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Views Types

Vitessce supports several view types for visualization of single-cell data, and several view types for updating visualization parameters. The view names found on this page are all valid values for the field layout[].component in the view config. On this page you will also find screenshots of each view.

scatterplot

The scatterplot view displays 2-dimensional (pre-computed) embeddings / projections (such as t-SNE or UMAP). Use with the embeddingType coordination type to specify which embedding to use when mapping cells onto scatterplot points. Use with datasets containing the cells data type. Optionally, the cell-sets and genes data types can be used for coloring cells on the plot.

Screenshot of Scatterplot View

heatmap

The heatmap view displays a (normalized) cell-by-gene (or gene-by-cell) matrix visualization. This view uses the expression-matrix data type, and optionally displays cell set color assignments if a file with the cell-sets data type is available in the same dataset. The heatmap can support very large matrices (~6,000 x ~9,000) when using Zarr-based file types (best performance can be acheived when arrays are saved with the type uint8).

Screenshot of Heatmap ViewScreenshot of Heatmap View

spatial

The spatial view is meant to display data with spatial coordinates, including spatially-resolved cell segmentations as polygons (from the cells data type) and molecule positions as points (from the molecules data type). The spatial view also includes a multiplexed and multi-scale image viewer (implemented with Viv). Image files can be defined with the raster data type. Cell segmentations can be colored by gene expression data through the expression-matrix data type or cell set color assignments through the cell-sets data type.

Screenshot of Spatial ViewScreenshot of Spatial View

layerController

The layer controller view provides an interface for manipulating the visualization layers displayed in the spatial view. The image layers are coordinated through the spatialImageLayer coordination type.

Screenshot of Layer Controller View

genomicProfiles

The genomic profiles view displays genome browser tracks (using the genomic-profiles data type) containing bar plots, where the genome is along the x-axis and the value at each genome position is encoded with a bar along the y-axis. Genome tracks may be colored by corresponding cell set color assignments if the cell-sets data type is available in the same dataset, coordinated on the cellSetSelection coordination type. This view was implemented with HiGlass.

Screenshot of Genomic Profiles View

genes

The genes view displays an interactive list of genes when used with datasets containing the expression-matrix data type.

Screenshot of Expression Levels View

cellSets

The cell sets view displays an interactive list of (potentially hierarchical) cell sets when used with datasets containing the cell-sets data type. This can be useful for managing cell sets representing clustering algorithm outputs or cell type annotations.

Screenshot of Cell Set Manager View

cellSetSizes

The cell set sizes view displays a bar plot with the currently-selected cell sets (using the cell-sets data type and cellSetSelection coordination type) on the x-axis and bars representing their size (by number of cells) on the y-axis. This view was implemented with Vega-Lite.

Screenshot of Cell Set Sizes View

description

The description view can be used to display text content. This may be useful for communicating the details of a dataset or a data analysis process. When the spatial view is used for visualization of imaging data, the description view also renders a dropdown containing image metadata.

Screenshot of Description View

status

The status view displays debugging messages, including app-wide error messages when datasets fail to load or when schemas fail to validate. Details about the entity under the mouse cursor (cell, gene, and/or molecule) are displayed during hover interactions.

Screenshot of Status View

cellSetExpression

The cell set expression view displays a violin plot with expression values for the selected gene, implemented with Vega-Lite.

Screenshot of Cell Set Expression View

expressionHistogram

The expression histogram view displays a bar plot with the distribution of expression values for the selected gene, implemented with Vega-Lite.

Screenshot of Expression Histogram View