Visualizations overview

Many interactive visualizations are available in Single Cell Portal. They are automatically generated when the appropriate data is uploaded to the portal.

Scatter plots (e.g. PCA, t-SNE, UMAP) (Details)

Visualization used to show (at a high level) cells that are related. Clusters of cells are often of interest. These (scatter) plots are available in either 2 or 3 dimensions. Correlation plots and spatial plots are  also available.

Violin plots (Details)

Plotted to show a gene / isoform's expression over groups of cells (or other labels provided by study creators). Violin plots tend to work better than boxplots given the zero-inflated or multimodal nature of the data.

Dot plots (Details)

Often used when visualizing multiple genes / isoforms over groups of cells (or other labels provided by the study creators). These plots show both the magnitude of expression (eg. average expression over the group) and prevalence (eg. the proportion of cells expressing the gene / isoform) of the gene's activity. These summaries combined help give an overview of sparse measurements as often found in single-cell transcriptomics.

Heat maps (Details)

This visualization is used in many fields that leverage multivariate statistics and is commonly used in computational biology. In the portal, this visualization shows the gene/isoform expression of multiple genes in individual cells. This visualization is used as a higher resolution representation of portal dot plots.

Ideograms (Details)

This visualization enables one to view gene expression organized by genomic region. Specifically, average gene expression is shown along chromosomes and stratified by cell groups (or other labels provided by study creators).

Genome browser (IGV) (Details)

Sequence data provided in BAMs can be explored in genome browsers in the portal. This allows read-level data to be viewed and explored.