Create a highSpaClone object.
Usage
createObject(
counts,
location,
min_avg_expression = 0.01,
min_gene_counts = 100,
gene_order_file = NULL,
annotations_file = NULL,
project = ""
)Arguments
- counts
Gene-by-cell raw count matrix.
- location
A data.frame or matrix of spatial coordinates for each cell, with three columns (cell.id, x, y). The row names of location must match with the column names of counts.
- min_avg_expression
Minimum average expression per gene.
- min_gene_counts
Minimum total counts per cell.
- gene_order_file
The gene order file, contains chromosome, start, and stop position for each gene.
- annotations_file
Cell type annotation information. Should contain two columns: cell.id and cell.label. Must be a data.frame, .csv or .txt file.
- project
The name of the project.