R/core_venn.R

In MayaGans/CoreMicro: Testing Widely Used Core Microbiome Assignment Methods

#' Core Venn Diagram
#'
#' Create a venn diagram using the output of core_methods to find which core taxa are included
#' in which methods
#'
#' @param combined_taxa_data the taxa data of type \code{core_methods}
#' @param category_names the names of the core inclusion methods.
#' @param low the low hexedicmal color
#' @param high the high hexidecimal color
#'
#' @examples
#' \dontrun{
#' core_arabidopsis <- core_methods(arabidopsis)
#' core_venn(core_arabidopsis)
#' }
#' @export
core_venn <- function(combined_taxa_data,
                             category_names = c("Summation of \n Sequence Reads",
                                                "Proportion of \n Sequence Replicates",
                                                "Proportion of \n Sequence Reads and Replicates",
                                                "Hard Cut Off"),
                             low = "white",
                             high = "#7E191B") {

  UseMethod("core_venn", combined_taxa_data)

}


#' @return NULL
#' @export
#' @rdname core_venn
core_venn.default <- function(combined_taxa_data,
                             category_names = c("Summation of \n Sequence Reads",
                                                "Proportion of \n Sequence Replicates",
                                                "Proportion of \n Sequence Reads and Replicates",
                                                "Hard Cut Off"),
                             low = "white",
                             high = "#7E191B") {

  x <- deparse(substitute(combined_otu_data))

  rlang::abort(
    glue::glue("to create plot,
               {x} must be of type core_methods.
               Please run core_methods({x})  prior to plotting")
  )

}

#' @return a venn diagram of the taxa included within each core method
#'
#' @export
#' @rdname core_venn
core_venn.core_methods <- function(combined_taxa_data,
                                     category_names = c("Summation of \n Sequence Reads",
                                                        "Proportion of \n Sequence Replicates",
                                                        "Proportion of \n Sequence Reads and Replicates",
                                                        "Hard Cut Off"),
                                     low = "white",
                                     high = "#7E191B") {

    temp <-
      data.frame(combined_taxa_data) %>%
      dplyr::filter(.data$value == 1) %>%
      dplyr::select(.data$X, .data$name)

    temp <- lapply(split(temp, temp$name), `[[`, "X")

    suppressMessages(
      suppressWarnings(
        ggVennDiagram::ggVennDiagram(temp, category.names = category_names, set_size = 12, label_size = 10) +
          ggplot2::scale_fill_gradient(low=low,high = high) +
          scale_color_manual(values = rep("black", 4))
      )
    )

}