R/long_wide_convertor.R

In tidymass/tinytools: All the usefull tools for MS data processing and analysis

#' ##------------------------------------------------------------------------------
#' #' @title convert2long
#' #' @description Convert from wide data to long data.
#' #' @author Xiaotao Shen
#' #'\email{shenxt1990@@outlook.com}
#' #' @param expression_data expression_data
#' #' @param sample_info sample_info
#' #' @param variable_info variable_info
#' #' @importFrom magrittr %>%
#' #' @importFrom tibble rownames_to_column
#' #' @importFrom tidyr pivot_longer
#' #' @importFrom dplyr left_join
#' #' @importFrom dplyr select
#' #' @importFrom dplyr everything
#' #' @export
#'
#' convert2long <-
#'   function(expression_data,
#'            sample_info,
#'            variable_info) {
#'     final_data <-
#'       expression_data %>%
#'       as.data.frame() %>%
#'       tibble::rownames_to_column(var = "variable_id") %>%
#'       tidyr::pivot_longer(
#'         cols = -variable_id,
#'         names_to = "sample_id",
#'         values_to = "value"
#'       ) %>%
#'       dplyr::left_join(sample_info, by = "sample_id") %>%
#'       dplyr::left_join(variable_info, by = "variable_id") %>%
#'       dplyr::select(sample_id, variable_id, value, dplyr::everything())
#'     return(final_data)
#'   }
#'
#'
#' ##------------------------------------------------------------------------------
#' ##------------------------------------------------------------------------------
#' #' @title convert2wide
#' #' @description Convert from wide data to long data.
#' #' @author Xiaotao Shen
#' #'\email{shenxt1990@@outlook.com}
#' #' @param data data
#' #' @param sample_info_name sample_info_name
#' #' @param variable_info_name variable_info_name
#' #' @importFrom magrittr %>%
#' #' @importFrom tibble rownames_to_column
#' #' @importFrom tibble column_to_rownames
#' #' @importFrom dplyr distinct
#' #' @importFrom tidyr pivot_longer
#' #' @importFrom dplyr left_join
#' #' @importFrom dplyr select
#' #' @importFrom dplyr everything
#' #' @export
#'
#' # sample_info_name = c(
#' #   "sample_id",
#' #   "subject_id",
#' #   "accurate_time",
#' #   "day",
#' #   "time",
#' #   "time_window",
#' #   "seconds",
#' #   "hour"
#' # )
#' #
#' # variable_info_name = c("variable_id", "mol_name", "class")
#'
#' convert2wide <-
#'   function(data,
#'            sample_info_name = c("sample_id"),
#'            variable_info_name = c("variable_id")) {
#'     variable_info <-
#'       data %>%
#'       dplyr::select(variable_info_name) %>%
#'       dplyr::distinct(.keep_all = TRUE) %>%
#'       as.data.frame() %>%
#'       dplyr::select(variable_id, dplyr::everything())
#'
#'     expression_data <-
#'       data %>%
#'       dplyr::select(sample_id, variable_id, value) %>%
#'       tidyr::pivot_wider(names_from = sample_id,
#'                          values_from = value) %>%
#'       as.data.frame() %>%
#'       tibble::column_to_rownames(var = "variable_id")
#'
#'     sample_info <-
#'       data %>%
#'       dplyr::select(sample_info_name) %>%
#'       dplyr::distinct(.keep_all = TRUE) %>%
#'       as.data.frame() %>%
#'       dplyr::select(sample_id, dplyr::everything())
#'
#'     expression_data =
#'       expression_data[, sample_info$sample_id]
#'     expression_data =
#'       expression_data[variable_info$variable_id, ]
#'
#'
#'     final_data <-
#'       list(
#'         sample_info = sample_info,
#'         variable_info = variable_info,
#'         expression_data = expression_data
#'       )
#'     return(final_data)
#'   }