tSNEplots

Description

An R script for automatically creating coloured tSNE plots. Follow the instructions within the R script to execute.

There are two versions of this script. In the main script (tSNEplots.R), the colour scale for each sample is handled independently. In the new script (tSNEplots_global_scaling.R) the colour, X, and Y scales are 'global', so for any given marker the maximum and minimum will be the same between samples.

This script accepts .csv files as input. A version to read straight from .fcs files will follow soon.

How to download

Go to 'releases' above (https://github.com/sydneycytometry/tSNEplots/releases) and download source code for the latest version. There is a PDF with some visual instructions, along with comments in the code to guide you.

Citation

If you use this script in your work, please citing: please consider citing Ashhurst TM, Marsh-Wakefield F, Putri GH, et al. (2020). bioRxiv. 2020.10.22.349563. You can also refer to the github repository in your methods section using information below. You can use the specific version that you used in your work.

Version history

v1.4 - updated main script and arranged some files

Ashhurst, T. M. (2017). tSNEplots v1.4. GitHub repository. Repository: https://github.com/sydneycytometry/tSNEplots/releases.

v1.3 - updated to ignore columns with non-numeric values

Ashhurst, T. M. (2017). tSNEplots v1.3. GitHub repository. Repository: https://github.com/sydneycytometry/tSNEplots.

v1.2.0 - updated to include 'global' colour, X, and Y scaling (most recent)

Ashhurst, T. M. (2017). tSNEplots v1.2.0. GitHub repository. DOI: http://doi.org/10.5281/zenodo.893859, repository: https://github.com/sydneycytometry/tSNEplots.

v1.1.0 - original script

Ashhurst, T. M. (2017). tSNEplots v1.1.0. GitHub repository. DOI: http://doi.org/10.5281/zenodo.851736, repository: https://github.com/sydneycytometry/tSNEplots.