Nothing
#' Automatic Exploratory Data Analysis PDF Report
#'
#' @description This function automatically generates a PDF report with different exploratory plots and tables from an MSnSet object.
#'
#' @param data A MSnSet object. First `pData` column must be the subject group/type.
#' @param imputation Imputation method. Options are "none", "half_min", "median", "mean", "min" and "knn" (default). If "none", all missing values will be replaced by zero.
#' @param normalization Normalization method. Options are "none", "auto_scaling", "level_scaling", "log_scaling", "log_transformation", "vast_scaling" and "log_pareto" (default).
#' @param clean_outliers Logical. If it's set to TRUE, outliers will be removed from EDA.
#' @param coeff_outliers This value corresponds to the classical 1.5 in \eqn{Q3 + 1.5*IQR} formula to detect outliers. By changing this value, the permissiveness in outlier detection will change.
#' @param username This name will be included as a report subtitle.
#'
#' @export
#'
#' @return An exploratory data analysis PDF report.
#' @author Pol Castellano-Escuder
#'
#' @importFrom rmarkdown render
#' @import knitr
#' @import patchwork
#' @importFrom crayon red
#' @importFrom clisymbols symbol
PomaEDA <- function(data, # nocov start
imputation = "knn",
normalization = "log_pareto",
clean_outliers = TRUE,
coeff_outliers = 1.5,
username = "Username"){
if (missing(data)) {
stop(crayon::red(clisymbols::symbol$cross, "data argument is empty!"))
}
if(!is(data[1], "MSnSet")){
stop(paste0(crayon::red(clisymbols::symbol$cross, "data is not a MSnSet object."),
" \nSee POMA::PomaMSnSetClass or MSnbase::MSnSet"))
}
if (!(imputation %in% c("none", "half_min", "median", "mean", "min", "knn"))) {
stop(crayon::red(clisymbols::symbol$cross, "Incorrect value for imputation argument!"))
}
if (!(normalization %in% c("none", "auto_scaling", "level_scaling", "log_scaling",
"log_transformation", "vast_scaling", "log_pareto"))) {
stop(crayon::red(clisymbols::symbol$cross, "Incorrect value for normalization argument!"))
}
rmarkdown::render(system.file("rmd", "POMA_EDA_report.Rmd", package = "POMA"), "pdf_document")
} # nocov end
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.