It yields a scatter plot in png format, wherein cells are placed in space of reduced dimensionality and coloured by attribute of choice.
Requires calculating the specified embeddings first. For example, to make UMAP/TSNE plots, run Scanpy RunUMAP/Scanpy RunTSNE first, then enter "umap"/"tsne" as the name of the embedding to plot here.
More information can be found at https://scanpy.readthedocs.io
126.96.36.199+galaxy0: Upate to scanpy-scripts 1.1.1 build 1 (running scanpy ==1.8.1), including improved Scrublet integration with batch handling.
1.8.1+galaxy0: Upate to scanpy-scripts 1.0.1 (running scanpy ==1.8.1), including Scrublet integration.
1.7.2+galaxy0: Upate to scanpy-scripts 0.3.3 (running scanpy ==1.7.2) to incorporate fix for object output from PAGA plotting, to allow PAGA init of FDG.
1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/
1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca.
1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes.
1.4.3+galaxy10: Use profile 18.01 for modules.
1.4.3+galaxy6: Update to scanpy-scripts 0.2.8 (running scanpy ==1.4.3) and wider compatibility with other Galaxy modules. Bug fixes in filtering and plotting improvements.
1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).
1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).
1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.