Giotto import functionalities for Visium HD datasets. This function generates a `VisiumHDReader` instance that has convenient reader functions for converting individual pieces of Visium HD data into Giotto-compatible representations when the param `visiumHD_dir` is provided. A function that creates the full `giotto` object is also available. These functions should have all param values provided as defaults, but can be flexibly modified to do things such as look in alternative directories or paths.
importVisiumHD(
visiumHD_dir = NULL,
expression_source = "raw",
gene_column_index = 2,
barcodes = NULL,
array_subset_row = NULL,
array_subset_col = NULL,
pxl_subset_row = NULL,
pxl_subset_col = NULL
)
Visium HD output directory (e.g. square_016um)
character. Raw or filter expression data. Defaults to 'raw'
numeric. Expression column to use for gene names 1 = Ensembl and 2 = gene symbols
character vector. (optional) Use if you only want to load a subset of the pixel barcodes
numeric vector. (optional) Vector with min and max values to subset based on array rows
numeric vector. (optional) Vector with min and max values to subset based on array columns
numeric vector. (optional) Vector with min and max values to subset based on row pixels
numeric vector. (optional) Vector with min and max values to subset based on column pixels
VisiumHDReader object
Loading functions are generated after the `visiumHD_dir` is added.