ppreshant/flow_cytometry

analyzing .fcs2.0/3.0 files with semi-automated gating and plotting

flow_cytometry's Issues

Replace ` /` with `_` in the name column in pData and flowworkspace_summary

in get_and_parse_plate_layout() : I added the / to between assay_variable and sample_category but don't recall the reason for making this new column when the sample_name_bulk already has a _ delimiter?

Am later replacing the / with _ with str_replace while renaming fcs files before write.FCS() in 7-exploratory..R for saving aggregated data from multiple runs/plates`

Make a wrapper to speed up manual checking of gating

Make a wrapper function : select_and_show_gating() that takes in the well number (ex: B04), and gating fraction and calls

           scatter_channels, fluorescence_channels, density_gating_fraction=.3,
           make_plots = True)```

Error with `fcssummary.subset` for single fluorophore data

There's a problem with pivoting the summary of fl.set when there's only 1 fluorophore in analyze_fcs.R. This is when the fluor_channel subset of the arrau returns a named vector (names of mean, median, quartiles etc.) but leaves out the channel name.

How to fix?

• need to check for only 1 row, reshape and add back a name? -- *too indirect
• convert the array to a tibble before selecting the desired channels - *issue : the tibble's columns are named after the names of fluor_channels, instead of values
  • select by values only then..

Check line 104.
pivot_wider(names_from = measurement, values_from = value) %>% # put mean, median .. in separate columns

Caused by error in `all_of()`: ! Can't subset elements that don't exist. ✖ Element `mScarlet-I-A` doesn't exist.

Possible reason : there is no names_glue = "{statistic}_{.value} format when there's only 1 fluorophore :(