get_table: Create a data frame of left/right counts and their ratio of...

In jdknguyen/SMART: SMART (Semi-manual alignment to reference template): a pipeline for whole brain mapping projects

Create a data frame of left/right counts and their ratio of regions of interest

Description

Generates a dataframe showing region acronyms, their full name, hierachical paths, total cell counts, left and right counts, and cell count percentages.

Usage

get_table(dataset, rois = c("CH", "BS"), base = "grey")

Arguments

dataset	(required) Whole brain dataset returned as an output of the forward_warp() function.
rois	(optional, default = c("CH", "BS")) The acronyms of the regions of interest. Acronyms must follow Allen Brain Atlas abbreviation standards.
base	(optional, default = "grey") The base parent region you want subregions traced back to. Note, base region MUST be a higher parent level or the same level of the roi/rois provided to the rois argument.

Value

Returns table, a dataframe showing total, left and right cell counts and count percentages according region acryonym.

Examples

# Get cell counts of the hypothalamus
table <- get_table(dataset, rois = "HY", base = "HY")

# Get cell counts of all grey matter
table <- get_table(dataset, rois = "grey", base = "grey")

# Get cell counts of hypothalamus and all parent structures of the hypothalamus up to gray matter
table <- get_table(dataset, rois = "HY", base = "grey")

jdknguyen/SMART documentation built on May 30, 2022, 10:51 p.m.