run.prepare.chronoclust: run.prepare.chronoclust

In ImmuneDynamics/Spectre: High-dimensional cytometry and imaging analysis.

run.prepare.chronoclust

Description

This function will prepare a Python environment to run ChronoClust. You need to install anaconda package management software for this to work. If Reticulate is kind, it might prompt you to install it when running this function if you haven't got it installed. However, please do not count on it. If it does not prompt you, and you encounter an error such as no anaconda installation is found, please visit https://www.anaconda.com/products/individual to manually download and install anaconda.

Usage

run.prepare.chronoclust(environment_name, environment_path, create_environment, install_dependencies)

Arguments

environment_name	NO DEFAULT. Character. The name of the anaconda environment where chronoclust will execute.
environment_path	DEFAULT NULL. Character. For expert users only. If you have custom anaconda installation i.e. not installed to default location, you can specify the location here.
create_environment	DEFAULT TRUE. Logical. Whether to newly create the environment or not. If FALSE, make sure the environment exists in your anaconda installation.
install_dependencies	DEFAULT TRUE. Logical. Whether to install chronoclust and all its dependencies into the environment. If TRUE, it will install all the dependencies, and restart R session. When R session is restarted, the variables you have previously assigned will remain intact, but you will need to reload all the libraries again.

Details

For advanced users, if your anaconda is installed in custom location, you can specify this location as environment_path parameter.

Author(s)

Givanna Putri, [e-mail]

References

https://sydneycytometry.org.au/spectre.

Examples

run.prepare.chronoclust(environment_name = "chronoclust-R", create_environment = TRUE, install_dependencies = TRUE)

ImmuneDynamics/Spectre documentation built on Nov. 12, 2023, 8:12 a.m.