read_xenium_folder: Read a structured xenium folder

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Read a structured xenium folder

Description

Read a structured xenium folder

Usage

read_xenium_folder(
  xenium_dir,
  data_to_use = "subcellular",
  bounds_to_load = c("cell"),
  load_format = "csv",
  h5_expression = FALSE,
  verbose = TRUE
)

Arguments

xenium_dir	full path to the exported xenium directory
data_to_use	which type(s) of expression data to build the gobject with (e.g. default: 'subcellular', 'aggregate', or 'all')
bounds_to_load	vector of boundary information to load (e.g. 'cell' or 'nucleus' by themselves or c('cell', 'nucleus') to load both at the same time.)
load_format	files formats from which to load the data. Either 'csv' or 'parquet' currently supported.
h5_expression	(boolean) whether to load cell_feature_matrix from .h5 file. Default is TRUE
verbose	be verbose when building Giotto object

Value

path_list a list of xenium files discovered and their filepaths. NULL values denote missing items

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