Merge pull request #32 from microbiome/bioreview

Generate panels when elements are available + warnings
microbiome · Jul 16, 2024 · 2332829 · 2332829
2 parents 7eab2ab + 590957b
commit 2332829
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -15,7 +15,7 @@ Description:
     TreeSummarizedExperiment objects. Not surprisingly, it also depends on the
     generic panels from iSEE.
 biocViews: Microbiome, Software, Visualization, DataImport
-License: Artistic-2.0 + file LICENSE
+License: Artistic-2.0
 Encoding: UTF-8
 Depends:
     R (>= 4.4.0),

diff --git a/LICENSE b/LICENSE
diff --git a/R/iSEE-default.R b/R/iSEE-default.R
@@ -52,30 +52,37 @@ setGeneric("iSEE", iSEE::iSEE)
 #'   ComplexHeatmapPlot RowDataTable ColumnDataTable
 #' @importFrom TreeSummarizedExperiment TreeSummarizedExperiment rowLinks
 #' @importFrom SingleCellExperiment reducedDims
+#' @importFrom SummarizedExperiment rowData colData
+#' @importFrom mia taxonomyRanks
 setMethod("iSEE", "TreeSummarizedExperiment",
     function(se, initial = c(RowDataTable(), ColumnDataTable(), RowTreePlot(),
         AbundancePlot(), AbundanceDensityPlot(), ReducedDimensionPlot(),
         ComplexHeatmapPlot()), extra = NULL, colormap = ExperimentColorMap(),
         landingPage = createLandingPage(), tour = NULL, appTitle = NULL,
         runLocal = TRUE, voice = FALSE, bugs = FALSE, saveState = NULL, ...) {
 
+    initial <- .check_panel(se, initial, "RowDataTable", rowData)
+    initial <- .check_panel(se, initial, "ColumnDataTable", colData)
     initial <- .check_panel(se, initial, "RowTreePlot", rowLinks)
+    initial <- .check_panel(se, initial, "AbundancePlot", taxonomyRanks)
     initial <- .check_panel(se, initial, "ReducedDimensionPlot", reducedDims)
 
-    iSEE::iSEE(se, initial = initial, extra = extra, colormap = colormap,
+    iSEE::iSEE(se, initial = initial, extra = initial, colormap = colormap,
         landingPage = landingPage, tour = tour, appTitle = appTitle,
         runLocal = runLocal, voice = voice, bugs = bugs,
         saveState = saveState, ...)
 })
 
 #' @importFrom S4Vectors isEmpty
 #' @importFrom methods is
-.check_panel <- function(se, panel_list, panel_class, panel_fun) {
+.check_panel <- function(se, panel_list, panel_class, panel_fun, wtext) {
 
     no_keep <- unlist(lapply(panel_list, function(x) is(x, panel_class)))
 
     if( any(no_keep) && (is.null(panel_fun(se)) || isEmpty(panel_fun(se))) ){
         panel_list <- panel_list[!no_keep]
+        warning("no valid ", as.character(substitute(panel_fun)),
+            " fields for ", panel_class, call. = FALSE)
     }
 
     return(panel_list)