pairwise_activation: Calculate pairwise activation across groups

In valeriabonapersona/abc4d: Analysis of Brain Cells in 4 Dimensions

Usage

pairwise_activation(region_df, against_group = "0", heatmap = FALSE)

Arguments

region_df	region_based dataframe. It can be the output of preprocess_per_region(). Each row corresponds to a brain area ("my_grouping") per sample, with (corrected) counts ("cells_perthousand_box_scaled"). The variable "group" refers to the experimental groups. The variable "batch" is used for pairwise comparisons. Of note, for each "batch" there can be only a sample per group.
against_group	group from "group" var against which comparisons will be made
heatmap	if TRUE, the function returns a list where the first element is the dataframe, and the second element is a visualization with heatmap.
count_var	string with the name of the variable on which to perform the analyses

Examples

dat <- data.frame(
group = rep(c("0", "30", "90"), each = 50),
my_grouping = rep(c(1:50), 3),
my_counts = rnorm(150)
)
res <- pairwise_activation(dat)
res_with_visualization <- pairwise_activation(dat, heatmap = TRUE, classifications_df = cat, classifications_cat = "parents")

valeriabonapersona/abc4d documentation built on Dec. 23, 2021, 2:09 p.m.