voxel_map: Project single cell gene expression data to spatial...
In quadbiolab/VoxHunt: Projecting single-cell transcriptomes to spatial brain maps

voxel_map

R Documentation

Project single cell gene expression data to spatial expression patterns in the mouse brain

Description

Calculates correlation between single-cell gene expression and in situ hybridization data of the developing mouse brain from the Allen Brain Atlas.

Usage

voxel_map(object, ...)

## Default S3 method:
voxel_map(
  object,
  stage = "E13",
  groups = NULL,
  method = "pearson",
  genes_use = NULL,
  allow_neg = FALSE,
  pseudobulk_groups = TRUE
)

## S3 method for class 'Seurat'
voxel_map(
  object,
  stage = "E13",
  group_name = NULL,
  method = "pearson",
  genes_use = NULL,
  allow_neg = FALSE,
  pseudobulk_groups = TRUE
)

Arguments

`stage`	The developmental stage in the ABA to map single cells to.
`groups`	A character or factor vector or for grouping of cells, e.g. clusters, cell types.
`method`	A character string indicating which correlation coefficient to compute.
`genes_use`	A character vector with genes to use for computing the correlation. We recommend to use 150 - 500 genes.
`allow_neg`	Logical. Whether to allow negative correlations or set them to 0.
`pseudobulk_groups`	Logical. Whether to summarizse the group expression before computing the correlation.
`group_name`	A string indicating the metadata column for grouping the cells, e.g. clusters, cell types.