VRland
This file will become the README and documentation index for the upcoming standalone implementation of the Valley-Ridge score landscapes.
VRland allows to visualise single-cell differentiation processes on a Waddington-like landscape by combining the global cellular relationships captured by PHATE as ‘longitude and latitude’ axes, with a Valley-Ridge (VR) score based on cellular pluripotency and RNA velocity. The resulting VR landscape altitude captures the differentiation potential of a cell population, with the valley-ridge topology delineating local plasticity.
For an example of the current implementation as a single Jupyter Notebook, please see the work on Qin & Cardoso Rodriguez et al. 2023 and it’s associated GitHub repository (VR score and landscape generation can be found within the Figure 7 directory).
This repository contains a development version of VRland where additional distance metrics to determine the Ridge component will be explored.
Ultimately, the aim is to deploy this notebook-based tool as an interactive web-app.
How to use
A brief tutorial will be coming soon…
For now refer to the individual score and landscape notebooks in this repo, or to the work on Qin & Cardoso Rodriguez et al. 2023 and it’s associated GitHub repository.
Install
Currently, the pre-release VRland tool can be used by cloning its GitHub repository and locally installing the package from the repo root directory with:
pip install -e ".[dev]" It will eventually be available on Python Package Index.