read_10x_for_spaco: Read in 10x Visium spatial transcriptomics data

In SPACO: Spatial Component Analysis for Spatial Sequencing Data

Read in 10x Visium spatial transcriptomics data

Description

Read in 10x Visium spatial transcriptomics data

Usage

read_10x_for_spaco(
  data_dir,
  slice,
  filename,
  variable_features_n = variable_features_n,
  spatial_file = spatial_file,
  vars_to_regress = NULL
)

Arguments

data_dir	Directory containing the H5 file specified by file name and the image data in a sub directory called spatial
slice	Name for the stored image of the tissue slice
filename	Filename of data to be read
variable_features_n	Number of most variable features to keep.
spatial_file	Name of csv file from which to read tissue positions.
vars_to_regress	Names of features to be regressed against using PercentageFeatureSet

Value

Retuns a ready to run SPaCoObject.

SPACO documentation built on March 31, 2026, 5:07 p.m.