ggpubr: 'ggplot2' Based Publication Ready Plots

Documented in compare_means

#' @include utilities.R
NULL
#'Comparison of Means
#'@description Performs one or multiple mean comparisons.
#'@param formula a formula of the form \code{x ~ group} where \code{x} is a
#'  numeric variable giving the data values and \code{group} is a factor with
#'  one or multiple levels giving the corresponding groups. For example,
#'  \code{formula = TP53 ~ cancer_group}.
#'
#'  It's also possible to perform the test for multiple response variables at
#'  the same time. For example, \code{formula = c(TP53, PTEN) ~ cancer_group}.
#'@param data a data.frame containing the variables in the formula.
#'@param method the type of test. Default is \link[stats]{wilcox.test}. Allowed
#'  values include: \itemize{ \item \code{\link[stats]{t.test}} (parametric) and
#'  \code{\link[stats]{wilcox.test}} (non-parametric). Perform comparison
#'  between two groups of samples. If the grouping variable contains more than
#'  two levels, then a pairwise comparison is performed. \item
#'  \code{\link[stats]{anova}} (parametric) and
#'  \code{\link[stats]{kruskal.test}} (non-parametric). Perform one-way ANOVA
#'  test comparing multiple groups. }
#'@param paired a logical indicating whether you want a paired test. Used only
#'  in \code{\link[stats]{t.test}} and in \link[stats]{wilcox.test}.
#'@param group.by  a character vector containing the name of grouping variables.
#'@param ref.group a character string specifying the reference group. If
#'  specified, for a given grouping variable, each of the group levels will be
#'  compared to the reference group (i.e. control group).
#'
#'  \code{ref.group} can be also \code{".all."}. In this case, each of the
#'  grouping variable levels is compared to all (i.e. basemean).
#'@param symnum.args a list of arguments to pass to the function
#'  \code{\link[stats]{symnum}} for symbolic number coding of p-values. For
#'  example, \code{symnum.args <- list(cutpoints = c(0, 0.0001, 0.001,
#'  0.01, 0.05, Inf), symbols = c("****", "***", "**", "*",  "ns"))}.
#'
#'  In other words, we use the following convention for symbols indicating
#'  statistical significance: \itemize{ \item \code{ns}: p > 0.05 \item
#'  \code{*}: p <= 0.05 \item \code{**}: p <= 0.01 \item \code{***}: p <= 0.001 \item \code{****}:  p <= 0.0001 }
#'@param p.adjust.method method for adjusting p values (see
#'  \code{\link[stats]{p.adjust}}). Has impact only in a situation, where
#'  multiple pairwise tests are performed; or when there are multiple grouping
#'  variables. Allowed values include "holm", "hochberg", "hommel",
#'  "bonferroni", "BH", "BY", "fdr", "none". If you don't want to adjust the p
#'  value (not recommended), use p.adjust.method = "none".
#'
#'  Note that, when the \code{formula} contains multiple variables, the p-value
#'  adjustment is done independently for each variable.
#'@return return a data frame with the following columns:
#'\itemize{
#'\item \code{.y.}: the y variable used in the test.
#'\item \code{group1,group2}: the compared groups in the pairwise tests.
#'Available only when \code{method = "t.test"} or \code{method = "wilcox.test"}.
#'\item \code{p}: the p-value.
#'\item \code{p.adj}: the adjusted p-value. Default for \code{p.adjust.method = "holm"}.
#'\item \code{p.format}: the formatted p-value.
#'\item \code{p.signif}: the significance level.
#'\item \code{method}: the statistical test used to compare groups.
#'
#'
#'}
#'@param ... Other arguments to be passed to the test function.
#' @examples
#' # Load data
#' #:::::::::::::::::::::::::::::::::::::::
#' data("ToothGrowth")
#' df <- ToothGrowth
#'
#' # One-sample test
#' #:::::::::::::::::::::::::::::::::::::::::
#' compare_means(len ~ 1, df, mu = 0)
#'
#' # Two-samples unpaired test
#' #:::::::::::::::::::::::::::::::::::::::::
#' compare_means(len ~ supp, df)
#'
#' # Two-samples paired test
#' #:::::::::::::::::::::::::::::::::::::::::
#' compare_means(len ~ supp, df, paired = TRUE)
#'
#' # Compare supp levels after grouping the data by "dose"
#' #::::::::::::::::::::::::::::::::::::::::
#' compare_means(len ~ supp, df, group.by = "dose")
#'
#' # pairwise comparisons
#' #::::::::::::::::::::::::::::::::::::::::
#' # As dose contains more thant two levels ==>
#' # pairwise test is automatically performed.
#' compare_means(len ~ dose, df)
#'
#' # Comparison against reference group
#' #::::::::::::::::::::::::::::::::::::::::
#' compare_means(len ~ dose, df, ref.group = "0.5")
#'
#' # Comparison against all
#' #::::::::::::::::::::::::::::::::::::::::
#' compare_means(len ~ dose, df, ref.group = ".all.")
#'
#' # Anova and kruskal.test
#' #::::::::::::::::::::::::::::::::::::::::
#' compare_means(len ~ dose, df, method = "anova")
#' compare_means(len ~ dose, df, method = "kruskal.test")

#' @rdname compare_means
#' @export
compare_means <- function(formula, data, method = "wilcox.test",
                          paired = FALSE,
                          group.by = NULL, ref.group = NULL,
                          symnum.args = list(), p.adjust.method = "holm", ...)
{

  . <- NULL

  method.info <- .method_info(method)
  method <- method.info$method
  method.name <- method.info$name

  if(.is_empty(symnum.args))
    symnum.args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05,  1),
                        symbols = c("****", "***", "**", "*",  "ns"))

  if(!inherits(data, "data.frame"))
    stop("data must be a data.frame.")

  variables <- response.var <- .formula_left_variables(formula)
  group <- .formula_right_variables(formula)
  if(group == "1") group <- NULL # NULL model

  if(!.is_empty(group)){
    group.vals <- .select_vec(data, group)
    if(!is.factor(group.vals)) data[[group]] <- factor(group.vals, levels = unique(group.vals))
  }

  # Keep only variables of interest
  data <- data %>%
    df_select(vars = c(group.by, group, variables))

  # Case of formula with multiple variables
  #   1. Gather the data
  #   2. group by variable
  #   3. Perform pairwise test between levels of each grouing variable
  #:::::::::::::::::::::::::::::::::::::::::::::::::::::
  # ex: formula = c(GATA3, XBP1, DEPDC1) ~ group
  if(.is_multi_formula(formula)){
    data <- df_gather(data, cols = variables, names_to = ".y.", values_to = ".value.") %>%
      dplyr::mutate(.y. = factor(.data$.y., levels = unique(.data$.y.)))
    response.var <- ".value."
    group.by = c(group.by,  ".y.")
    formula <- .collapse(response.var, group, sep = " ~ ") %>% stats::as.formula()
  }

  # Check if comparisons should be done against a reference group
  #:::::::::::::::::::::::::::::::::::::::::::::::::::::
  if(!is.null(ref.group)){

    group.vals <- .select_vec(data, group)
    if(is.factor(group.vals)) group.levs <- levels(group.vals)
    else group.levs <- unique(group.vals)

    if(ref.group %in% group.levs){
      data[[group]] <- stats::relevel(group.vals, ref.group)
    }

    if(ref.group == ".all."){
      data <- data %>%
        mutate(.group. = as.character(group.vals),
               .all. = ".all.") # Add 'all' column
      # Create a new grouping column gathering group and the .all. columns
      .group.name. <- NULL
      data <- data %>%
        df_gather(cols = c(".group.", ".all."), names_to =  ".group.name.", values_to = ".group.") %>%
        dplyr::select(-.group.name.)
      data[[".group."]] <- factor(data[[".group."]], levels = c(".all.", group.levs))
      group <- ".group."
      formula <- .collapse(response.var, group, sep = " ~ ") %>% stats::as.formula()

    }
    else if(!(ref.group %in% group.levs)){
      stop("Can't find specified reference group: ", ref.group, ". ",
           "Allowed values include one of: ", .collapse(group.levs, sep = ", "), call. = FALSE)
    }
  }

  # Peform the test
  #:::::::::::::::::::::::::::::::::::::::::::::::::::::
  test.func <- .test_pairwise
  if(method %in% c("anova", "kruskal.test"))
    test.func <- .test_multigroups

  if(is.null(group.by)){
    res <- test.func(formula = formula, data = data, method = method,
                     paired = paired, p.adjust.method = "none", ...)
  }
  else{
    grouped.d <- .group_by(data, group.by)
    res <- grouped.d %>%
      mutate(p = purrr::map(
        data,
        test.func, formula = formula,
        method = method, paired = paired, p.adjust.method = "none",...)
      ) %>%
      df_select(vars = c(group.by, "p")) %>%
      unnest(cols = "p")
  }

  # Add response variables to the result
  #:::::::::::::::::::::::::::::::::::::::::::::::::::::
  if(!c(".y." %in% colnames(res)))
    res <- res %>%
    dplyr::mutate(.y. = variables) %>%
    dplyr::select(!!!syms(c(group.by, ".y.")), dplyr::everything())

  # Select only reference groups if any
  #::::::::::::::::::::::::::::::::::::::::::::::::::::::::
  if(!is.null(ref.group)){
    group.levs <- .select_vec(data, group) %>% .levels()
    group1 <- NULL
    res <- res %>% dplyr::filter(group1 == ref.group | group2 == ref.group)
    # ref.group should be always in group1 column
    # swap group1 and group2 if group2 contains ref.group
    group2 <- res$group2
    res <- transform(res,
                    group1 = ifelse(group2 == ref.group, group2, group1),
                    group2 = ifelse(group2 == ref.group, group1, group2))
  }
  # Formatting and adjusting pvalues, and adding significance symbols
  #:::::::::::::::::::::::::::::::::::::::::::::::::::::
  symnum.args$x <- res$p
  pvalue.signif <- do.call(stats::symnum, symnum.args) %>%
    as.character()

  pvalue.format <- format.pval(res$p, digits = 2)

  .y. <- p.adj <- NULL
  .p.adjust <- function(d, ...) {data.frame(p.adj = stats::p.adjust(d$p, ...))}
  by_y <- res %>% group_by(.y.)
  pvalue.adj <- do(by_y, .p.adjust(., method = p.adjust.method))
  res <- res %>%
    dplyr::ungroup() %>%
    mutate(p.adj = pvalue.adj$p.adj, p.format = pvalue.format, p.signif = pvalue.signif,
           method = method.name)

  res %>%
    mutate(p.adj = signif(p.adj, digits = 2)) %>%
    tibble::as_tibble()
}


# Check and get test method info
#:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
# return a list(method, name)
.method_info <- function(method){

  if(is.null(method))
    method = "wilcox.test"

  allowed.methods <- list(
    t = "t.test", t.test = "t.test", student = "t.test",
    wiloxon = "wilcox.test", wilcox = "wilcox.test", wilcox.test = "wilcox.test",
    anova = "anova", aov = "anova",
    kruskal = "kruskal.test", kruskal.test = "kruskal.test")

  method.names <- list(
    t.test = "T-test", wilcox.test = "Wilcoxon",
    anova = "Anova", kruskal.test = "Kruskal-Wallis")

  if(!(method %in% names(allowed.methods)))
    stop("Non-supported method specified. Allowed methods are one of: ",
         .collapse(allowed.methods, sep =", "))
  method <- allowed.methods[[method]]
  method.name <- method.names[[method]]

  list(method = method, name = method.name)
}

# Comparing two groups
#:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
.test <- function(data, formula, method = "t.test",  ...)
{
  test <- match.fun(method)

  x <- deparse(formula[[2]])
  group <- attr(stats::terms(formula), "term.labels")

  if(.is_empty(group)) # Case of null model
    test.opts <- list(x = .select_vec(data, x), ...)
  else test.opts <- list(formula = formula, data = data, ...)

  res <- data.frame(p = suppressWarnings(do.call(test, test.opts)$p.value))
  group1 <- group2 <- NULL

  if(!.is_empty(group)){
    group.lev <- .select_vec(data, group) %>% levels()
    res <- res %>%
      dplyr::mutate(
        group1 = group.lev[1],
        group2 = group.lev[2]
      ) %>%
      dplyr::select(group1,group2, dplyr::everything())
  }
  else res <- res %>% dplyr::mutate(group1 = 1, group2 = "null model") %>%
    dplyr::select(group1, group2, everything())
  res
}


# pairwise test
#:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
.test_pairwise <- function(data, formula, method = "wilcox.test",
                           paired = FALSE, pool.sd = !paired,
                           ...)
{

  x <- deparse(formula[[2]])
  group <- attr(stats::terms(formula), "term.labels")

  # One sample test
  if(.is_empty(group)){
    res <- .test(data, formula, method = method,  ...)
    return(res)
  }

  # Pairwise test
  method <- switch(method,
                   t.test = "pairwise.t.test",
                   wilcox.test = "pairwise.wilcox.test")
  test <- match.fun(method)

  test.opts <- list(x = .select_vec(data, x),
                    g = .select_vec(data, group),
                    paired = paired,
                    ...)
  # if(method == "pairwise.wilcox.test") test.opts$exact <- FALSE
  if(method == "pairwise.t.test"){
    if(missing(pool.sd)){
      if(!paired) pool.sd <- FALSE
    }
    test.opts$pool.sd <- pool.sd
  }

  pvalues <- suppressWarnings(do.call(test, test.opts)$p.value) %>%
    as.data.frame()
  ..group1.. <- ..group2.. <- p <- NULL
  pvalues$..group2.. <- rownames(pvalues)
  pvalues <- pvalues %>%
    tidyr::gather(key = "..group1..", value = "p", -..group2..) %>%
    dplyr::select(group1 = ..group1.., group2 = ..group2.., p) %>%
    dplyr::filter(!is.na(p))
  pvalues
}

# Compare multiple groups
#::::::::::::::::::::::::::::::::::::::::::::::::::

.test_multigroups <- function(data, formula, method = c("anova", "kruskal.test"), ...){

  method <- match.arg(method)
  . <- NULL

  if(method == "anova")
    pvalue <- stats::lm(formula, data = data) %>%
    stats::anova(.) %>%
    .$`Pr(>F)` %>%
    .[1]
  else if(method == "kruskal.test"){
    pvalue <- stats::kruskal.test(formula, data = data)$p.value
  }

  data.frame(p = pvalue)
}



# Formula with multiple response variables
#:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
# ex formula = c(GATA3, XBP1, DEPDC1) ~ group
.is_multi_formula <- function(formula){
  x <- grep(",", formula)
  !.is_empty(x)
}

# Get formula variables
.formula_left_variables <- function(formula){
  . <- NULL
  x <- deparse(formula[[2]]) %>%
    gsub("c\\(|\\)|\\s", "", .) %>%
    strsplit(",") %>%
    unlist()
  x
}
.formula_right_variables <- function(formula){
  group <- attr(stats::terms(formula), "term.labels")
  if(.is_empty(group)) group <- "1"
  group
}

.update_test_arguments <- function(formula, data, group.by){

  variables <- .formula_left_variables(formula)
  group <- .formula_right_variables(formula)

  data <- data %>%
    df_gather(cols = variables, names_to = ".y.", values_to = ".value.") %>%
    dplyr::mutate(.y. = factor(.data$.y., levels = unique(.data$.y.)))
  formula <- .collapse(".value.", group, sep = " ~ ") %>% stats::as.formula()
  group.by = c(group.by, ".y.")

}