Scanpy PlotEmbed (version 1.9.3+galaxy0)

Input object in AnnData/Loom format:

Format of input object:

name of the embedding to plot:

color by attributes, comma separated texts:

Key for categorical in `.obs`:

You can pass your predefined groups by choosing any categorical annotation of observations.

Field for gene symbols:

The field used in the AnnData object to store gene symbols, leave blank for the default (index), else a common value is 'gene_symbols'

Use raw attributes:

Using this option means that scanpy will expect to find the raw data object. The job will fail if the raw data object is not present within the supplied AnnData file.

Name of the AnnData object layer to plot:

By default adata.raw.X is plotted. If use_raw=False is set, then adata.X is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over use_raw.

Where to look for neighbors connectivities.:

If not specified, this looks in .obsp[‘connectivities’] for connectivities (default storage place for pp.neighbors). If specified, this looks .obsp[.uns[neighbors_key][‘connectivities_key’]] for connectivities.

Location of legend:

Legend font size:

Point size:

Automatically determined if not specified.

Show edges?:

Width of edges:

Color of edges:

Plot in order?:

For continuous annotations used as 'color parameter, plot data points with higher values on top of others.

Components to plot:

Comma-separated list, e.g. '1,2', '2,3'. To plot all available components use 'all'.

Plot projection:

Figure title:

Figure size as 'width,height', e.g, '7,7':

Figure dpi:

Figure font size:

Show plot frame:

Plot embeddings of a given method of dimensionality reduction

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

Version history 1.9.301+galaxy0: Moves to Scanpy 1.9.3

1.8.1+galaxy9: Fixes version label to get versions sorted properly on Galaxy (equivalent to 1.8.1+3+galaxy0). In addition, adds ability to make fields unique in AnnData operations, adds additional handler on Scrubblet for workflows convenience, enables Scanpy tools to avoid outputing AnnData/matrix files when not required.

1.8.1+3+galaxy0: Upate to scanpy-scripts 1.1.3 (running scanpy ==1.8.1), including a fix to MTX output and a bugfix for the Scrublet wrapper.

1.8.1+2+galaxy0: Upate to scanpy-scripts 1.1.2 (running scanpy ==1.8.1), including improved boolean handling for mito etc.

1.8.1+1+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.

1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.