R/Features.R

In ddiez/CanekDebug: Functions to Evaluate Canek Integration

#' SummarizeHVF
#'
#' @param x Seurat object.
#'
#' @export
#'
SummarizeHVF <- function(x) {
  if (inherits(x, "Seurat")) x <- list(Seurat = x)
  total_datasets <- length(x)
  x <- lapply(names(x), function(n) {
    tibble(dataset = n, feature = VariableFeatures(x[[n]]))
  }) %>% bind_rows()
  total_features <- length(unique(x$feature))
  x %>% gather("dataset", "feature") %>% count(.data[["feature"]], sort = TRUE, name = "n_datasets") %>% count(.data[["n_datasets"]], name = "n_features") %>% mutate(total_datasets = total_datasets, percentage_datasets = .data[["n_datasets"]] / .data[["total_datasets"]], total_features = total_features, percentage_features = 100 * .data[["n_features"]] / .data[["total_features"]], cumsum_features = rev(cumsum(rev(.data[["n_features"]]))), cumsum_percentage_features = rev(cumsum(rev(.data[["percentage_features"]])))) %>% select("n_datasets", "total_datasets", "percentage_datasets", "n_features", "cumsum_features", "total_features", "percentage_features", "cumsum_percentage_features")
}


#' TabulateHVF
#'
#' @param x Seurat object.
#'
#' @export
#'
TabulateHVF <- function(x) {
  if (inherits(x, "Seurat")) x <- list(Seurat = x)
  lapply(names(x), function(n) {
    tibble(dataset = n, feature = VariableFeatures(x[[n]]), n = 1)
  }) %>% bind_rows() %>%
    group_by(.data[["feature"]]) %>% mutate(total = sum(.data[["n"]])) %>%
    spread(.data[["dataset"]], .data[["n"]], fill = 0)
}

#' IntersectFeatures
#'
#' @param x Seurat object.
#' @param assay assay name.
#' @param slot slot name.
#' @param use.hvf whether to use HVF.
#' @param cutoff cutoff for gene expression.
#'
#' @export
#'
IntersectFeatures <- function(x, assay = "RNA", slot = "data", use.hvf = TRUE, cutoff = 0) {
  features <- lapply(names(x), function(n) {
    if (use.hvf) {
      return(VariableFeatures(x[[n]]))
    } else {
      tmp <- GetAssayData(x[[n]], assay = assay, slot = slot)
      return(rownames(tmp)[rowSums(tmp) > cutoff] )
    }
  })
  Reduce(intersect, features)
}