load_xenium_folder: Load xenium data from folder

load_xenium_folderR Documentation

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.