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

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

voxel_map(object, ...)

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

# S3 method for 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.

Value

A VoxelMap object with a cell x voxel correlation matrix and metadata.