Example

This package use simplex barycentric coordinate approach to assist exploration in the similarity between single cells between selected cell clusters. We denote a number (2-4) of selected clusters, or groups of clusters, as vertices. We calculate the similarity between each single cell and the average point of each vertex. By normalizing the similarity between each single cell and all specified vertices to a unit sum, we can derive the barycentric coordinates for each single cell. Visualization method for binary (ended line), ternary (equilateral triangle) and quaternary (tetrahedron) simplex are developed. The main plotting functions are plot_binary(), plot_ternary() and plot_quaternary(), respectively.

Test Dataset

The dataset used in all example can be found on figshare. This is a small subset of publicly available single cell RNA-seq data from the human bone marrow mononuclear cells (BMMC) generated in our previous study 1. The data is stored in a .h5ad file format, which can be read by the AnnData package. Users can load the dataset following the code below.

import CytoSimplex as csx
import scanpy as sc
adata = sc.read(filename='test.h5ad',
                backup_url="https://figshare.com/ndownloader/files/41034857")

The contents included in the adata object include:

• adata.X: A CSR sparse matrix of 250 rows (cells) by 20,243 columns (genes) containing the raw gene count matrix.

• adata.obs["cluster"]: A categorical annotation of cell clusters. There are totally 12 clusters which can be viewed via adata.obs["cluster"].cat.categories. Namingly, ‘Chondrocyte_1’, ‘Chondrocyte_2’, ‘Chondrocyte_3’, ‘OCT_Stem’, ‘ORT_1’, ‘ORT_2’, ‘ORT_3’, ‘Osteoblast_1’, ‘Osteoblast_2’, ‘Osteoblast_3’, ‘Reticular_1’ and ‘Reticular_2’.

• adata.uns["velo"]: A 250 by 250 CSR sparse matrix of velocity neighbor graph. This is derived with veloVAE 2. We will have more introduction to this in detailed examples.

Contents:

• Select Top Features
• Create Ternary Simplex (Triangle) Plot
  • Adding velocity information to ternary plot
  • Exploration with each cluster
• Create Binary Simplex (Ended Line) Plot
• Create Quaternary Simplex (Tetrahedron) Plot

1

Matsushita, Y., Liu, J., Chu, A.K.Y. et al. Bone marrow endosteal stem cells dictate active osteogenesis and aggressive tumorigenesis. Nat Commun 14, 2383 (2023). https://doi.org/10.1038/s41467-023-38034-2

2

Gu, Y., Blaauw, D., Welch, J. D.. Bayesian Inference of RNA Velocity from Multi-Lineage Single-Cell Data. bioRxiv (2022). https://doi.org/10.1101/2022.07.08.499381