plot_faust_count: Plot counts of FAUST pops by sample
In MiguelRodo/faustutils: Additional functions to extract and plot FAUST output

Description Usage Arguments Details Examples

Saves plots of counts to project_path/faustData/plotData/pop_stats for specified FAUST-identified subsets.

plot_faust_count(
  project_path,
  pop,
  font_size = 10,
  point_size_max = 2,
  breaks = NULL,
  trans_x = "asinh",
  p_width = NULL,
  p_height = NULL,
  exhaustive = FALSE,
  limitsize = FALSE
)

`project_path`	character. FAUST project directory.
`pop`	`list` or `named character vector`. If a `character vector`, then counts of all subsets matching the set of marker levels are plotted. If a `list`, then each list element must be a character vector. In that case, one boxplot of frequencies is plotted for each element of the list of where the frequency is the sum of all cells that match the population specified. If `NULL`, then all subsets found are plotted.
`breaks`	numeric vector. If supplied, then this is the breaks for the x-axis. If not supplied, then the default breaks are used of `c(0, 0.001, 0.005, 0.01, 0.02, 0.5, 0.1, 0.5, 1, 2, 5, 10, 20, 50, 100)`.
`trans_x`	`character` or `Transformation` object (from `scales` package). the name of a transformation object or the object itself. Built-in transformations include "asinh", "asn", "atanh", "boxcox", "date", "exp", "hms", "identity", "log", "log10", "log1p", "log2", "logit", "modulus", "probability", "probit", "pseudo_log", "reciprocal", "reverse", "sqrt" and "time". Default is `asinh`.
`p_width`	`numeric`. Width of saved plot in cm. If `NULL`, then set to 40.
`p_height`	`numeric`. Height of saved plot in cm. If `NULL`, then it is set to `max(5, n_pop * 1.25)`, where `n_pop` is the number of sub-populations in `pop`.
`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`.
`limitsize`	logical. If `TRUE`, then plots of size 125cm x 125cm or more are not saved but an error is returned when `cowplot::ggsave2` is run. Default is `FALSE`.

The key parameter is pop. If pop is a list, then each element is treated as a population for which counts are required on aggregate (rather than for individual subsets of that population). If pop is a character vector, then it is treated as a population for which counts are required for individual subsets.

project_path <- usethis::proj_path(ext = "/inst/extdata")
# plot all subsets of pop, as it is a character vector
pop <- c("CD3" = "+", "CD4" = "+", "CD8-IgD" = "-",
         "CD20" = "-", "CD33" = "-", "CD14" = "-",
         "TCRgd-CD19" = "-")
plot_faust_count(project_path = project_path,
                 pop = pop)
# plot counts of cells matching annotation of each
# element in pop, as pop is a list
pop <- list(c("CD3" = "+", "CD4" = "+", "CD8-IgD" = "-",
"CD20" = "-", "CD33" = "-", "CD14" = "-",
"TCRgd-CD19" = "-"),
c("CD3" = "+", "CD4" = "-", "CD8-IgD" = "+",
  "CD20" = "-", "CD33" = "-", "CD14" = "-",
 "TCRgd-CD19" = "-"))
plot_faust_count(project_path = project_path,
pop = pop)