This GitHub repository contains the Python code for reproducing the analysis and figures in the following manuscript:
Van Hoan Do, Stefan Canzar, A generalization of t-SNE and UMAP to single-cell multimodal omics, bioRxiv (2021). doi: https://doi.org/10.1101/2021.01.10.426098
The instruction of how to install the package: https://github.com/canzarlab/JVis-learn
1/ Section "Proofs of principle". Here we analyzed a SNARE-seq data set and performed a number of experiments to validate the ability of Jvis to learn the correct representation under the noise. The data and python scripts to reproduce this section are provided in the directory "proof_of_principle". In addition, we simulated 8 multimodal synthetic data sets using Splatter (R scripts are in the directory 'proof_of_principle/sim_splat'). The model parameters in Splatter are learned from the healthy human PBMC data set, which can be downloaded from the Gene Expression Omnibus with the accession code GSE126310 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126310). The Python scripts for performing the benchmark Jvis againts competting approaches are available in the directory 'proof_of_principle/python_scripts'.
2/ Section "Jvis utilizes multi-modal data to resolve subtle transcriptomic difference". We ran Jvis on two CITE-seq datasets and compared it to the visualizations based on each modality alone. The data and python scripts to reproduce this section are provided in the directory "cell_heterogeneity"
3/ Section "Jvis improves the visualization of joint velocity landscapes of protein and RNA". In this section we visualized the single cell acceleration on the joint visualization in constrast to the transcriptomic space as in the original publication [1]. The datasets are download from the paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1945-3#availability-of-data-and-materials
- Gorin G, Svensson V, Pachter L. CITE-seq protein and mRNA counts. figshare; 2019 [cited 2020 Jan 20]. Available from: https://figshare.com/articles/CITE-seq_protein_and_mRNA_counts/8309696
- Gorin G, Svensson V, Pachter L. REAP-seq protein and mRNA counts. figshare; 2019 [cited 2020 Jan 20]. Available from: https://figshare.com/articles/REAP-seq_protein_and_mRNA_counts/8309708
- Gorin G, Svensson V, Pachter L. ECCITE-seq protein and mRNA counts. figshare; 2019 [cited 2020 Jan 20]. Available from: https://figshare.com/articles/ECCITE-seq_protein_and_mRNA_counts/8309714
- Gorin G, Pachter L, Svensson V. 10X protein and mRNA counts. figshare; 2019 [cited 2020 Jan 20]. Available from: https://figshare.com/articles/10X_protein_and_mRNA_counts/9912734/1
The Python scripts for reproducing this section are given in the directory "sc_velocity"
[1] Gorin, G., Svensson, V. & Pachter, L. Protein velocity and acceleration from single-cell multiomics experiments. Genome Biol 21, 39 (2020). https://doi.org/10.1186/s13059-020-1945-3