R/molecules.R

In mojaveazure/ggseurat: ggplot2 Bindings for Seurat Objects

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# Methods for ggplot2-defined generics
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#' @method autolayer Molecules
#' @export
#'
autolayer.Molecules <- function(
  object,
  feature,
  na.rm = TRUE,
  show.legend = NA,
  nmols = NULL,
  seed = NA_integer_,
  ...
) {
  coords <- ggplot2::fortify(
    model = object,
    data = feature,
    nmols = nmols,
    seed = seed
  )
  if (isTRUE(x = na.rm)) {
    coords <- stats::na.omit(object = coords)
  }
  return(ggplot2::geom_point(
    mapping = ggplot2::aes_string(x = 'y', y = 'x', color = 'molecule'),
    data = coords,
    show.legend = show.legend,
    ...
  ))
}

#' @method fortify Molecules
#' @export
#'
fortify.Molecules <- function(
  model,
  data,
  nmols = NULL,
  seed = NA_integer_,
  ...
) {
  coords <- SeuratObject::GetTissueCoordinates(object = model, features = data)
  if (!is.null(x = nmols)) {
    if (!is.na(x = seed)) {
      set.seed(seed = seed)
    }
    coords <- lapply(
      X = unique(x = coords$molecule),
      FUN = function(m) {
        df <- coords[coords$molecule == m, , drop = FALSE]
        if (nrow(x = df) > nmols) {
          idx <- sample(x = seq_len(length.out = nrow(x = df)), size = nmols)
          df <- df[idx, , drop = FALSE]
        }
        return(df)
      }
    )
    coords <- do.call(what = 'rbind', args = coords)
  }
  return(coords)
}

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# Internal
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