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 is implemented with RStudio's Shiny, with a multi-panel 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
The interface is proposed to contain the following features in its first iteration:
✅ multiple interactive scatter plots with selectable points
✅ colouring of samples by metadata or expression values
dynamic updating of cell-level metadata on hover/click
✅ zooming in to a particular subregion of the plot, if requested
✅ scatter plots can be generated from reduced dimensionality data, or with biaxial plots of existing metadata columns.
The interface is proposed to contain the following features in its first iteration:
✅ 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
✅ integrated brushing in cell-based scatter plots with cell identities in gene-level plots
✅ 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.