Description Usage Arguments Value See Also
View source: R/compute_density.R
Compute cell density from a table of cell counts and tissue areas read from a summary cell seg data file.
1 2 3 4 5 6 7 | compute_density_from_cell_summary(
counts,
summary_path,
tissue_categories,
pixels_per_micron = getOption("phenoptr.pixels.per.micron"),
.by = "Slide ID"
)
|
counts |
A data frame with columns for |
summary_path |
Path(s) to cell seg data summary table(s) containing
sample names and tissue categories matching |
tissue_categories |
A character vector of tissue category names of interest. |
pixels_per_micron |
Conversion factor to microns. |
.by |
Column to aggregate by |
A data table with counts converted to density in cells / mm^2.
Other aggregation functions:
compute_density_from_table()
,
compute_h_score_from_score_data()
,
compute_h_score()
,
compute_mean_expression_many()
,
compute_mean_expression()
,
compute_positivity_many()
,
compute_positivity()
,
count_phenotypes()
,
counts_to_percents()
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