iSEE/interactiveSummarizedExperimentExplorer

Overview

The iSEE package aims to provide an interactive user interface for exploring data in objects derived from the SummarizedExperiment class. Particular focus will be given to single-cell data in the SingleCellExperiment derived class. The interface will be implemented with RStudio's Shiny, with a multi-tab setup for ease of navigation.

This initiative was proposed at the European Bioconductor Meeting in Cambridge, 2017. Current contributors include:

• Charlotte Soneson
• Aaron Lun
• Federico Marini
• Kevin Rue-Albrecht

Cell-based visualizations

The interface is proposed to contain the following features in its first iteration:

:white_check_mark: multiple interactive scatter plots with selectable points

:white_check_mark: colouring of samples by metadata or expression values

dynamic updating of cell-level metadata on hover/click

:white_check_mark: zooming in to a particular subregion of the plot, if requested

:white_check_mark: scatter plots can be generated from reduced dimensionality data, or with biaxial plots of existing metadata columns.

Gene-based visualization

The interface is proposed to contain the following features in its first iteration:

:white_check_mark: boxplots of expression values for a single gene, stratified by metadata level

heatmaps of multiple genes for groups of cells or for individual ordered cells

:white_check_mark: integrated brushing in cell-based scatter plots with cell identities in gene-level plots

Miscellaneous

:white_check_mark: The interface will contain a continually updated R interface that provides the R code corresponding to each user interaction. This can be copy-pasted into R scripts for batch generation of figures.