The MDSvis package implements visualization of Multi Dimensional Scaling (MDS) objects representing a low dimensional projection of cytometry samples. Such objects can be obtained using the functionalities implemented in the CytoMDS package. The visualization is realised via a Shiny app that allows the user to interactively customise the plots depending on a series of input parameters.
Below a screenshot of the app ‘View’ tab. The controls on the side allow to choose the projection axes, colour, label, facet or shape the points according to phenodata variables, add biplot, show a plotly plot for interactive plot exploration or flip axes.
Installation
To install the package run the following lines:
if (!require("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github(repo = 'https://github.com/UCLouvain-CBIO/MDSvis')Note that CytoMDS version 1.3.5 or above needs to be installed before.
License
The MDSvis code is provided under GPL license version 3.0 or higher. The documentation, including the manual pages and the vignettes, are distributed under a CC BY-SA 4.0 license.
Citation
If you use MDSvis in your research, please use the following citation:
Hauchamps, Philippe, Simon Delandre, Stéphane T. Temmerman, Dan Lin, and Laurent Gatto. 2025. “Visual Quality Control with CytoMDS, a Bioconductor Package for Low Dimensional Representation of Cytometry Sample Distances.” Cytometry. Part A: The Journal of the International Society for Analytical Cytology 107 (3): 177–86.