load_xenium_folder | R Documentation |
Load xenium data from folder
load_xenium_folder(
path_list,
load_format = "csv",
data_to_use = "subcellular",
h5_expression = "FALSE",
h5_gene_ids = "symbols",
gene_column_index = 1,
cores,
verbose = TRUE
)
load_xenium_folder_csv(
path_list,
cores,
data_to_use = "subcellular",
h5_expression = FALSE,
h5_gene_ids = "symbols",
gene_column_index = 1,
verbose = TRUE
)
load_xenium_folder_parquet(
path_list,
cores,
data_to_use = "subcellular",
h5_expression = FALSE,
h5_gene_ids = "symbols",
gene_column_index = 1,
verbose = TRUE
)
path_list |
list of full filepaths from read_xenium_folder |
load_format |
files formats from which to load the data. Either 'csv' or 'parquet' currently supported. |
data_to_use |
which type(s) of expression data to build the gobject with (e.g. default: 'subcellular', 'aggregate', or 'all') |
h5_expression |
(boolean) whether to load cell_feature_matrix from .h5 file.
Default is |
h5_gene_ids |
use gene symbols (default) or ensembl ids for the .h5 gene expression matrix |
gene_column_index |
which column from the features or genes .tsv file to use for row ids |
cores |
how many cores or threads to use to read data if paths are provided |
verbose |
be verbose when building Giotto object |
list of loaded in xenium data
load_xenium_folder_csv()
: Load from csv files
load_xenium_folder_parquet()
: Load from parquet files
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