R/forceatlas2.R

In milescsmith/ReductionWrappers: Wrapper exposing several Python dimensional reduction tools

#' @title ForceAtlas2
#'
#' An R wrapper around the Python implementation of ForceAtlas2 found at
#' https://github.com/bhargavchippada/forceatlas2
#'
#' Currently a very restricted version
#'
#' @param init_pos Array of initial positions, i.e. PCA or PAGA embeddings
#' @param adjacencies A graph in 2D format
#' @param iterations Number of times to iterate the main loop
#' @param ... Additional arguments to pass to the forceatlas2 object instantiation
#'
#' @importFrom reticulate import
#' @importFrom glue glue
#' 
#' @rdname fa2
#'
fa2 <- function(init_pos,
                adjacencies,
                iterations = 500,
                ...){

  required_modules <- c("fa2","numpy")
  for (i in required_modules) {
    if (!py_module_available(i)) {
      stop(glue::glue("The {i} module is unavailable.
         Please activate the appropriate environment or
         install the module."))
    }
  }

  fa2 <- reticulate::import(module = "fa2", delay_load = TRUE)
  np <- reticulate::import(module = "numpy", delay_load = TRUE)

  # shamelessly based from the fantastic Scanpy package
  forceatlas2 <-
    fa2$ForceAtlas2(
      outboundAttractionDistribution=FALSE,  # Dissuade hubs
      linLogMode=FALSE,  # NOT IMPLEMENTED
      adjustSizes=FALSE,  # Prevent overlap (NOT IMPLEMENTED)
      edgeWeightInfluence=1.0,
      # Performance
      jitterTolerance=1.0,  # Tolerance
      barnesHutOptimize=TRUE,
      barnesHutTheta=1.2,
      multiThreaded=FALSE,  # NOT IMPLEMENTED
      # Tuning
      scalingRatio=2.0,
      strongGravityMode=FALSE,
      gravity=1.0,
      # Log
      verbose=TRUE
    )

  fa_results <-
   forceatlas2$forceatlas2(
     G = adjacencies,
     pos = init_pos,
     iterations = as.integer(iterations)
    )
  fa_embeddings <- np$array(fa_results)
  rownames(fa_embeddings) <- rownames(init_pos)
  colnames(fa_embeddings) <- as.character(glue::glue("fa_{seq(ncol(fa_embeddings))}"))
  
  fa_embeddings
}