Unravelling three-dimensionally dynamics of spatial multi-modal data with RidgeSpace

You can freely use RidgeSpace for illustrating, comparing, and tracking the spatial dynamics of molecular signals.

Overview of RidgeSpace.

Under construction ......

Prerequisites

"matplotlib", "numpy", "pandas", "scipy"

Installation

I suggest that you can freely install RidgeSpace with pip.

pip install RidgeSpace

You can also use a separate conda environment for installing RidgeSpace.

conda create -y -n RidgeSpace_env python=3.7
source activate RidgeSpace_env
pip install RidgeSpace

Basic Examples

Single-gene spatial depiction:

RidgeSpace.pl_single(adata, plot_name = 'Mbp', obs_cluster='Clusters', elev=30, azim=160))

Multi-modal spatial comparison:

RidgeSpace.pl_multipleOUT(adata, plot_nameA = 'Tnnt1', plot_nameB = 'Tnnt2', obs_cluster='Clusters', elev=20, azim=160, plot_HE_bg=True)

Pseudotime spatial trajectory representation:

RidgeSpace.pl_trajectory(adata, plot_name = 'Pseudotime', obs_cluster='Clusters', elev=45, azim=165, HE_z=10)

Further tutorials please refer to https://RidgeSpace.readthedocs.io/.