R/convenience.R

In lambdamoses/SeuratBasics: Slimmed down version of Seurat

#' @include generics.R
#' @include visualization.R
#'
NULL

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Functions
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

#' @param ... Extra parameters passed to \code{DimHeatmap}
#'
#' @rdname DimHeatmap
#' @export
#'
PCHeatmap <- function(object, ...) {
  args <- list('object' = object)
  args <- c(args, list(...))
  args$reduction <- "pca"
  return(do.call(what = 'DimHeatmap', args = args))
}

#' @param ... Extra parameters passed to \code{DimPlot}
#'
#' @rdname DimPlot
#' @export
#'
PCAPlot <- function(object, ...) {
  return(SpecificDimPlot(object = object, ...))
}

#' @rdname DimPlot
#' @export
#'
TSNEPlot <- function(object, ...) {
  return(SpecificDimPlot(object = object, ...))
}

#' @rdname DimPlot
#' @export
#'
UMAPPlot <- function(object, ...) {
  return(SpecificDimPlot(object = object, ...))
}

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Methods for Seurat-defined generics
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Methods for R-defined generics
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Internal
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

# @rdname DimPlot
#
SpecificDimPlot <- function(object, ...) {
  funs <- sys.calls()
  name <- as.character(x = funs[[length(x = funs) - 1]])[1]
  name <- tolower(x = gsub(pattern = 'Plot', replacement = '', x = name))
  args <- list('object' = object)
  args <- c(args, list(...))
  reduc <- grep(
    pattern = name,
    x = names(x = object),
    value = TRUE,
    ignore.case = TRUE
  )
  reduc <- grep(pattern = DefaultAssay(object = object), x = reduc, value = TRUE)
  args$reduction <- ifelse(test = length(x = reduc) == 1, yes = reduc, no = name)
  tryCatch(
    expr = return(do.call(what = 'DimPlot', args = args)),
    error = function(e) {
      stop(e)
    }
  )
}