UMAP and t-SNE Analysis

Prerequisites

Run the following before the first analysis to install all required R packages:

Rscript scripts/install_dependencies.R

Alternative manual installation:

Rscript -e "install.packages(c('optparse','data.table','Rtsne','umap','ggplot2','vegan','R.utils'), repos='https://cloud.r-project.org')"

Note: R.utils is only required when --timeout > 0, but pre-installing it avoids environment drift across runs. testthat is installed by scripts/install_dependencies.R as the development test dependency.

The skill cannot run until these packages are installed. In new or bare R environments, always run the prerequisite step first.