Merge pull request #8 from ropensci/gganimate

Gganimate

Author: rmendels

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: plotdap
 Title: Easily Visualize Data from 'ERDDAP' Servers via the 'rerddap' Package
-Version: 0.0.4
-Date: 2019-10-14
+Version: 0.0.8
+Date: 2020-10-23
 Authors@R: c(
     person("Carson", "Sievert", role = "aut"),
     person("Roy", "Mendelssohn", role = c("aut", "ctb", "cre"), email = "roy.mendelssohn@noaa.gov"))
@@ -10,10 +10,12 @@ License: MIT + file LICENSE
 URL: https://github.com/ropensci/plotdap
 BugReports: https://github.com/ropensci/plotdap/issues
 Depends: 
-   R (>= 3.6.0)
+   R (>= 4.0.0)
 Imports:
+  cmocean,
   dplyr,
   gganimate,
+  ggnewscale (>= 0.4.1),
   ggplot2 (>= 3.1.0),
   lazyeval,
   lubridate,
@@ -24,7 +26,8 @@ Imports:
   rgeos,
   scales,
   sf,
-  tidyr
+  tidyr,
+  viridis
 Suggests:
   Cairo,
   knitr,
@@ -33,7 +36,7 @@ Suggests:
   rgdal,
   rmarkdown,
   testthat
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1
 LazyData: true
 Encoding: UTF-8
 VignetteBuilder: knitr

NAMESPACE

@@ -17,6 +17,7 @@ importFrom(ggplot2,coord_sf)
 importFrom(ggplot2,geom_sf)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,guide_colorbar)
 importFrom(ggplot2,guides)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,scale_colour_gradientn)

NEWS.md

@@ -1,3 +1,23 @@
+# plotdap 0.0.8
+
+fixed animation bug in 'add_griddap()' not finding the correct number
+of frames
+
+# plotdap 0.0.7
+
+* fixed problem with \dontrun example not finding rerddap::griddap()
+
+* fixed problem in vignette to URL link to R docs
+
+# plotdap 0.0.6
+* fixed problem when no time coordinate in dataset
+* 'add_tabledap()' overlays on gridded maps now work for 'ggplot2'
+
+# plotdap 0.0.5
+* fixed problem with animation in 'add_griddap()'
+* fixed bad URL for sardine example
+* changed to use colors in package 'cmocean' instead of in 'rerddap'
+
 # plotdap 0.0.4
 * fixed changed SODA datasetid in vignette
 * fixed Namespace and Import problems

R/add_griddap.R

@@ -5,8 +5,9 @@
 #' @param plot a \link{plotdap} object.
 #' @param grid a \link{griddap} object.
 #' @param var a formula defining a variable, or function of variables to visualize.
-#' @param fill either a character string of length 1 matching a name in \\link[rerddap]{colors}
-#' or a vector of color codes. This defines the colorscale used to encode values
+#' @param fill either a character string of length 1 matching a name in the
+#' package \code{cmocean} or a vector of color codes.
+#' This defines the colorscale used to encode values
 #' of \code{var}.
 #' @param maxpixels integer > 0. Maximum number of cells to use for the plot.
 #' If maxpixels < ncell(x), sampleRegular is used before plotting.
@@ -34,12 +35,12 @@
 #' # actual datasets in data folder to meet execution timings
 #'
 #'\donttest{
-#'  murSST <- griddap(
-#'    'jplMURSST41', latitude = c(35, 40), longitude = c(-125, -1205),
+#'  murSST <- rerddap::griddap(
+#'    'jplMURSST41', latitude = c(35, 40), longitude = c(-125, -120.5),
 #'    time = c('last', 'last'), fields = 'analysed_sst'
 #'   )
 #'
-#'  QMwind <- griddap(
+#'  QMwind <- rerddap::griddap(
 #'    'erdQMwindmday', time = c('2016-11-16', '2017-01-16'),
 #'    latitude = c(30, 50), longitude = c(210, 240),
 #'    fields = 'x_wind'
@@ -133,8 +134,15 @@ add_griddap <- function(plot, grid, var, fill = "viridis",
     )
     if (inherits(r, "RasterBrick")) {
       for (i in seq_len(raster::nlayers(r))) {
-        r[[i]] <- raster::resample(r[[i]], rnew, method = 'bilinear')
+        #r[[i]] <- raster::resample(r[[i]], rnew, method = 'bilinear')
+        junk <- raster::resample(r[[i]], rnew, method = 'bilinear')
+        if (i == 1) {
+          temp <- junk
+        } else {
+          temp <- raster::addLayer(temp, junk)
+        }
       }
+      r <- raster::brick(temp)
     } else {
       r <- raster::resample(r, rnew, method = 'bilinear')
     }
@@ -152,18 +160,30 @@ add_griddap <- function(plot, grid, var, fill = "viridis",
   }
 
   # color scale
-  cols <- if (length(fill) == 1) rerddap::colors[[fill]] else fill
+  # cols <- if (length(fill) == 1) rerddap::colors[[fill]] else fill
+  if (length(fill) == 1) {
+     if (fill == 'viridis') {
+       cols <- viridis::viridis(256)
+     } else {
+       cols <- cmocean::cmocean(fill)(256)
+
+     }
+  }  else {
+     cols <- fill
+  }
 
   if (is_ggplotdap(plot)) {
     # TODO: not the most efficient approach, but it will have to do for now
     # https://twitter.com/hadleywickham/status/841763265344487424
     s <- sf::st_as_sf(raster::rasterToPolygons(r))
     vars <- setdiff(names(s), "geometry")
-    sg <- sf::st_as_sf(tidyr::gather_(s, "variable", "value", vars))
+    var_name <- lazyeval::f_text(var)
+    variable_name <- "variable"
+    sg <- sf::st_as_sf(tidyr::gather(s, {{variable_name}},{{var_name}}, vars))
     if (animate) {
       try_gganimate()
       plot$animate <- TRUE
-      plot$nper <- length(sg)
+      plot$nper <- length(s) - 1
       plot$ggplot <- plot$ggplot +
         gganimate::transition_manual(variable, cumulative = cumulative) +
         ggplot2::labs(title = "{current_frame}")
@@ -173,10 +193,10 @@ add_griddap <- function(plot, grid, var, fill = "viridis",
       add_ggplot(
         plot,
         geom_sf(data = sg,
-                mapping = aes_string(fill = "value", colour = "value"), ...),
-        scale_fill_gradientn(name = lazyeval::f_text(var), colors = cols),
-        scale_colour_gradientn(colors = cols),
-        guides(colour = FALSE)
+              mapping = ggplot2::aes_string(fill = var_name, colour = var_name), ...),
+        scale_fill_gradientn(name = var_name, colors = cols),
+        scale_colour_gradientn(colors = cols)
+        #ggplot2::guides(colour = "none")
       )
     )
   }

R/add_tabledap.R

@@ -5,7 +5,7 @@
 #' @param plot a \link{plotdap} object.
 #' @param table a \link{tabledap} object.
 #' @param var a formula defining a variable, or function of variables to visualize.
-#' @param color either a character string of length 1 matching a name in \link[rerddap]{colors}
+#' @param color either a character string of length 1 matching a name in \code{cmocean}
 #' or a vector of color codes. This defines the colorscale used to encode values
 #' of \code{var}.
 #' @param size the size of the symbol.
@@ -29,11 +29,11 @@
 #' # code given to extract the data
 #'
 #'\donttest{
-#' sardines <- tabledap(
+#' sardines <- rerddap::tabledap(
 #'  'FRDCPSTrawlLHHaulCatch',
 #'  fields = c('latitude',  'longitude', 'time', 'scientific_name', 'subsample_count'),
 #'   'time>=2010-01-01', 'time<=2012-01-01',
-#'   scientific_name="Sardinops sagax"
+#'   'scientific_name="Sardinops sagax"'
 #'   )
 #'}
 #'
@@ -77,7 +77,17 @@ add_tabledap <- function(plot, table, var, color = c("#132B43", "#56B1F7"),
   }
 
   # color scale
-  cols <- if (length(color) == 1) rerddap::colors[[color]] else color
+  # cols <- if (length(color) == 1) rerddap::colors[[color]] else color
+
+  if (length(color) == 1) {
+    if (color == 'viridis') {
+      cols = viridis::viridis(256)
+    } else{
+      cols <- cmocean::cmocean(color)(256)
+    }
+  }  else {
+    cols <- color
+  }
 
   if (is_ggplotdap(plot)) {
 
@@ -89,15 +99,27 @@ add_tabledap <- function(plot, table, var, color = c("#132B43", "#56B1F7"),
         gganimate::transition_manual(factor(time), cumulative = cumulative) +
         ggplot2::labs(title = "{current_frame}")
     }
-
-    return(
-      add_ggplot(
-        plot,
-        geom_sf(data = table, mapping = aes_(colour = var),
-                size = size, pch = shape, ...),
-        scale_colour_gradientn(name = lazyeval::f_text(var), colours = cols)
+    if (length(plot$ggplot$layers) == 1) {
+      return(
+        add_ggplot(
+          plot,
+          geom_sf(data = table, mapping = aes_(colour = var),
+                  size = size, pch = shape, ...),
+          scale_colour_gradientn(name = lazyeval::f_text(var), colours = cols)
+        )
       )
-    )
+    } else {
+      #plot$ggplot <- plot$ggplot + ggnewscale::new_scale_colour() + ggnewscale::new_scale_fill()
+      return(
+        add_ggplot(
+          plot,
+          ggnewscale::new_scale_colour(),
+          geom_sf(data = table, mapping = aes_(colour = var),
+                  size = size, pch = shape, ...),
+          scale_colour_gradientn(name = lazyeval::f_text(var), colours = cols))
+          #scale_colour_gradientn(colours = cols)
+      )
+    }
   }
 
 

R/imports.R

@@ -7,8 +7,8 @@
 #' @importFrom scales rescale col_numeric
 #' @importFrom lazyeval is_formula f_text f_eval
 #' @importFrom sf st_as_sf st_transform st_crs st_bbox st_graticule
-#' @importFrom ggplot2 ggplot geom_sf coord_sf theme_bw scale_colour_gradientn
-#' scale_fill_gradientn ggtitle aes_string aes_ guides labs
+#' @importFrom ggplot2 aes_ aes_string ggplot geom_sf guides guide_colorbar coord_sf theme_bw scale_colour_gradientn
+#' scale_fill_gradientn ggtitle labs
 #' @importFrom raster raster nlayers calc ncell nrow ncol crs extent resample
 #' projectRaster rasterToPolygons values plot brick setExtent isLonLat
 NULL

R/plotdap.R

@@ -104,7 +104,7 @@ print.ggplotdap <- function(x, ...) {
   gg <- x$ggplot
   dots <- list(...)
   if (isTRUE(dots$landmask)) {
-    gg$layers <- rev(gg$layers)
+    gg$layers[1:2] <- rev(gg$layers[1:2])
     layer_data <- lapply(gg$layers, function(y) y$layer_data(gg$data))
     bbs <- lapply(layer_data[1], sf::st_bbox)
     x$ggplot <- gg
@@ -257,7 +257,11 @@ get_raster <- function(grid, var) {
   r <- if (length(times) > 1) {
     # ensure values appear in the right order...
     # TODO: how to detect a south -> north ordering?
-    d <- dplyr::arrange(grid$data, time, desc(lat), lon)
+    if ("lat" %in% names(grid$data)) {
+      d <- dplyr::arrange(grid$data, time, desc(lat), lon)
+    } else {
+      d <- dplyr::arrange(grid$data, time, desc(latitude), longitude)
+    }
     b <- raster::brick(
       nl = length(times),
       nrows = length(lats),
@@ -266,7 +270,11 @@ get_raster <- function(grid, var) {
     raster::values(b) <- lazyeval::f_eval(var, d)
     raster::setExtent(b, ext)
   } else {
-    d <- dplyr::arrange(grid$data, desc(lat), lon)
+    if ("lat" %in% names(grid$data)) {
+      d <- dplyr::arrange(grid$data, desc(lat), lon)
+    } else {
+      d <- dplyr::arrange(grid$data, desc(latitude), longitude)
+    }
     raster::raster(
       nrows = length(lats),
       ncols = length(lons),
@@ -279,7 +287,7 @@ get_raster <- function(grid, var) {
 }
 
 
-utils::globalVariables(c("time", "desc", "lat", "lon"))
+utils::globalVariables(c("time", "desc", "lat", "lon", "latitude", "longitude"))
 
 latlon_is_valid <- function(x) {
   if (is_raster(x)) {

R/utils.R

@@ -32,7 +32,7 @@ try_require <- function(package, fun) {
 
 try_gganimate <- function() {
   if (system.file(package = "gganimate") != "") {
-    if (utils::packageVersion("gganimate") > "0.1") {
+    if (utils::packageVersion("gganimate") > "1.0.0") {
       return(TRUE)
     }
   }
@@ -87,6 +87,11 @@ format_table <- function(table, .info) {
   table
 }
 
+# sf is not properly importing rgeos.
+# I need to import it, but causes note if not
+# referenced. Here is a dummy function.
+dummy <- function() rgeos::getScale()
+# dummy2 <- function() rgdal::checkCRSArgs("+proj=laea +y_0=0 +lon_0=155 +lat_0=-90 +ellps=WGS84 +no_defs")
 
 # This is likely WRONG, SAD!
 # rescale_lims <- function(x, .info = info(attr(x, "datasetid"))) {

cran-comments.md

@@ -1,33 +1,32 @@
-## This is a minor update 
+## This is a minor bugfix update 
 
-- fixed URL change in vignette
-- fixed Import and Namespace problems reported on CRAN checks
-- On Windows,  previous version built with --no-vignettes please continue that
-if Vignette build takes too long
 
 
 ## Test environments
-* local OS X install, R 3.6.1
-* Fedora Linux on RHub)
+* local OS X install, R 4.0.3
+* local Fedora, R 4.0.2 
 * win-builder (devel and release)
 
 ## R CMD check results
 
 ### OS X
 
-Duration: 3m 53s
+Duration: 4m 23.5s
 
-0 errors ✔ | 0 warnings ✔ | 0 notes ✔
+0 errors ✓ | 0 warnings ✓ | 0 notes ✓
 
 ### Winbuilder release
+
 OK
 
 ### Winbuilder devel
 
 OK
 
-### RHUb Windows Server 2008 R2 SP1, R-devel, 32/64 bit
 
-OK
-### RHub Fedora
-OK
+### Local Fedora
+
+Duration: 3m 08s
+
+0 errors ✓ | 0 warnings ✓ | 0 notes ✓
+