- Add plot_time_var argument to autoplot() for 3D plotting (#197)

R/ResamplingSptCVCstf.R

@@ -106,13 +106,13 @@ ResamplingSptCVCstf = R6Class("ResamplingSptCVCstf",
 sample_cast = function(task, stratify = FALSE, folds) {
 
   if (length(task$col_roles$time) && length(task$col_roles$space)) {
-    lg$info(sprintf("Using column roles 'space' (var. '%s') and 'time' (var. '%s') for partitioning", task$col_roles$space, task$col_roles$time))
+    lg$info(sprintf("Using column roles 'space' ('%s') and 'time' ('%s') for partitioning", task$col_roles$space, task$col_roles$time))
 
   } else if (length(task$col_roles$time)) {
-    lg$info(sprintf("Using column role 'time' (var. '%s') for partitioning", task$col_roles$time))
+    lg$info(sprintf("Using column role 'time' ('%s') for partitioning", task$col_roles$time))
   }
   else if (length(task$col_roles$space)) {
-    lg$info(sprintf("Using column role 'space' (var. '%s') for partitioning", task$col_roles$space))
+    lg$info(sprintf("Using column role 'space' ('%s') for partitioning", task$col_roles$space))
   }
 
   target = if (stratify) task$target_names else NULL

R/TaskClassifST.R

@@ -20,7 +20,6 @@
 #' @export
 #' @examples
 #' if (mlr3misc::require_namespaces(c("sf", "blockCV"), quietly = TRUE)) {
-#'
 #'   data = mlr3::as_data_backend(ecuador)
 #'   task = TaskClassifST$new("ecuador",
 #'     backend = data, target = "slides",
@@ -43,7 +42,6 @@
 #' }
 TaskClassifST = R6::R6Class("TaskClassifST",
   inherit = TaskClassif,
-
   public = list(
 
     #' @description
@@ -65,8 +63,8 @@ TaskClassifST = R6::R6Class("TaskClassifST",
     initialize = function(id, backend, target, positive = NULL,
       extra_args = list(
         coords_as_features = FALSE, crs = NA,
-        coordinate_names = NA)) {
-
+        coordinate_names = NA
+      )) {
       assert_string(target)
 
       # restore extra_args defaults
@@ -85,7 +83,8 @@ TaskClassifST = R6::R6Class("TaskClassifST",
 
       super$initialize(
         id = id, backend = backend, target = target,
-        positive = positive, extra_args = extra_args)
+        positive = positive, extra_args = extra_args
+      )
 
       self$extra_args$coordinate_names = extra_args$coordinate_names
 
@@ -98,7 +97,8 @@ TaskClassifST = R6::R6Class("TaskClassifST",
 
       self$properties = union(
         self$properties,
-        if (length(levels) == 2L) "twoclass" else "multiclass")
+        if (length(levels) == 2L) "twoclass" else "multiclass"
+      )
       if (!is.null(positive)) {
         self$positive = positive
       }
@@ -116,7 +116,8 @@ TaskClassifST = R6::R6Class("TaskClassifST",
       if (!extra_args$coords_as_features) {
         self$col_roles$feature = setdiff(
           self$col_roles$feature,
-          extra_args$coordinate_names)
+          extra_args$coordinate_names
+        )
       }
     },
 
@@ -138,6 +139,16 @@ TaskClassifST = R6::R6Class("TaskClassifST",
       super$print(...)
       cat("* Coordinates:\n")
       print(self$coordinates())
+      if (length(self$col_roles$time) && length(self$col_roles$space)) {
+        cat(
+          "* Column roles:\n- Time:", self$col_roles$time,
+          "\n- Space:", self$col_roles$space, "\n"
+        )
+      } else if (length(self$col_roles$time)) {
+        cat("* Column roles:\n- Time:", self$col_roles$time, "\n")
+      } else if (length(self$col_roles$space)) {
+        cat("* Column roles:\n- Space:", self$col_roles$space, "\n")
+      }
     },
 
     #' @field extra_args (named `list()`)\cr

R/TaskRegrST.R

@@ -108,8 +108,6 @@ TaskRegrST = R6::R6Class("TaskRegrST",
         cat("* Column roles:\n- Time:", self$col_roles$time, "\n")
       } else if (length(self$col_roles$space)) {
         cat("* Column roles:\n- Space:", self$col_roles$space, "\n")
-      } else if (length(self$col_roles$plot)) {
-        cat("* Column roles:\n- Plot:", self$col_roles$plot, "\n")
       }
     },
 

R/autoplot.R

@@ -1631,13 +1631,9 @@ autoplot_spatiotemp = function(
     if (!plot_as_grid) {
       return(invisible(plot_list))
     } else {
-      messagef("Unfortunately plotly does not support a dynamic
-       arrangement of multiple subplots.
-       See article 'Visualization of spatiotemporal clusters'
-       (https://mlr3spatiotempcv.mlr-org.com/articles/spatiotemp-viz) for a
-       manual workaround.
-       Use the objects in the returned list to arrange a custom grid.",
-        wrap = TRUE)
+      lg$warn("Unfortunately plotly does not support a dynamic arrangement of multiple subplots.
+       See article 'Visualization of spatiotemporal clusters' (https://mlr3spatiotempcv.mlr-org.com/articles/spatiotemp-viz) for a manual workaround.
+       Use the objects in the returned list to arrange a custom grid.")
 
       return(invisible(plot_list))
     }

R/autoplot_spcv_cstf.R

@@ -4,12 +4,13 @@
 #'   visualize mlr3 spatiotemporal resampling objects.
 #'
 #' @details
-#' This method requires to set argument `fold_id` and no plot containing all
-#' partitions can be created. This is because the method does not make use of
-#' all observations but only a subset of them (many observations are left out).
+#' This method requires to set argument `fold_id`.
+#' No plot showing all folds in one plot can be created.
+#' This is because the LLTO method does not make use of all observations but only
+#' a subset of them (many observations are omitted).
 #' Hence, train and test sets of one fold are not re-used in other folds as in
-#' other methods and plotting these without a train/test indicator would not
-#' make sense.
+#' other methods and plotting these without a train/test indicator would be
+#' misleading.
 #'
 #' @section 2D vs 3D plotting:
 #' This method has both a 2D and a 3D plotting method.
@@ -52,6 +53,10 @@
 #' @param plot3D `[logical]`\cr
 #'   Whether to create a 2D image via \pkg{ggplot2} or a 3D plot via
 #'   \pkg{plotly}.
+#' @param plot_time_var `[character]`\cr
+#'   The variable to use for the z-axis (time).
+#'   Remove the column role `feature` for this variable to only use
+#'   it for plotting.
 #' @param ... Passed down to `plotly::orca()`. Only effective when
 #' `static_image = TRUE`.
 #' @export
@@ -75,7 +80,7 @@
 #'   resampling = rsmp("sptcv_cstf", folds = 5)
 #'   resampling$instantiate(task_st)
 #'
-#'   # with both `space_var` and `time_var` (LLTO), the omitted observations per
+#'   # with both `"space"` and `"time"` column roles set (LLTO), the omitted observations per
 #'   # fold can be shown by setting `show_omitted = TRUE`
 #'   autoplot(resampling, task_st, fold_id = 1, show_omitted = TRUE)
 #' }
@@ -95,6 +100,7 @@ autoplot.ResamplingSptCVCstf = function( # nolint
   static_image = FALSE,
   show_omitted = FALSE,
   plot3D = NULL,
+  plot_time_var = NULL,
   ...) {
 
   dots = list(...)
@@ -118,11 +124,10 @@ autoplot.ResamplingSptCVCstf = function( # nolint
     resampling_sub$instance = resampling_sub$instance[[repeats_id]]
   }
 
-  # FIXME: check space and time var from column roles!
   # check if we are in a 2D or 3D scenario
   if (is.null(plot3D)) {
-    if (!is.null(resampling_sub$space_var) &&
-      !is.null(resampling_sub$time_var)) {
+    if (length(task$col_roles$space) &&
+      length(task$col_roles$time)) {
       plot3D = TRUE
     } else {
       plot3D = FALSE
@@ -163,6 +168,18 @@ autoplot.ResamplingSptCVCstf = function( # nolint
 
         data_coords = format_resampling_list(task, resampling_sub)
 
+        if (length(task$col_roles$time)) {
+          data_coords$Date = as.Date(task$data(cols = task$col_roles$time)[[1]])
+        } else {
+          # if time col is not set, check for plot_time col role
+          if (!is.null(plot_time_var)) {
+            data_coords$Date = as.Date(task$data(cols = plot_time_var)[[1]])
+          } else {
+            lg$error("Neither 'time' or 'plot' column roles are set. At least one is required for 3D plotting. If the variable is only used for plotting purposes, please define argument 'plot_time_var' in `autoplot()` and remove the column role 'feature' for this variable.")
+            stop()
+          }
+        }
+
         # suppress undefined global variables note
         data_coords$indicator = ""
 
@@ -303,7 +320,8 @@ autoplot.ResamplingSptCVCstf = function( # nolint
     }
 
     else {
-      stop("This method requires to set argument 'fold_id'. See ?autoplot.ResamplingSptCVCstf for more information.") # nolint
+      lg$fatal("This method requires to set argument 'fold_id'. See ?autoplot.ResamplingSptCVCstf for more information.") # nolint
+      stop()
     }
 
     # is a grid requested?
@@ -313,13 +331,9 @@ autoplot.ResamplingSptCVCstf = function( # nolint
       }
       return(plot)
     } else {
-      messagef("Unfortunately plotly does not support a dynamic
-       arrangement of multiple subplots.
-       See article 'Visualization of spatiotemporal clusters'
-       (https://mlr3spatiotempcv.mlr-org.com/articles/spatiotemp-viz) for a
-       manual workaround.
-       Use the objects in the returned list to arrange a custom grid.",
-        wrap = TRUE)
+      lg$warn("Unfortunately plotly does not support a dynamic arrangement of multiple subplots.
+       See article 'Visualization of spatiotemporal clusters' (https://mlr3spatiotempcv.mlr-org.com/articles/spatiotemp-viz) for a manual workaround.
+       Use the objects in the returned list to arrange a custom grid.")
 
       if (static_image) {
         plotly::orca(plot, ...)
@@ -347,6 +361,7 @@ autoplot.ResamplingRepeatedSptCVCstf = function( # nolint
   point_size = 3,
   axis_label_fontsize = 11,
   plot3D = NULL,
+  plot_time_var = NULL,
   ...) {
 
   autoplot.ResamplingSptCVCstf(
@@ -361,7 +376,8 @@ autoplot.ResamplingRepeatedSptCVCstf = function( # nolint
     nticks_y = nticks_y,
     point_size = point_size,
     axis_label_fontsize = axis_label_fontsize,
-    plot3D = plot3D,
+    plot3D = plot3D, ,
+    plot_time_var = plot_time_var,
     ...,
     # ellipsis
     repeats_id = repeats_id

R/helper_autoplot.R

@@ -27,11 +27,6 @@ format_resampling_list = function(task, resampling) {
     data$train[data$row_id %in% row_id_train] = i
   }
 
-  # FIXME: this is just an escape, fix before merging
-  if (length(task$col_roles$time)) {
-    data$Date = as.Date(task$data(cols = task$col_roles$time)[[1]])
-  }
-
   # merge the coords for the 3D plot
   data_coords = merge(data, coords, by = "row_id")
   return(data_coords)

R/zzz.R

@@ -59,17 +59,17 @@ register_mlr3 = function() { # nocov start
   )), "type")
 
   # append "coordinates" to col_roles
-  x$task_col_roles$classif_st = append(x$task_col_roles$classif, "coordinates")
-  x$task_col_roles$regr_st = append(x$task_col_roles$regr, "coordinates")
+  # x$task_col_roles$classif_st = append(x$task_col_roles$classif, "coordinates")
+  # x$task_col_roles$regr_st = append(x$task_col_roles$regr, "coordinates")
 
   # append "space" and "time" to col_roles
   # used in CAST
-  # prevent redudant addition when calling pkgload::load_all()
-  if (!any(c("space", "time") %in% x$task_col_roles$classif)) {
-    x$task_col_roles$classif = c(x$task_col_roles$classif, "space", "time")
-    x$task_col_roles$regr = c(x$task_col_roles$regr, "space", "time")
-    x$task_col_roles$classif_st = c(x$task_col_roles$classif_st, "space", "time")
-    x$task_col_roles$regr_st = c(x$task_col_roles$regr_st, "space", "time")
+  # prevent redundant addition when calling `pkgload::load_all()`
+  if (!any(c("space", "time", "plot_time", "coordinates") %in% x$task_col_roles$classif)) {
+    x$task_col_roles$classif = append(x$task_col_roles$classif, c("coordinates", "space", "time"))
+    x$task_col_roles$classif_st = append(x$task_col_roles$classif_st, c("coordinates", "space", "time"))
+    x$task_col_roles$regr = append(x$task_col_roles$regr, c("coordinates", "space", "time"))
+    x$task_col_roles$regr_st = append(x$task_col_roles$regr_st, c("coordinates", "space", "time"))
   }
 
   # tasks --------------------------------------------------------------------