UI components for single-cell

Single-cell data will require additional UI components for visualizing. In many cases, we can repurpose the components we have by adding some capabilities. In other cases, we will need brand new tabs or endpoints.

single-cell exploration (navigate
cell type assignments view
single-cell QC
sub-biomaterial view
subset view (see #1182)

Single-cell exploration

links for navigating to cell type subsets

Having subset navigation is also something we currently lack for regular bulk datasets.

Single-cell assignments

visualize specific cell-type assignments (preferred by default)
display the protocol for cell-typing

Single cell QC

Include single-cell specific diagnostics in the "Diagnostics" tab of an EE.

Sub-biomaterial View

In the /bioMaterial/showBioMaterial.html endpoint, include a table of sub-biomaterials derived from the sample with their specific characteristics and factor values.

Also include characteristics and factor values inherited from source biomaterials.

Subset View

Single-cell datasets are represented using EE subsets where the bioassays are attached to sub-biomaterials (each one representing a cell population of a given type from a parent subject).

For existing Gemma subsets, this would be a good addition to see specific slices of a dataset.

It appears that /expressionExperiment/showExpressionExperiment.html is meant to support viewing subsets, although it seems to be broken right now.

There's also /expressionExperiment/showExpressionExperimentSubSet.html that can be used for this purpose.

I think we need to explore the possibility of using GemBrow's or Vue.js for developing any new components for viewing the single-cell aspect of a dataset. There might even be a way of nesting a Vue.js component within our Ext.js app.

PavlidisLab / Gemma