R/getStatAnnotationAnchorLines.R

In cusom/CUSOM.ShinyHelpers: CU School of Medicine Helper Functions for Shiny Applications

#' function to generate list of line anchors for stat annotations
#'
#' @param .data dataframe
#' @param group column of group labels used to calcualte statistic
#' @param groupMembers string/vector - all possible group labels
#' from group column
#' @param significanceVariable column containing statistical variable
#' result (i.e. p.value from statistical test)
#' @param groupIsSignificant column - logical indicating whether
#' significanceVariable value is significant.
#' @param includeInsignificantValues logical - whether to include
#' results that are not significant. Defaults to FALSE
#' @return list of position references for each annotation
#' @importFrom rlang enquo
#' @import dplyr
#' @export

getStatAnnotationAnchorLines <- function (
  .data,
  group,
  groupMembers,
  significanceVariable,
  groupIsSignificant,
  includeInsignificantValues = FALSE
) {

  group <- rlang::enquo(group)
  significanceVariable <- rlang::enquo(significanceVariable)
  groupIsSignificant <- rlang::enquo(groupIsSignificant)

  dataGroupMembers <- .data |>
    dplyr::select(!!group) |>
    dplyr::distinct() |>
    dplyr::pull()

  allGroupMembers <- intersect(groupMembers, dataGroupMembers)

  line <- list(
    type = "line",
    x = 0,
    y = 0,
    line = list(
      color = "grey"
    ), 
    xref = "x",
    yref = "paper",
    showarrow = FALSE
  )

  lines <- list()

  xpositions <- seq(-0.2, length(allGroupMembers) - 1, 1)

  i <- 0

  for (igroup in allGroupMembers) {

    i <- i + 1

    statResult <- .data |>
      dplyr::filter(!!group == igroup) |>
      dplyr::select(!!significanceVariable) |>
      dplyr::distinct() |>
      dplyr::pull()

    isSignificant <- .data |>
      dplyr::filter(!!group == igroup) |>
      dplyr::select(!!groupIsSignificant) |>
      dplyr::distinct() |>
      dplyr::pull()

    if (!is.na(statResult) || includeInsignificantValues) {
      line[["x0"]] <- xpositions[i]
      line[["x1"]] <- xpositions[i] + 0.5
      line[["y0"]] <- 1
      line[["y1"]] <- 1
      line[["statResult"]] <- statResult
      line[["isSignificant"]] <- isSignificant
      line[["group"]] <- igroup
      lines <- c(lines, list(line))
    }
  }
  return(lines)
}