R/ba_chart-methods.R

In c5sire/brapix: Additional Convenience Tools to Tnteract with BrAPI Compatible Databases

#' ba_chart.ba_locations
#'
#' method for an object of class brapi_locations, which will only display the crop, database address:port and user
#'
#' @param x a brapi_locations data.frame/tibble or a numeric vector of longitudes
#' @param ... other plot parameters
#' @example inst/examples/ex-chart_locations.R
#' @author Reinhard Simon
#' @family brapiutils
#' @import magrittr
#' @export
ba_chart.ba_locations <- function(x, ...) {
  prms <- list(...)
  chart_type <- ifelse(!is.null(prms$chart_type), prms$chart_type, "plot")
  stopifnot(chart_type %in% c("plot", "map"))
  locs <- x
  with_geo <- locs[!is.na(locs$latitude), ]
  stopifnot(nrow(with_geo) > 0)
  if (chart_type == "plot") {
    graphics::plot(x = locs$longitude, y = locs$latitude)
  }
  if (chart_type == "map") {
    can_map <- exists(x = "worldMapEnv")
    if (can_map) {
      maps::map()
      with_geo$latitude <- with_geo$latitude %>% as.numeric()
      with_geo$longitude <- with_geo$longitude %>% as.numeric()
      xr <- range(with_geo$longitude)
      yr <- range(with_geo$latitude)
      maps::map(database = "world", xlim = xr, ylim = yr)
      graphics::title(main = paste0("Locations from database"))
      graphics::points(x = with_geo$longitude, y = with_geo$latitude, col = "red")
      maps::map.axes()
    } else {
      message(paste0("Please install and load: library(maps)"))
    }
  }
  return(invisible())
}

#' ba_chart.ba_genomemaps
#'
#' print method for an object of class brapi_brapi_genomemaps, which will only display the crop,  database address:port and user
#'
#' @param x a brapi_locations data.frame/tibble or a numeric vector of longitudes
#' @param ... other plot parameters
#' @example inst/examples/ex-chart_genome_maps.R
#' @author Reinhard Simon
#' @family brapiutils
#' @export
ba_chart.ba_genomemaps <- function(x, ...) {
  prms <- list(...)
  stopifnot(!is.null(x$numberMarkers & !is.null(x$mapDbId)))
  chart_type <- ifelse(!is.null(prms$chart_type), prms$chart_type, "plot")
  stopifnot(chart_type %in% c("plot"))
  if (chart_type == "plot") {
    ttl <- paste0("Comparative view of genome maps")
    graphics::barplot(height = x$numberMarkers,
                      horiz = T,
                      axisnames = T,
                      names.arg = x$linkageGroupId,
                      las = 1,
                      main = ttl,
                      xlab = "Number of markers")
  }
  return(invisible())
}

#' ba_chart.ba_genomemaps_details
#'
#' print method for an object of class brapi_brapi_genomemaps_details, which will only display the crop,  database address:port and user
#'
#' @param x a brapi_genomemaps_details_data data.frame/tibble or a numeric vector of longitudes
#' @param ... other plot parameters
#' @example inst/examples/ex-chart_genome_maps_details.R
#' @author Reinhard Simon
#' @family brapiutils
#' @export
ba_chart.ba_genomemaps_details <- function(x, ...) {
  prms <- list(...)
  chart_type <- ifelse(!is.null(prms$chart_type), prms$chart_type, "plot")
  stopifnot(chart_type %in% c("plot"))
  if (chart_type == "plot") {
    ttl <- paste0("Linkage groups")
    cnid <- which(stringr::str_detect(string = colnames(x), pattern = "Id"))
    graphics::barplot(height = x$numberMarkers,
                      horiz = T,
                      axisnames = T,
                      names.arg = x[[c(cnid)]],
                      las = 1,
                      main = ttl,
                      xlab = "Number of Markers")
  }
  return(invisible())
}