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nemoarchive / analytics

Repository for the NeMO Analytics project.
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cant display continuous/numeric sample metadata in colorized legend in static tsne/umap plots #148

Open carlocolantuoni opened 3 years ago

carlocolantuoni commented 3 years ago

it looks like all of my curated views using the static tsne option can no longer handle continuous variables for the colorized legend. i can get categoricals to work fine, but not anything numeric/continuous. this is odd because i had set up many curated views previously using numeric columns for coloring the legend, but none of them load anymore when looking at the profiles and i cant create new ones either - the little load symbol just keeps going as it tries to create the preview, but it never finishes.

shaun thinks "this may be because I added the ability to select the legend colors and legend order, which assumed the data was discrete."

(btw - adding that coloring and ordering of the legend would be great - sounds like you are in the middle of it becasue i dont see it in NeMO Analytics)

carlo

adkinsrs commented 3 years ago

@carlocolantuoni can you link a URL of an example dataset with a numerical legend so I can poke around?

(btw - adding that coloring and ordering of the legend would be great - sounds like you are in the middle of it becasue i dont see it in NeMO Analytics)

This should be finished and merged. Coloring happens if there is a column of hexcodes named "{group}_colors" in the observation table (substitute {group} with legend group name). Ordering happens if both split_plot_groups and colorize_legend_by have dropdown values selected in the dataset curator.

carlocolantuoni commented 3 years ago

this is one that had a numeric colored legend that stopped working some time ago: https://nemoanalytics.org/dataset_curator.html#/dataset/f265f0cf-c975-498a-864a-17b4ec514720/displays

in case i cpoied the wrong URL, the datasest titel is: " Embryonic stem cell neural differentiation scRNAseq (Yao et al. 2017 Cell Stem Cell) "

carlocolantuoni commented 3 years ago

hey guys, i still cant display continuous variables as color in the colorized legend of static tsne/umap plots - am i missing something, or can we fix this?

adkinsrs commented 3 years ago

Currently the static plots only supports a categorical variable in the colorized legend. I believe Scanpy does not allow for continuous variable for colorized legends. If you wish to do this, I would recommend making a dynamic tsne/umap plot

carlocolantuoni commented 3 years ago

ok, thanks, but this is odd as i used to have several of these type of plots working in the static tSNE visualizations. i think this is functionality worth having in the static tSNEs, so maybe i'll bring it up in a planning meeting thanks shaun

On Fri, Aug 20, 2021 at 8:17 AM Shaun Adkins @.***> wrote:

Currently the static plots only supports a categorical variable in the colorized legend. I believe Scanpy does not allow for continuous variable for colorized legends. If you wish to do this, I would recommend making a dynamic tsne/umap plot

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-- Carlo