voxelize: Generate voxel-based heatmaps

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

Generate voxel-based heatmaps

Description

Generate voxel-based cell density heatmaps based on datasets from SMART analysis. Generate group mean and SD heatmaps to show trends across test groups. Generate .csv files containing raw heatmap data for downstream statistical analysis.

Usage

voxelize(
  brains_list = c(),
  data_list = c(),
  datasets = c(),
  groups_list = c(),
  groups = c(),
  ML_bounds = c(-5, 5),
  DV_bounds = c(-8, 1),
  detection_bounds = c(0.1, 0.1),
  resolution = 50,
  ticks = 10,
  display_bounds = NULL,
  heatmaps = TRUE,
  save = TRUE,
  output = NULL
)

Arguments

data_list	(required, default = c()) Vector of .RData files (including file paths) to be accessed.
datasets	(required, default = c()) Vector of dataset names (in quotes) corresponding to the relevant dataset in each .RData file. To generate heatmaps for individual brain slices, use isolate_dataset() to isolate cells from a specific plate.
groups_list	(required, default = c()) Vector corresponding to brains_list that specifies the group name for each brain.
groups	(required, default = c()) Vector of groups.
ML_bounds	(optional, default = c(-5, 5)) Bounds for ML axis.
DV_bounds	(optional, default = c(-8, 1)) Bounds for DV axis.
detection_bounds	(optional, default = c(0.1, 0.1)) Side length (in mm) of detection square around each search point.
resolution	(optional, default = 50) Number of search points in each dimension, per millimeter (e.g. resolution 50 divides each square mm into a 50 x 50 grid with 2,500 search points).
ticks	(optional, default = 10) Number of tick marks to show on scale.
display_bounds	(optional) Range of cell densities to display on heatmaps.
heatmaps	(optional, default = TRUE) Specify whether to output heatmaps.
save	(optional, default = TRUE) Specify whether to save .csv files.
output	(required, default = NULL) Specify path to output folder to output .csv files, heatmaps, and .RData files.

Value

Returns group_matrices an object containing all brain matrices, as well as group mean and SD matrices.

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