lysogeny / kalvosto

A simple, modular and fast single-cell sequencing exploration shiny app

lysogeny

I like julia.

kalvosto's Issues

Add Swap button for twin view

Add a button that swaps the x/y combination for the two panels in twin view

Violin plots?

Maybe add a violin plot module?

Check that h5ad will properly be read

Currently there are no checks to see if the h5ad will have:

• Unique column names
• Unique row names

The app will fail with a cryptic error if the column names are non-unique.
Further, categorical indices can cause issues and should be checked for.

Restructure dropdowns for anndata-like choices

Possibly having a first dropdown with X, 'obs' and all options from 'obsm', and a second dropdown for the column within the specified dataset might make more sense for users (avoids having to scroll past 50 PCs).

This would also be less arbitrary, as the 'gene' name that is added to the first dropdown might also be given as a column. What happens then is not known.

Consider automatically locking axes when multi-panel created by grouping variable

Discourage including variables in grouping variables with many unique values

Grouping variables with highly unique values will probably cause problems.
How do we avoid these?

Log and normalisation

What is the current strategy for log normalisation and what should the strategy be?