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IGS / gEAR

The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
https://umgear.org
GNU Affero General Public License v3.0
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Spatial data plot visualization requirements #913

Open adkinsrs opened 2 days ago

adkinsrs commented 2 days ago
  1. spatial image
  2. UMAP and violin plots
  3. Focus on smaller region
  4. ProjectR integration
    1. This leads to visualizing cell types.

This is a list in flux

adkinsrs commented 2 days ago

Potentially 3-4 panel plot

adkinsrs commented 2 days ago

Opened branch "feature-spatial-visualization" to address this

adkinsrs commented 1 day ago

image

First pass at a 4-panel plot using a selection of genes. This was made in a Jupyter notebook, hence the dark theming. I used a combination of scanpy and matplotlib to make this. Note I removed the colorbar from the stacked violin plot because the scanpy people removed the colorbar with their own horizontal "legend" object, and I could not create a vertical colorbar using their StackedViolin figure object.

adkinsrs commented 1 day ago

Notebook found at 809996e