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TopKAT: Topological Kernel Association Test

TopKAT is a global test of association between the topological (geometric) structure of cells in cell-level imaging data and patient-level outcomes. The goal of the TopKAT package is to provide the software to run this test and do post-hoc analyses of the results.

Installation

You can install the development version of TopKAT from Github via:

# First, install devtools
if (!require("devtools", quietly = TRUE)) {
  install.packages("devtools")
}

# Install from Github
devtools::install_github("sarahsamorodnitsky/TopKAT")

TopKAT relies on several dependencies: MiRKAT, RcppAlgos, TDAstats, dplyr, ggplot2, ggtda, reshape2, tidyr, viridis, igraph, and magrittr. The underlying engine for running persistent homology is TDAstats. ggtda, which facilitates visualization of the filtration process and persistence diagrams is available only on Github.

Vignettes

Example usage of TopKAT to analyze data is provided in two vignetes:

  1. Getting Started: illustrates the application of TopKAT to a simulated dataset containing contrived shapes.
  2. Simulated Tissue: illustrates the application of TopKAT to a dataset simulated using the scSpatialSIM package. [1]
  3. Application of TopKAT to a study of Triple Negative Breast Cancer: reproduces the triple negative breast cancer analysis described in the main manuscript using data from [2]

References

[1] Soupir, A. C., Wrobel, J., Creed, J. H., Ospina, O. E., Wilson, C. M., Manley, B. J., … & Fridley, B. L. (2025). scSpatialSIM: a simulator of spatial single-cell molecular data. SoftwareX, 31, 102223.

[2] Keren, L., Bosse, M., Marquez, D., Angoshtari, R., Jain, S., Varma, S., … & Angelo, M. (2018). A structured tumor-immune microenvironment in triple negative breast cancer revealed by multiplexed ion beam imaging. Cell, 174(6), 1373-1387.