getSODBDataset

getSODBDataset

Usage

getSODBDataset(
  dataset_name = NULL,
  experiment_name = "default",
  env_name = "giotto_env"
)

Arguments

dataset_name

name of dataset to pull from the SODB. Must exist within the SODB.

experiment_name

name of one experiment associated with `dataset_name` By default, the first experiment will be used.

env_name

name of the conda environment within which pysodb is already installed, or within which installation of pysodb will be prompted

Details

Interface with the Spatial Omics DataBase (SODB) using the python extension, pysodb, from TenCent.

This function will write an anndata h5ad file for a provided dataset name to the current working directory and will then convert the h5ad into a Giotto Object.

Run

listSODBDatasetNames()

to find names of SODB datasets. Run

listSODBDatasetExperimentNames()

to find names of experiments associate with a provided dataset.

This function will not run if pysodb is not installed in the active conda environment. It will prompt the user to install pysodb automatically if it is not detected.

*Note that manual installation is more stable.* To install manually within the giotto environment, follow the steps below:

1. Run

checkGiottoEnvironment()

in R to find the installation location of the Giotto conda environment.

2. Open a terminal.

3. Clone the source code and change into the pysodb directory.

  git clone https://github.com/TencentAILabHealthcare/pysodb.git
  cd pysodb

4. Activate the giotto environment.

conda activate your/path/to/giotto_env

5. Install pysodb as a dependency or third-party package with pip:

pip install .

Examples

if (FALSE) {

sodb_dataset_names = listSODBDatasetNames()
desired_dataset = sodb_dataset_names[[15]] # Arbitrary

dataset_experiment_names = listSODBDatasetExperimentNames(dataset_name = desired_dataset)
desired_experiment = dataset_experiment_names[[1]] # Arbitrary

gobject = getSODBDataset(dataset_name = desired_dataset,
                         experiment_name = desired_experiment)}