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10XGenomics / loupeR

Convert Seurat objects to 10x Genomics Loupe files.
https://10xgen.com/louper
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Expression Distribution (Violin plots) remains empty #45

Open kloot opened 5 months ago

kloot commented 5 months ago

Hi,

Thanks for making this tool available - most parts work on first attempt ;-) However, the 'Expression Distribution' panel remains empty. Only horizontal gridlines and y-axis labels are visible, even if I choose highly expressed genes/features. The 'Differential Expression Output' panel shows gene names in both the Feature Table and the Heatmap, indicating that Loupe has recognised the gene symbols/names

Is this 'expected behaviour'?

gmjoseph commented 4 months ago

👋 Thanks for raising this issue. Let me look into reproducing it on our end and I can get back to you as to whether it's a bug that we'll fix or whether it's working as intended.

esiegel commented 2 months ago

Are you still having this issue?

Is it possible that you have deselected all of the clusters? Besides doing this I'm unable to reproduce.

A couple of questions:

  1. What platform are you on (windows/mac)?
  2. What version of Loupe

Here are some pictures. The first shows the expression distribution plot working when all clusters are enabled, and the second shows an empty screen when all clusters are disabled.

image image

Tanyazwantig commented 1 month ago

Hi, this tool makes ScRNA visualization super easy for me . I know violin plots can be exported as SVG or PNG. Due to clustered y-axis, I would like to export the metadata/values as csv and replot in R. Is this possible? Thanks.