count_cell_types default parameters issue

[leealj]

I'm currently troubleshooting CSIDE on my dataset, and I noticed that the count_cell_types function isn't working for me since I get the following error:

Error in choose_cell_types(myRCTD, barcodes, doublet_mode, cell_type_threshold, : argument "cell_type_filter" is missing, with no default

I see that in the CSIDE code, choose_cell_types is also used to determine which cell types are used in the analysis, and this works since the cell_type_filter argument is set inside of the CSIDE function, along with an optional parameter for cell_type_filter in the CSIDE function call. However, there is no option to set cell_type_filter when running count_cell_types, and cell_type_filter is not set in the choose_cell_types function call inside of the count_cell_types code, resulting in the above error. I think I'll move forward with using choose_cell_types directly for my own purposes, but I think this could be a fairly straightforward fix for the count_cell_types function, which is currently unusable.

Thanks, Alex

[dmcable]

Hi Alex,

You are right, thank you. I am not sure how this happened, but I have fixed the bug as you suggested.

Best, Dylan