Gene expression page with linked charts

Idea / Use case

Users often wish to visualize expression of certain genes on a reduced dimension. The idea is to present a certain reduced dimension (e.g. obtained by PCA, t-SNE or UMAP) side-by-side with a box plot showing expression stratified by a metadata variable. The user should be able to choose the gene to show (also in static mode).

Implementation

A function that takes

• the report object
• the 2D coordinates of the reduced dimension
• a matrix / data frame of gene expression (possibly limited to "interesting" genes)
• a metadata variable for stratification
• the page title

and generates a static page with linked charts. Implementation of the interactive version will be done later.

See also

Plotly has a lot of capability to create client-side linked charts (no need for shiny): https://plotly-r.com/client-side-linking.html

Extensions

1. Interactive version: The user can choose the metadata variable for stratification. The function has to be changed to take a dataframe of metadata variables for this to work.
2. Wrapper functions for popular classes: SingleCellExperiment, seurat
3. In addition, the boxplot could show certain summary statistics per variable level: The number of observations with positive (>0) expression and the percentage of such observations (e.g. 14 cells (75%))