Project Minimum Viable Product Brief

[ljjh20]

A list of features already implemented and all those still required to deliver a viable tool.

[ljjh20]

Under the hood and smaller scope

• [x] Display UMAP data from csv as a scatter plot in three dimensions
• [x] Encode cell type as color of points
• [x] Encode Gene expression as color of points
• [x] Be able to switch between different genes
• [x] Encode expression of 3 genes as stretch in x,y,z of points (ellipsoids)
• [x] Add text labels to cell types
• [x] Allow user to expand and contract scale of the scene for their viewing convenience
• [x] Load cells as instances to improve performance
• [x] Allow loading of different datasets, given they follow a certain flexible structure
• [x] Allow color marking and deletion of points with laser pointers from controllers
• [x] Update instances on button press only, running on version of scenery with per frame instance updating turned off
• [x] update TSNEVisualization to work with multiple master instances

[ljjh20]

• [ ] 7: Implement analytical features of CellxGene

• [ ] (lasso?) cell selection (currently with laser) - bubble selection with expandable translucent sphere?

• [ ] see top 10 deferentially expressed genes from selection

• [ ] Clip all continuous values to percentile range (clip color encoding if gene expression is outside of a given percentile range - see website)

• [ ] 2D bar graph representation of gene (see website). n_genes vs n_cells, n_counts vs n_cells. Tracks changes to parameters and data. Could be on far wall.

[ljjh20]

• Texboards appear when close
• reimplement "selected" metadata
• reimplement deleted cells