easy-vitessce 0.0.1

A package to easily use Vitessce to create interactive plots for single-cell data

Easy Vitessce

🪄 Magic in a single line of code!

Turn your static Scanpy and SpatialData plots into interactive Vitessce visualizations with Easy Vitessce for spatial and single-cell data just by adding the easy_vitessce package!

Supported Plots

• UMAP
• PCA
• t-SNE
• Spatial (Scanpy version)
• Spatial (SpatialData version)
• Violin
• Dotplot
• Heatmap

Installation

Install package using pip:

pip install 'easy_vitessce @ git+https://github.com/luoselena/easy_vitessce@main'

How to Use

Importing Easy Vitessce

from easy_vitessce import configure_plots

🪄 All interactive plots are enabled magically.

Note that Scanpy is also required to run the package: import scanpy as sc

Supported Functions and Parameters

embedding:

basis: Plot type. "umap", "pca", or "tsne".

color: gene, e.g. "CD79A".

color_map: color map. "viridis", "plasma", or "jet".

spatial (Scanpy ver.):

color: annotations of observations, e.g. "log1p_n_genes_by_counts".

color_map: color map. "viridis", "plasma", or "jet".

Spatial (SpatialData ver.)

spatialdata_filepath: filepath of spatialdata zarr file containing image data.

zip_filepath: filepath of zip folder.

render_images(): renders image.

• element: image data location.

render_shapes(): renders shapes, e.g. spots.

• element: element to be rendered, e.g. "cells".
• color: gene.
• color_map: color map. "viridis", "plasma", or "jet".

render_labels(): renders labels.

• element: label data location.

show(): displays interactive plot.

violin:

markers: list of genes. groupby: observation grouping, e.g. "bulk_labels"

dotplot:

markers: list of genes, e.g. ['C1QA', 'PSAP', 'CD79A', 'CD79B', 'CST3', 'LYZ'].

groupby: observation grouping, e.g. "bulk_labels"

heatmap:

color_map: colormap. "viridis", "plasma", or "jet".

markers: list of genes.

groupby: observation grouping.

Deactivating Interactive Plots:

configure_plots(disable_plots = ["spatial", "violin"]

Reactivating Interactive Plots:

configure_plots(enable_plots = ["spatial", "violin"]