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maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
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If colors.tsv defined, anything not in colors.tsv defaulted to gray #104

Closed matthewspeir closed 5 years ago

matthewspeir commented 5 years ago

If I don't define a color for something in colors.tsv, why not just default to whatever coloring is used if colors.tsv isn't defined? Basically, I want to define colors for some fields, but not others.

maximilianh commented 5 years ago

good point... there are technical reasons for the current behavior but technical reasons are rarely good reasons...

On Thu, Apr 25, 2019 at 12:42 AM Matt Speir notifications@github.com wrote:

If I don't define a color for something in colors.tsv, why not just default to whatever coloring is used if colors.tsv isn't defined? Basically, I want to define colors for some fields, but not others.

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matthewspeir commented 5 years ago

Haha, makes sense.

My use case for this is the Mouse Gastrulation dataset: https://hgwdev.gi.ucsc.edu/~mspeir/cb_demo/?ds=mouse_gastrulation. I was able to extract celltype coloring from the metadata and I was able to use the OSX Color Meter tool to find the colors of metadata fields with few (<10) values (Stage, Theiler) on the website (https://marionilab.cruk.cam.ac.uk/MouseGastrulation2018/), but wasn't able to do anything for fields that didn't have colors in the metadata and didn't want to spend the time using the Color Meter for those fields with lots of values (cluster, cluster.theiler, etc). Because I couldn't get colors for these other fields, they now just default to gray.

maximilianh commented 5 years ago

OK, this should be done now, 0.5.17

matthewspeir commented 5 years ago

This is looking good. Thanks, Max!