Linked table (DT) and plotly graph
Idea / use case
For exploration of marker genes for each cluster, a user often has a table containing those genes, with additional data like p-values, fold changes etc. It would be nice, if this table could be shown in the report as well (1), along with a reduced dimension view colored by gene expression (2). Additionally, if a user clicks on a row in the table, the dimension reduction plot is colored according to the selected genes expression.
Example
The table might look like this:
Gene | Cluster | p-value | FDR | logFC | Action |
---|---|---|---|---|---|
geneA | cluster1 | 0.001 | 0.01 | 2.05 | View |
geneB | cluster2 | 0.005 | 0.02 | 1.4 | View |
If the user now clicks on the View-Link, JavaScript is executed that triggers Plotly.update with the corresponding expression data.
Unsolved questions
- How can expression data be stored? Can it be transmitted via the link? Can it be baked into the plotly and simply switched to visible?
Intermediate goals
- Extend
i2dash
to include objects of type DT. - Create a new page, that links a DT with a dimension reduction plot.
- Create wrappers for
Seurat
andSingleCellExpression
objects.