cluster_characterization() method with validation

R/cluster_characterization_barplot.R

+#' Renders a barplot for cluster characterization
+#'
+#' @param object A \linkS4class{i2dash::i2dashboard} object.
+#' @param cluster Values for the membership to clusters. In case of a nested list, a dropdown menu will be provided in the interactive mode.
+#' @param x Numeric values mapped to the x-axis. In case of a nested list, a dropdown menu will be provided in the interactive mode. If x is NULL then a barplot for "Number of cells" per cluster will be created. If x is not NULL a barplot for "Fraction per cell" per cluster will be created.
+#' @param title A title that will be displayed on top.
+#'
+#' @return A string containing markdown code for the rendered textbox
+cluster_characterization_barplot <- function(object, x, cluster, title = "Characterization of clusters") {
+  # Create random env id
+  env_id <- paste0("env_", stringi::stri_rand_strings(1, 6, pattern = "[A-Za-z0-9]"))
+
+  # validate input, create environment variables, save environment object
+  .validate_input_cluster_characterizatio_barplot(object@workdir, env_id, x, cluster)
+
+  timestamp <- Sys.time()
+  expanded_component <- knitr::knit_expand(file = system.file("templates", "cluster_characterization_barplot_template.Rmd", package = "i2dash.scrnaseq"), title = title, env_id = env_id, date = timestamp)
+  return(expanded_component)
+}
+
+.validate_input_cluster_characterizatio_barplot <- function(workdir, env_id, x, cluster) {
+  env <- new.env()
+  env$x_selection <- FALSE
+  env$cluster_selection <- FALSE
+
+  # Check existence of cluster
+  if(is.null(cluster)) stop("cluster is required.")
+
+  # Create lists if needed
+  if(!is.list(x) & !is.null(x)) x <- list(x)
+  if(!is.list(cluster)) cluster <- list(cluster)
+
+  # should I use magrittr::%<>% ?
+  # name the lists
+  library(magrittr)
+  if(is.null(names(cluster))) x %<>% magrittr::set_names("clustering.1")
+  if(is.null(names(x)) & !is.null(x)) x %<>% magrittr::set_names("x")
+
+  # Check validity
+  if(!all(sapply(cluster, is.factor))) stop("'cluster' should only contain factorial values.")
+  if(!all(sapply(x, is.factor))) stop("'x' should only contain factorial values.")
+
+  # Check if lengths in a list are the same and if x and y and label and color_by are the same length
+  #if(length(unique(sapply(x, length))) != 1) stop("list x should contain elements with the same length.")
+  #if(length(unique(sapply(y, length))) != 1) stop("list y should contain elements with the same length.")
+
+  #if(!identical(length(x[[1]]), length(y[[1]]))) stop("all arguments should be of the the same length.")
+  #if(!identical(length(x[[1]]), length(colour_by[[1]])) & !is.null(colour_by)) stop("all arguments should be of the the same length.")
+  #if(!identical(length(x[[1]]), length(labels[[1]])) & !is.null(labels)) stop("all arguments should be of the the same length.")
+
+  # Add objects to env
+  env$x <- x
+  env$x_selection <- length(env$x) > 1
+
+  env$cluster <- cluster
+  env$cluster_selection <- length(env$cluster) > 1
+
+  # save environment as rds-object
+  saveRDS(env, file = file.path(workdir, "envs", paste0(env_id, ".rds")))
+  print("validation TRUE")
+}