get_pop_counts: Get counts of subsets identified by FAUST
In MiguelRodo/faustutils: Additional functions to extract and plot FAUST output

Description Usage Arguments Value Examples

Get counts of subsets identified by FAUST

get_pop_counts(
  project_path = NULL,
  data = NULL,
  pop = NULL,
  dem_col = c("sample", "exp_unit", "tot_count", "sampleName", "experimentalUnit"),
  exhaustive = FALSE
)

`project_path`	character. FAUST project directory.
`data`	dataframe. Dataframe where columns specify counts. If `NULL`, then it is read in from `project_path/faustData/faustCountMatrix.rds`.
`pop`	`named character vector` or `list`. If a `character vector`, then names specify markers and values specify levels, e.g. c("CD4" = "-", "CD8" = "+"). Counts of all annotations will be returned that match these annotations separately, i.e. not summed. If a `list`, then each element must be a character vector as above. For a given list element, instead of all returning all subsets individually that have the correct level for the specified markers, we sum over all the subsets matching the specified annotation and plot the final count. If `NULL`, then all subsets are returned.
`dem_col`	`character vector`. Specifies names of columns in `data` that we wish to keep, regardless of if they match a FAUST annotation.
`exhaustive`	logical. If `TRUE`, then counts are taken from the exhaustive FAUST count matrix rather than the count matrix after excluding subsets that don't appear in sufficiently many experimental units. Default is `FALSE`.

A dataframe with columns as specified in dem_col, tot_count (total number of cells classified for a sample), pop (population name) and count (number of cells in population).

# get counts for cells matching one annotation
pop <- c("CD4"  = "-", "CD8"  = "+")
get_pop_counts(pop = pop)
# get counts for cells matching either of the two annotations
pop <- list(c("CD4"  = "-", "CD8"  = "+"), c("CD8" = "-", "CD4" = "+"))
get_pop_counts(pop = pop)