load_xenium_folder: Load xenium data from folder

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Load xenium data from folder

Description

Load xenium data from folder

Usage

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
)

Arguments

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 TRUE
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

Value

list of loaded in xenium data

Functions

• load_xenium_folder_csv(): Load from csv files

• load_xenium_folder_parquet(): Load from parquet files

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.