R/config_process_single_sample.R

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

#' @rdname process_config
.process_input_qc_config <- function(cfg, other_variables) {
  if (!cfg$ENABLE_CELL_FILTERING) {
    cli_alert_info(str_space(
      "Cell filtering is disabled ({.field ENABLE_CELL_FILTERING} is {.val {FALSE}}),",
      "setting all filtering thresholds to cell-always-pass values."
    ))

    cfg$MAD_THRESHOLD <- Inf
    cfg$MIN_UMI_CF <- -Inf
    cfg$MAX_UMI_CF <- Inf
    cfg$MIN_FEATURES <- -Inf
    cfg$MAX_MITO_RATIO <- Inf
  }

  if (!cfg$ENABLE_GENE_FILTERING) {
    cli_alert_info(str_space(
      "Gene filtering is disabled ({.field ENABLE_GENE_FILTERING} is {.val {FALSE}}),",
      "setting all filtering thresholds to gene-always-pass values."
    ))

    cfg$MIN_UMI <- 0
    cfg$MIN_RATIO_CELLS <- 0
  }

  possible_input_data_types <- c("cellranger", "table", "sce", "sce_drake_cache")
  assert_that_(
    !is_null(cfg$INPUT_DATA$type), cfg$INPUT_DATA$type %in% possible_input_data_types,
    msg = "{.var input_data$type} must be {.vals possible_input_data_types}. Current value: {.val {cfg$INPUT_DATA$type}}"
  )

  possible_filters_operators <- c("&", "|")
  for (param_name in c("DATASET_SENSITIVE_FILTERS_OPERATOR", "CUSTOM_FILTERS_OPERATOR")) {
    val <- cfg[[param_name]]
    assert_that_(
      val %in% possible_filters_operators,
      msg = "{.field {param_name}} must be one of {.vals {possible_filters_operators}}. Current value: {.val {val}}"
    )
  }

  assert_that_(
    !is_null(cfg$INPUT_DATA$path),
    msg = "{.field INPUT_DATA$type} is not set, data cannot be loaded later."
  )
  cfg$INPUT_DATA$path <- here(cfg$INPUT_DATA$path)
  cfg <- .hereize_paths(cfg, "INPUT_QC_REPORT_RMD_FILE")
  cfg <- .paths_to_base_dir(cfg, other_variables$BASE_OUT_DIR, "INPUT_QC_BASE_OUT_DIR")
  cfg <- .paths_to_base_dir(cfg, cfg$INPUT_QC_BASE_OUT_DIR, "INPUT_QC_REPORT_HTML_FILE")

  return(cfg)
}

#' @rdname process_config
.process_norm_clustering_config <- function(cfg, other_variables) {
  if (is_empty(cfg$SCT_VARS_TO_REGRESS)) {
    cfg <- add_item_to_list(cfg, "SCT_VARS_TO_REGRESS")
  }

  cfg$CELL_GROUPINGS <- .get_dict_param(cfg$CELL_GROUPINGS, not_empty = FALSE, empty_to_null = FALSE)
  NORM_CLUSTERING_REPORT_DIMRED_PLOTS_OTHER <- .get_dict_param(
    cfg$NORM_CLUSTERING_REPORT_DIMRED_PLOTS_OTHER,
    not_empty = FALSE, empty_to_null = TRUE
  )

  if (!is_null(NORM_CLUSTERING_REPORT_DIMRED_PLOTS_OTHER)) {
    NORM_CLUSTERING_REPORT_DIMRED_PLOTS_OTHER <- purrr::map(
      names(NORM_CLUSTERING_REPORT_DIMRED_PLOTS_OTHER),
      ~ list(name = ., label = NORM_CLUSTERING_REPORT_DIMRED_PLOTS_OTHER[[.]])
    ) %>%
      set_names(names(NORM_CLUSTERING_REPORT_DIMRED_PLOTS_OTHER))
  }

  cfg$NORM_CLUSTERING_REPORT_DIMRED_PLOTS_OTHER <- NORM_CLUSTERING_REPORT_DIMRED_PLOTS_OTHER

  if (cfg$NORMALIZATION_TYPE == "scran") {
    assert_that_(
      cfg$HVG_METRIC != "sctransform",
      msg = "{.field HVG_METRIC} of {.val sctransform} can be used only if {.field NORMALIZATION_TYPE} is {.val sctransform}"
    )
  }

  if (is_empty(cfg$CELL_ANNOTATION_SOURCES)) {
    cfg <- add_item_to_list(cfg, "CELL_ANNOTATION_SOURCES")
  } else {
    cfg$CELL_ANNOTATION_SOURCES <- .prepare_cell_annotation_sources_params(
      cfg$CELL_ANNOTATION_SOURCES, cfg$CELL_ANNOTATION_SOURCES_DEFAULTS
    )
  }

  input_files <- c("NORM_CLUSTERING_REPORT_RMD_FILE", "NORM_CLUSTERING_REPORT_SIMPLE_RMD_FILE")
  if (!is_null(cfg$SELECTED_MARKERS_FILE)) {
    input_files <- c("SELECTED_MARKERS_FILE", input_files)
  }

  cfg <- .hereize_paths(cfg, input_files)
  cfg <- .paths_to_base_dir(cfg, other_variables$BASE_OUT_DIR, "NORM_CLUSTERING_BASE_OUT_DIR")
  cfg <- .paths_to_base_dir(
    cfg, cfg$NORM_CLUSTERING_BASE_OUT_DIR, c(
      "NORM_CLUSTERING_SELECTED_MARKERS_OUT_DIR", "NORM_CLUSTERING_CELL_ANNOTATION_OUT_DIR",
      "NORM_CLUSTERING_DIMRED_PLOTS_OUT_DIR", "NORM_CLUSTERING_OTHER_PLOTS_OUT_DIR",
      "NORM_CLUSTERING_REPORT_HTML_FILE", "NORM_CLUSTERING_REPORT_SIMPLE_HTML_FILE"
    )
  )

  return(cfg)
}