mye-infobank / simba-downstream Goto Github PK

Plotly should support this, but requires the pipeine to create an according entry in obsm

Currently, the name showed in the application navbar is based on the file name provided in the input.txt file. Since the file names are not remarkably beautiful, it would be better to have a separate field for the pretty name.
Since the way shiny apps are deployed does not allow setting values via CLI, the easiest way would probably be to add a second line to input.txt and use the first line as input file and the second line as page title.

Currently the values are labeled as Upregulated or Downregulated. For biologists it would be interesting, in which of the compared categories they are higher. Better labels would be High in <reference> vs High in <alternative>.

Also, investigate if we can visualize the actual p-values in the field that pops up when hovering over a dot. Currently, only the negative log values are shown. I think, this was done this way because plotly had a problems with values too close to zero, but I don't remember exactly. Maybe we can find a clean solution for this. If not, we could show something like p-value: below <min_value> if the value is too low, to prevent errors.