493 FilteredDatasetDefault class

NAMESPACE

@@ -23,6 +23,7 @@ S3method(init_filter_states,data.frame)
 S3method(init_filter_states,matrix)
 S3method(init_filtered_dataset,MultiAssayExperiment)
 S3method(init_filtered_dataset,data.frame)
+S3method(init_filtered_dataset,default)
 S3method(print,teal_slice)
 S3method(print,teal_slices)
 S3method(variable_types,DFrame)

NEWS.md

@@ -8,6 +8,7 @@
 
 * `TealData` object is no longer supported by `teal.slice`.
 * `set_filter_state` no longer accepts a nested list. Use `teal_slices()` and `teal_slice()` instead.
+* Renamed `FilteredDataset` subclass that handles `data.frame`s from `DefaultFilteredDataset` to `DataframeFilteredDataset`. Added new class `DefaultFilteredDataset` that will store any type of object. Filtering will is not supported.
 
 ### Miscellaneous
 

R/FilteredData.R

@@ -60,7 +60,7 @@ FilteredData <- R6::R6Class( # nolint
     #' @description
     #' Initialize a `FilteredData` object
     #' @param data_objects (`list`)
-    #'   should named elements containing `data.frame` or `MultiAssayExperiment`.
+    #'   Named list of data objects.
     #'   Names of the list will serve as `dataname`.
     #' @param join_keys (`join_keys` or NULL) see [`teal.data::join_keys()`].
     #'
@@ -232,7 +232,8 @@ FilteredData <- R6::R6Class( # nolint
           private$get_filtered_dataset(dataname)$get_filter_overview()
         }
       )
-      dplyr::bind_rows(rows)
+      unssuported_idx <- vapply(rows, function(x) all(is.na(x[-1])), logical(1))
+      dplyr::bind_rows(c(rows[!unssuported_idx], rows[unssuported_idx]))
     },
 
     #' @description
@@ -254,7 +255,7 @@ FilteredData <- R6::R6Class( # nolint
     #' If this data has a parent specified in the `join_keys` object stored in `private$join_keys`
     #' then created `FilteredDataset` (child) gets linked with other `FilteredDataset` (parent).
     #' "Child" dataset return filtered data then dependent on the reactive filtered data of the
-    #' "parent". See more in documentation of `parent` argument in `FilteredDatasetDefault` constructor.
+    #' "parent". See more in documentation of `parent` argument in `DataframeFilteredDataset` constructor.
     #'
     #' @param data (`data.frame`, `MultiAssayExperiment`)\cr
     #'   data to be filtered.
@@ -265,7 +266,6 @@ FilteredData <- R6::R6Class( # nolint
     #' @return (`self`) invisibly this `FilteredData`
     #'
     set_dataset = function(data, dataname) {
-      checkmate::assert_multi_class(data, classes = c("data.frame", "MultiAssayExperiment"))
       checkmate::assert_string(dataname)
       logger::log_trace("FilteredData$set_dataset setting dataset, name: { dataname }")
       # to include it nicely in the Show R Code;
@@ -337,10 +337,16 @@ FilteredData <- R6::R6Class( # nolint
     #' @return `character(1)` the formatted string
     #'
     format = function(show_all = FALSE, trim_lines = TRUE) {
+      datasets <- lapply(self$datanames(), private$get_filtered_dataset)
+      ind <- vapply(datasets, inherits, logical(1L), what = "DefaultFilteredDataset")
+      states <- do.call(c, lapply(datasets[!ind], function(ds) ds$get_filter_state()))
+      states_fmt <- format(states, show_all = show_all, trim_lines = trim_lines)
+      holders_fmt <- vapply(datasets[ind], format, character(1L), show_all = show_all, trim_lines = trim_lines)
+
       sprintf(
         "%s:\n%s",
         class(self)[1],
-        format(self$get_filter_state(), show_all = show_all, trim_lines = trim_lines)
+        paste(c(states_fmt, holders_fmt), collapse = "\n")
       )
     },
 
@@ -830,7 +836,19 @@ FilteredData <- R6::R6Class( # nolint
               function(x) {
                 tags$tr(
                   tagList(
-                    lapply(x, tags$td)
+                    tags$td(
+                      if (all(x[-1] == "")) {
+                        icon(
+                          name = "exclamation-triangle",
+                          title = "Unsupported dataset",
+                          `data-container` = "body",
+                          `data-toggle` = "popover",
+                          `data-content` = "object not supported by the filter panel"
+                        )
+                      },
+                      x[1]
+                    ),
+                    lapply(x[-1], tags$td)
                   )
                 )
               }

R/FilteredDataset-utils.R

@@ -2,7 +2,7 @@
 #'
 #' @keywords internal
 #' @examples
-#' # DefaultFilteredDataset example
+#' # DataframeFilteredDataset example
 #' iris_fd <- teal.slice:::init_filtered_dataset(iris, dataname = "iris")
 #' app <- shinyApp(
 #'   ui = fluidPage(
@@ -89,7 +89,7 @@ init_filtered_dataset.data.frame <- function(dataset, # nolint
                                              parent = NULL,
                                              join_keys = character(0),
                                              label = attr(dataset, "label")) {
-  DefaultFilteredDataset$new(
+  DataframeFilteredDataset$new(
     dataset = dataset,
     dataname = dataname,
     keys = keys,
@@ -119,3 +119,19 @@ init_filtered_dataset.MultiAssayExperiment <- function(dataset, # nolint
     label = label
   )
 }
+
+#' @keywords internal
+#' @export
+init_filtered_dataset.default <- function(dataset, # nolint
+                                          dataname,
+                                          keys, # ignored
+                                          parent_name, # ignored
+                                          parent, # ignored
+                                          join_keys, # ignored
+                                          label = attr(dataset, "label")) {
+  DefaultFilteredDataset$new(
+    dataset = dataset,
+    dataname = dataname,
+    label = label
+  )
+}