scanpy_pbmc3k
Attributes
Functions
This is (will be) an example of how to build a set of views that are relevant to the given data... |
Module Contents
- scanpy_pbmc3k.setup_views()[source]
This is (will be) an example of how to build a set of views that are relevant to the given data… We could go into a bit of introspection on the project datasources & grouping columns based on what we can infer from names like “X_umap_1” “X_umap_2” being suited to making a 2D scatterplot… i.e. parse the ‘cells’ datasource columns & make charts for - 2D UMAP - 2D tsne - 3D pca All of those should be coloured by ‘louvain’ which we know from experience will show the clusters. The tooltip could be ‘cell_id’ so that the user can explore how particular gene sequences are distributed in those clusters. A table chart alongside that (perhaps not including the UMAP/tsne/PCA columns) can allow the user to see which values are represented as they interactively explore the data. This ‘view’ might only include ‘cells’.
There is also a ‘link’ in the project, which means that charts can be created dynamically in ‘cells’ based on interactions with ‘genes’. Some of the UX in this area, as well as the APIs, are subject to review in the near-term… but a second ‘view’ could be programmatically added with (for example) an empty ‘cells’ and a 3D scatterplot of ‘PCs’ & table in ‘genes’. Then the ‘+’ icon (‘Add Gene Expr’) in the ‘cells’ toolbar can be used by the user at runtime to populate ‘cells’ with charts corresponding to selections made in ‘genes’.