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Vitessce is a visual integration tool for exploration of spatial single-cell experiments. To learn more about the features of Vitessce, please visit our core docs.

Getting Started

The vitessceR package includes:

  • Vitessce as an htmlwidget

    • Use Vitessce directly within RStudio as an interactive widget

  • View config API

    • Create and edit Vitessce configurations using R6 object-oriented syntax

  • Data preparation

    • Use data conversion functions from the vitessceAnalysisR package to process data stored in common single-cell data structures including Seurat objects.

Installation

Installation requires R 4.0.0 or greater.

install.packages("devtools")
devtools::install_github("vitessce/vitessceR")

Examples

The simplest way to instantiate a Vitessce widget is to create a view config based on a single-cell dataset object and call the widget function on the view config instance:

library(vitessceR)

# Create Vitessce view config
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
dataset <- vc$add_dataset("My dataset")
scatterplot <- vc$add_view(dataset, Component$SCATTERPLOT, mapping = "pca")
status <- vc$add_view(dataset, Component$STATUS)
cell_sets <- vc$add_view(dataset, Component$OBS_SETS)
vc$layout(hconcat(scatterplot, vconcat(status, cell_sets)))

# Render the Vitessce widget
vc$widget()

For a full example, visit the Usage with JSON page.

To customize the view config passed into the widget (or to define a view config manually), please see the documentation for the VitessceConfig class.