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.
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.
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.
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.