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fungenomics / braindex

A web portal for exploring scRNAseq data in the developing brain, including our in-house atlas of the E10-P6 forebrain and brainstem
http://cc-shiny-01.functionalgenomics.ca/braindex/clusters/
GNU General Public License v3.0
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For 2D gene plotting, fix the case when a gene has 0 expression in all samples in one region #35

Open sjessa opened 3 years ago

sjessa commented 3 years ago

Ideally we could display an error, but otherwise we could display the plots with all 0 values, as we do in the case where only one sample has 0 expression across all cells?

In this case, the error shows up for forebrain, but not for pons:

image
bhavyaac commented 3 years ago

I plan to display a descriptive error message using validate() -"This gene has no detected expression in the selected brain region". I will display it in place of the expression-related dimensionality reduction plots & violin plots (Single cell expression by region & by sample tabs) as well as in the timecourse plot (which also displays an error in this case - see below).

Screen Shot 2021-06-28 at 11 12 17 AM
bhavyaac commented 3 years ago

Previews for dimensionality reduction plots and violin plots:

Screen Shot 2021-06-28 at 11 46 02 AM Screen Shot 2021-06-28 at 11 46 14 AM Screen Shot 2021-06-28 at 11 46 58 AM
sjessa commented 3 years ago

@bhavyaac I think that looks great! That validate() function looks like it will be super handy!

bhavyaac commented 3 years ago

Update: tested this in the server and it doesn't work currently, I'll have to do some more adjustments & try to test locally to get it working!