diff visualize.r @ 0:1015a0070bac draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/visualize.r	Thu Dec 29 13:05:04 2022 +0000
@@ -0,0 +1,56 @@
+#' Statically map indicators using ggplot
+#'
+#' @param grid spatial features, e.g. hexagons, to plot; requires a geometry
+#'   spatial column
+#' @param column column name with indicator; default="shannon"
+#' @param label label to show on legend
+#' @param crs coordinate reference system; see `sf::st_crs()`
+#' @param trans For continuous scales, the name of a transformation object or
+#'   the object itself. Built-in transformations include "asn", "atanh",
+#'   "boxcox", "date", "exp", "hms", "identity" (default), "log", "log10", "log1p",
+#'   "log2", "logit", "modulus", "probability", "probit", "pseudo_log",
+#'   "reciprocal", "reverse", "sqrt" and "time". See `ggplot2::continuous_scale`
+#'
+#' @return ggplot2 plot
+#' @concept visualize
+#' @export
+#' @import rnaturalearth viridis ggplot2
+#'
+#' @examples
+gmap_indicator <- function(
+    grid, column = "shannon", label = "Shannon index", trans = "identity",
+    crs = "+proj=robin +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs") {
+
+  world <- rnaturalearth::ne_countries(scale = "medium", returnclass = "sf")
+  bb <- sf::st_bbox(
+    sf::st_transform(grid, crs))
+
+  ggplot2::ggplot() +
+    ggplot2::geom_sf(
+      data = grid, ggplot2::aes_string(
+        fill = column, geometry = "geometry"), lwd = 0) +
+    viridis::scale_color_viridis(
+      option = "inferno", na.value = "white",
+      name = label, trans = trans) +
+    viridis::scale_fill_viridis(
+      option = "inferno", na.value = "white",
+      name = label, trans = trans) +
+    ggplot2::geom_sf(
+      data = world, fill = "#dddddd", color = NA) +
+    ggplot2::theme(
+      panel.grid.major.x = ggplot2::element_blank(),
+      panel.grid.major.y = ggplot2::element_blank(),
+      panel.grid.minor.x = ggplot2::element_blank(),
+      panel.grid.minor.y = ggplot2::element_blank(),
+      panel.background = ggplot2::element_blank(),
+      axis.text.x = ggplot2::element_blank(),
+      axis.text.y = ggplot2::element_blank(),
+      axis.ticks = ggplot2::element_blank(),
+      axis.title.x = ggplot2::element_blank(),
+      axis.title.y = ggplot2::element_blank()) +
+    ggplot2::xlab("") + ggplot2::ylab("") +
+    ggplot2::coord_sf(
+      crs  = crs,
+      xlim = bb[c("xmin", "xmax")],
+      ylim = bb[c("ymin", "ymax")])
+}