An R script for automatically creating coloured tSNE plots
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Using tSNEplots.pdf



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 ( and download source code for the latest version.


If you use this script in your work, please cite this github using the information below. You can cite the specific version that you used in your work (most recent version = v1.2.0).

Version history

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

Ashhurst, T. M. (2017). tSNEplots v1.3. GitHub repository. DOI: TBC, repository:

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:, repository:

v1.1.0 - original script

Ashhurst, T. M. (2017). tSNEplots v1.1.0. GitHub repository. DOI:, repository:

Citation in EndNote

In EndNote: citaton can be stored as ‘Computer Program’ or ‘Webpage’.

Author = Ashhurst, Thomas Myles

Year = 2017

Title = tSNEplots v1.2.0

Journal = GitHub repository

Publisher = Github

Website (copy the whole line) = DOI:, repository: