Normalize colabel counts over a designated denominator channel.

This function can only be run after running combine_norm_cell_counts(). It divides the colabelled cell counts by a designated normalization channel to provide a normalized ratio. Please note that the areas and volumes cancel out in this operation. This is not designed to work on multiple hemispheres. Please combine cell counts across multiple hemispheres when you run normalize_cell_counts().

Usage

normalize_colabel_counts(e, denominator_channel = "eyfp")

Arguments

e

experiment object

denominator_channel

(str, default = "eyfp") The exact name of the channel used for normalization

Value

e An experiment object with a new dataframe with the normalized ratios of colabelled counts over the designated denominator counts. Because the volumes and region areas cancel out, the values of count, normalized.count.by.area, and normalized.count.by.volume are all the same. This is to provide a consistent input dataframe into the analysis functions.

See also

combine_norm_cell_counts() & normalize_cell_counts()

Examples

e <- normalize_colabel_counts(e, denominator_channel = "eyfp")
#> Error in which(names(e$combined_normalized_counts$colabel) == "name"): object 'e' not found