . You are receiving this because you authored the thread.Message ID: @.***>

[adkinsrs]

Implemented and posted to nemo-devel. Do note that curation configuations are with respect to gene expression and while the configurations will be applied to the projections, PCAs will still implement their own two-way "unique" colorscale that will override the existing colorscale configuration.