Adapt estimation atlas from Erö et al. to be used in the analysis

Wrapper around dplyr functions to select only relevant brain areas of the cell estimation atlas. The atlas estimating the number of cells per brain area was generated in this publication (doi:10.3389/fninf.2018.00084). The atlas follows the Allen Brain Reference Atlas Categorization (mouse brain).

adapt_estimation_atlas(estimation_atlas, adj_aba_atlas)

Arguments

estimation_atlas	atlas from Erö et al. Use atlas as present in the package, or provide a dataframe where each row is a brain area. The dataframe must contain a variable called "Regions" with the names on the brain areas. The other variable(s) are the estimations, i.e "Neurons", "Glia", "Inhibitory" etc.
adj_aba_atlas	dataframe with Allen Brain Atlas tree, with an additional variable called "my_grouping" with the level of categorization of interest. The dataframe contains also the variable "name" specifying the name of the brain areas. For an example of how to create this dataframe, see X.

Value

Examples

x <- data.frame(
Regions = c("a_1", "a_2", "a_3", "b_1", "b_2"),
Cells = c(10000, 2100, 39847, 754, 923)
)

y <- data.frame(
name = c("a_1", "a_2", "a_3", "b_1", "b_2", "c_1", "c_2"),
my_grouping = c(rep("a",3), rep("b",2), rep("c", 2))
)

adapt_estimation_atlas(x,y)
#> Error in estimation_atlas %>% dplyr::rename_all(tolower) %>% dplyr::rename(name = regions) %>%     dplyr::full_join(adj_aba_atlas[, c("name", "my_grouping")],         by = "name") %>% dplyr::group_by(my_grouping) %>% dplyr::summarise(dplyr::across(-name,     ~sum(.x, na.rm = TRUE))) %>% dplyr::filter(!is.na(my_grouping)): could not find function "%>%"