easy_vitessce package

easy_vitessce package#

Submodules#

easy_vitessce.VitessceSpatialData module#

class easy_vitessce.VitessceSpatialData.VitessceSpatialData(sdata)[source]#

Bases: object

A class for configuring spatial plot with similar syntax to spatialdata from scverse.

render_images(element='', **kwargs)[source]#

Renders image.

Parameters:

element (str) – location of image data inside “images” folder.

Returns:

Self, allows for chaining.

render_labels(element='', **kwargs)[source]#

Renders label data.

Parameters:

element (str) – location of label data in “labels” folder.

Returns:

Self, allows for chaining.

render_points(element='', **kwargs)[source]#

Renders points.

Parameters:

element (str) – location of point data in “points” folder.

Returns:

Self, allows for chaining.

render_shapes(element='', **kwargs)[source]#

Renders shapes, e.g. “cells”.

Parameters:

  • element (str) – location of shape data inside “shapes” folder.

  • color (str) – gene.

  • color_map (str) – color map (viridis, plasma, jet).

Returns:

Self, allows for chaining.

show(**kwargs)[source]#

Displays spatial plot.

Returns:

Vitessce widget.

easy_vitessce.configuring_plots module#

easy_vitessce.configuring_plots.configure_plots(disable_plots=[], enable_plots=[])[source]#

Deactivates and reactivates interactive Vitessce plots.

Parameters:

  • disable_plots (list) – List of plots.

  • enable_plots (list) – List of plots.

easy_vitessce.configuring_plots.dotplot(adata, groupby, **kwargs)[source]#

Creates interactive dotplot.

Parameters:

  • adata (AnnData) – AnnData object.

  • groupby (str) – Category group.

  • markers (list[str]) – List of genes.

Returns:

Vitessce widget. Documentation can be found here.

easy_vitessce.configuring_plots.embedding(adata, basis, **kwargs)[source]#

Creates interactive versions of UMAP, PCA, t-SNE plots.

Parameters:

  • adata (AnnData) – AnnData object.

  • basis (str) – Name of plot (umap, pca, or tsne).

  • color (str) – Gene.

  • color_map (str) – Color map (viridis, plasma, jet). Defaults to viridis.

  • size ((float or int)) – Size of dots.

  • include_gene_list (bool) – If a list of genes is passed in, True will add a gene list for the last plot. False by default.

Returns:

Vitessce widget. Documentation can be found here.

easy_vitessce.configuring_plots.heatmap(adata, **kwargs)[source]#

Creates interactive heatmap.

Parameters:

  • adata (AnnData) – AnnData object.

  • groupby (str) – Category group.

  • markers (list[str]) – List of genes.

  • color_map (str) – Color map (viridis, plasma, jet). Defaults to viridis.

Returns:

Vitessce widget. Documentation can be found here.

easy_vitessce.configuring_plots.spatial(adata, **kwargs)[source]#

Creates interactive spatial plot. Similar syntax to Scanpy’s spatial plot.

Parameters:

  • adata (AnnData) – AnnData object.

  • color (str) – Gene.

  • color_map (str) – Color map (viridis, plasma, jet). Defaults to viridis.

Returns:

Vitessce widget. Documentation can be found here.

easy_vitessce.configuring_plots.violin(adata, groupby, **kwargs)[source]#

Creates interactive violin plot.

Parameters:

  • adata (Anndata) – AnnData object.

  • groupby (str) – Category group.

  • markers (list[str]) – Genes.

Returns:

Vitessce widget. Documentation can be found here.

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