R/validation.R

Defines functions validation.tidyHeatmap validation validation_default tidyHeatmap_to_tbl check_if_data_rectangular eliminate_sparse_transcripts check_if_attribute_present column_type_checking check_if_column_missing check_if_counts_is_na check_if_duplicated_genes check_if_wrong_input

Documented in check_if_counts_is_na check_if_duplicated_genes check_if_wrong_input

#' Check whether there are NA counts
#'
#' @import dplyr
#' @import tidyr
#' @importFrom purrr map
#'
#'
#' @param .data A tibble of read counts
#' @param list_input A list
#' @param expected_type A character string
#'
#' @return A tbl
#'
check_if_wrong_input = function(.data, list_input, expected_type) {
	# Do the check
	if (list_input %>%
			map( ~ .x %>% class() %>% `[` (1)) %>%
			unlist %>%
			equals(expected_type) %>%
			`!`)
		stop("tidyHeatmap says: You have passed the wrong argument to the function. Please check again.")
	
	# If all good return original data frame
	.data
}

#' Check whether there are duplicated genes/transcripts
#'
#' @import dplyr
#' @import tidyr
#'
#'
#' @param .data A tibble of read counts
#' @param .sample A character name of the sample column
#' @param .transcript A character name of the transcript/gene column
#' @param .abundance A character name of the read count column
#'
#' @return A tbl
check_if_duplicated_genes <- function(.data,
																			.sample,
																			.transcript,
																			.abundance ) {
	.sample = enquo(.sample)
	.transcript = enquo(.transcript)
	.abundance = enquo(.abundance)
	
	duplicates <-
		distinct(.data,!!.sample, !!.transcript, !!.abundance) %>%
		count(!!.sample, !!.transcript) %>%
		filter(n > 1) %>%
		arrange(n %>% desc())
	
	is_unique = duplicates %>% nrow() %>% equals(0)
	
	if (!is_unique) {
		writeLines("tidyHeatmap says: Those are the duplicated elements")
		duplicates %>% print()
	}
	
	is_unique
}

#' Check whether there are NA counts
#'
#' @import dplyr
#' @import tidyr
#'
#' @param .data A tibble of read counts
#' @param .abundance A character name of the read count column
#'
#' @return A tbl
#'
check_if_counts_is_na = function(.data, .abundance) {
	.abundance = enquo(.abundance)
	
	.data %>% filter(!!.abundance %>% is.na) %>% nrow %>% equals(0)
	
}

check_if_column_missing = function(.data, .sample, .transcript, .abundance) {
	# Parse column names
	.sample = enquo(.sample)
	.transcript = enquo(.transcript)
	.abundance = enquo(.abundance)
	
	# Check that the intersection is length 3
	.data %>% colnames %>%
		intersect(c(
			quo_name(.sample),
			quo_name(.transcript),
			quo_name(.abundance)
		)) %>%
		length %>%
		equals(3)
}

column_type_checking = function(.data, .sample, .transcript, .abundance) {
	# Parse column names
	.sample = enquo(.sample)
	.transcript = enquo(.transcript)
	.abundance = enquo(.abundance)
	
	.data %>% pull(!!.sample) %>% class %in% c("character", "factor") &
		.data %>% pull(!!.transcript) %>% class %in% c("character", "factor") &
		.data %>% pull(!!.abundance) %>% class %in% c("integer", "numeric", "double")
	
}

check_if_attribute_present = function(.data) {
	"tt_internals" %in% (.data %>% attributes %>% names) &&
		"tt_columns" %in% (.data %>% attr("tt_internals")  %>% names)
}

eliminate_sparse_transcripts = function(.data, .transcript){
	# Comply with CRAN NOTES
	my_n = NULL
	
	# Parse column names
	.transcript = enquo(.transcript)
	
	warning("
tidyHeatmap says: 
Some .row features have been omitted from the analysis because not present in every sample.
If you want to impute missing data use tidybulk::impute_abundance(~1, .column, .row, .abundance)
")
	
	.data %>%
		add_count(!!.transcript, name = "my_n") %>%
		filter(my_n == max(my_n)) %>%
		select(-my_n)
}

check_if_data_rectangular = function(.data, .sample, .transcript, .abundance, type = "hard"){
	
	# Parse column names
	.sample = enquo(.sample)
	.transcript = enquo(.transcript)
	.abundance = enquo(.abundance)
	
	.data %>%
		ungroup() %>%
		distinct(!!.sample, !!.transcript, !!.abundance) %>%
		count(!!.sample) %>%
		count(n) %>%
		nrow %>%
		equals(1)
	
}

tidyHeatmap_to_tbl = function(.data) {
	.data %>%	drop_class(c("tidyHeatmap", "tt"))
}

validation_default = function(.data,
															.sample,
															.transcript,
															.abundance,
															type = "hard",
															skip_dupli_check = FALSE) {
	# Parse column names
	.sample = enquo(.sample)
	.transcript = enquo(.transcript)
	.abundance = enquo(.abundance)
	
	# Type check
	is_missing = check_if_column_missing(.data,!!.sample,!!.transcript,!!.abundance)
	if (type == "hard" &
			!is_missing)
		stop(
			sprintf("tidyHeatmap says: One or more columns %s, %s or %s are missing from your data frame.", quo_name(.sample), quo_name(.transcript), quo_name(.abundance))
		)
	if (type == "soft" & !is_missing) {
		warning(
			sprintf("tidyHeatmap says: One or more columns %s, %s or %s are missing from your data frame.", quo_name(.sample), quo_name(.transcript), quo_name(.abundance))
		)
		return(.data %>% tidyHeatmap_to_tbl)
	}
	
	# Check if duplicated genes
	if (!skip_dupli_check) {
		is_unique = check_if_duplicated_genes(.data,!!.sample,!!.transcript,!!.abundance)
		if (type == "hard" &
				!is_unique)
			stop(
				"tidyHeatmap says: Your dataset include duplicated row/column pairs. Please, remove redundancies before proceeding."
			)
		if (type == "soft" & !is_unique) {
			warning(
				"tidyHeatmap says: Your dataset include duplicated row/column pairs. Please, remove redundancies before proceeding."
			)
			return(.data %>% tidyHeatmap_to_tbl)
		}
	}
	
	# # Check if NA in counts
	# is_count_good = check_if_counts_is_na(.data,!!.abundance)
	# if (type == "hard" &
	# 		!is_count_good)
	# 	stop("tidyHeatmap says: You have NA values in your counts. Please check your data frame.")
	# if (type == "soft" & !is_count_good) {
	# 	warning(
	# 		"tidyHeatmap says: You have NA values in your counts."
	# 	)
	# 	return(.data %>% tidyHeatmap_to_tbl)
	# }
	
}

validation <- function(.data,
											 .sample = NULL,
											 .transcript = NULL,
											 .abundance = NULL,
											 type = "hard",
											 skip_dupli_check = FALSE) {
	UseMethod("validation", .data)
}

validation.default =  validation_default

validation.tbl_df = validation_default
	
validation.tidyHeatmap = function(.data,
															 .sample = NULL,
															 .transcript = NULL,
															 .abundance = NULL,
															 type = "hard",
															 skip_dupli_check = FALSE) {
	# Check if attribute is present
	is_attr = check_if_attribute_present(.data)
	if (type == "hard" &
			!is_attr)
		stop(
			"tidyHeatmap says: The object provided has tidyHeatmap class but no attribute containing the column names. Insert a valid tidyHeatmap object or provide `.row`, `.column`, `.value` column names as arguments "
		)
	if (type == "soft" & !is_attr) {
		warning(
			"tidyHeatmap says: The object provided has tidyHeatmap class but no attribute containing the column names. The tidyHeatmap object has been converted to a `tbl`"
		)
		return(.data %>% tidyHeatmap_to_tbl)
	}
	
	# Get column names
	.sample = enquo(.sample)
	.transcript = enquo(.transcript)
	.abundance = enquo(.abundance)
	col_names = get_sample_transcript_counts(.data, .sample, .transcript, .abundance)
	.sample = col_names$.sample
	.transcript = col_names$.transcript
	.abundance = col_names$.abundance
	
	validation_default(
		.data,
		!!.sample,
		!!.transcript,
		!!.abundance,
		type = type,
		skip_dupli_check = skip_dupli_check
	)
	
}

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tidyHeatmap documentation built on July 7, 2021, 9:07 a.m.