#' Cell counts report.
#'
#' Generate plots and CSV files that report on cell counts over all cell
#' subsets. Report includes bar plots of cell counts by level.
#'
#' @param sample An Astrolabe samlpe.
#' @export
reportCellCounts <- function(sample) {
if (!isSample(sample)) stop("Expecting an Astrolabe sample")
subset_cell_counts <- sample$aggregate_statistics$subset_cell_counts
# Figure: Bar plot of subset cell counts, by level.
lapply(orloj::nameVector(colnames(sample$cell_subsets)), function(level) {
counts <- subset(subset_cell_counts, Parent == level)
# Order cell subsets by name.
counts$CellSubset <-
factor(counts$CellSubset, levels = unique(sample$cell_subsets[[level]]))
plt_list <-
orloj::plotBarPlot(counts,
x = "CellSubset",
y = "N",
title = paste0(level, ": Cell Counts"),
theme = NULL)
plt_list$plt <-
plt_list$plt + ggplot2::scale_y_continuous(labels = scales::comma)
plt_list
})
}
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