derektoms/interactive-3d-plotting-in-seurat-3.0.0

This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data

3D-Plotting-in-Seurat

The following code is used to generate nice interactive 3D tSNE and UMAP plots against Seurat objects created using the excellent single cell RNAseq analysis tool created by the Satijalab. V1 works for Seurat v2.3.4 + v3.0.2 and V2 (better interactive graphics, uses RShiny) of the code works for Seurat v3.0.0-v3.1.1

The engine behind this code uses plotly: Plotly Technologies Inc. Collaborative data science. Montréal, QC, 2015. https://plot.ly.

For more on Seurat please visit:https://satijalab.org/seurat/

News:

Code for analyzing UMAP embeddings and plotting in 3D are now added. Compatible with integrated/combined datasets created using new and improved sample integration systems in Seurat.

Cite

Please dont forget to acknowledge the contributors! Please cite as:

Qadir, M. M. F., Álvarez-Cubela, S., Klein, D., van Dijk, J., Muñiz-Anquela, R., Moreno-Hernández, Y. B., ... & Díaz, Á. (2020). Single-cell resolution analysis of the human pancreatic ductal progenitor cell niche. Proceedings of the National Academy of Sciences, 117(20), 10876-10887.https://doi.org/10.1073/pnas.1918314117

Fahd Qadir, Saad Sadiq, & Juan Domínguez-Bendala. (2019, October 11). 3D Plotting of scRNAseq data using Seurat objects (Version 1.3). Zenodo. http://doi.org/10.5281/zenodo.3483177

Contact

Fahd Qadir, Graduate Student. Molecular Cell and Dev. Biology Graduate Program, Dept. of Cell Biology, University of Miami, Miller School of Medicine. [email protected] [email protected]