Tests extended

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: iSEEfier
 Title: Streamlining the creation of initial states for starting an iSEE instance
-Version: 0.2.0
+Version: 0.3.0
 Authors@R:
     c(
     person(given = "Najla", family = "Abassi", role = c("aut", "cre"),
@@ -32,12 +32,14 @@ Imports:
     rlang,
     stats,
     SummarizedExperiment,
+    SingleCellExperiment,
     visNetwork
 Suggests:
     knitr,
     rmarkdown,
     scater,
     scRNAseq,
+    org.Mm.eg.db,
     scuttle,
     BiocStyle,
     testthat (>= 3.0.0)

NAMESPACE

@@ -11,6 +11,7 @@ importClassesFrom(iSEE,FeatureAssayPlot)
 importClassesFrom(iSEE,ReducedDimensionPlot)
 importClassesFrom(iSEE,RowDataTable)
 importClassesFrom(iSEEu,MarkdownBoard)
+importFrom(SingleCellExperiment,reducedDimNames)
 importFrom(SummarizedExperiment,colData)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,geom_tile)
@@ -27,6 +28,7 @@ importFrom(igraph,"V<-")
 importFrom(igraph,V)
 importFrom(igraph,graph.empty)
 importFrom(igraph,graph_from_data_frame)
+importFrom(methods,is)
 importFrom(methods,new)
 importFrom(rlang,.data)
 importFrom(stats,na.omit)

NEWS.md

@@ -1,3 +1,8 @@
+# iSEEfier 0.3.0
+
+* Main functions are equipped with extra parameters determining their behavior
+* Unit test suite is fully in!
+
 # iSEEfier 0.2.0
 
 * Functions renamed to the final version, in a more matching and descriptive manner

R/iSEEfier.R

@@ -1,5 +1,5 @@
 #' iSEEinit: Create an initial state of an iSEE instance for gene expression visualization
-#' 
+#'
 #' `iSEEinit()` defines the initial setup of an iSEE instance, recommending tailored visual elements to effortlessly illustrate the expression of a gene list in a single view.
 #'
 #' @param sce SingleCellExperiment object
@@ -14,13 +14,15 @@
 #' @export
 #' @importFrom methods new
 #' @importFrom SummarizedExperiment colData
+#' @importFrom SingleCellExperiment reducedDimNames
+#' @importFrom methods is
 #' @importClassesFrom iSEE ColumnDataPlot
 #' @importClassesFrom iSEE ReducedDimensionPlot
 #' @importClassesFrom iSEE FeatureAssayPlot
 #' @importClassesFrom iSEE RowDataTable
 #' @importClassesFrom iSEE ComplexHeatmapPlot
 #' @importClassesFrom iSEEu MarkdownBoard
-#' 
+#'
 #'
 #' @examples
 #' sce <- scRNAseq::RichardTCellData()
@@ -38,92 +40,169 @@ iSEEinit <- function(sce,
                      groups = colnames(colData(sce))[1],
                      markdownboard = FALSE,
                      dynamicMarkerTable = FALSE) {
+
+  ## Checks on arguments
+  if (!is(sce, "SingleCellExperiment"))
+    stop("Please provide a SingleCellExperiment as input!")
+
+  stopifnot(is.character(feature.list))
+  stopifnot(length(feature.list) > 0)
+
+  stopifnot(is.character(reddim.type))
+  stopifnot(length(reddim.type) == 1)
+
+  stopifnot(is.character(clusters))
+  stopifnot(length(clusters) == 1)
+
+  stopifnot(is.character(groups))
+  stopifnot(length(groups) == 1)
+
+  stopifnot(is.logical(markdownboard))
+  stopifnot(length(markdownboard) == 1)
+  stopifnot(is.logical(dynamicMarkerTable))
+  stopifnot(length(dynamicMarkerTable) == 1)
+
+  if (!(reddim.type %in% reducedDimNames(sce))) {
+    available_reddims <- reducedDimNames(sce)
+    stop("The selected reduced dimensionality embedding is not available!\n",
+         "Please select one of these: ",
+         paste(available_reddims, collapse = ", "))
+  }
+
+  if (!all(feature.list %in% rownames(sce))) {
+    not_available_features <- feature.list[!feature.list %in% rownames(sce)]
+    message("Some of the features specified are not available in the provided sce object!\n",
+            "Feature(s) not found: ",
+            paste(not_available_features, collapse = ", "))
+
+    feature.list <- feature.list[feature.list %in% rownames(sce)]
+    if (length(feature.list) == 0)
+      stop("No features available!")
+  }
+
+  if (!(clusters %in% colnames(colData(sce)))) {
+    if (ncol(colData(sce)) > 0) {
+      fallback_clusters <- colnames(colData(sce))[1]
+    } else {
+      stop("No colData provided for the `clusters`!")
+    }
+
+    message("colData column not found for the `clusters` parameter, defaulting to ",
+            fallback_clusters)
+  }
+
+  if (!(groups %in% colnames(colData(sce)))) {
+    if (ncol(colData(sce)) > 0) {
+      fallback_groups <- colnames(colData(sce))[1]
+    } else {
+      stop("No colData provided for the `groups`!")
+    }
+
+    message("colData column not found for the `groups` parameter, defaulting to ",
+            fallback_groups)
+  }
+
+
+
+
   initial <- list()
-  feature.list <- as.list(feature.list)
-  clusters <- as.character(clusters)
-  group <- as.character(groups)
-
-
+  ## TODO: do we need this to be enforced as list?
+  # feature.list <- as.list(feature.list)
+  # clusters <- as.character(clusters)
+  # groups <- as.character(groups)
+
+
   for (j in feature.list) {
-    initial[[paste0("ReducedDimensionPlot", which(feature.list == j))]] <- new("ReducedDimensionPlot",
-                                                                               Type = reddim.type,
-                                                                               ColorBy = "Feature name",
-                                                                               ColorByFeatureName = j,
-                                                                               ColorByFeatureSource = paste0("RowDataTable", which(feature.list == j)),
-                                                                               ColumnSelectionSource = "ColumnDataPlot1",
-                                                                               SelectionAlpha = 0.05
+    initial[[paste0("ReducedDimensionPlot", which(feature.list == j))]] <- new(
+      "ReducedDimensionPlot",
+      Type = reddim.type,
+      ColorBy = "Feature name",
+      ColorByFeatureName = j,
+      ColorByFeatureSource = paste0("RowDataTable", which(feature.list == j)),
+      ColumnSelectionSource = "ColumnDataPlot1",
+      SelectionAlpha = 0.05
     )
-
-    initial[[paste0("FeatureAssayPlot", which(feature.list == j))]] <- new("FeatureAssayPlot",
-                                                                           XAxis = "Column data",
-                                                                           XAxisColumnData = clusters,
-                                                                           YAxisFeatureName = j,
-                                                                           YAxisFeatureSource = paste0("RowDataTable", which(feature.list == j)),
-                                                                           ColorBy = "Column data",
-                                                                           ColorByColumnData = clusters
+
+    initial[[paste0("FeatureAssayPlot", which(feature.list == j))]] <- new(
+      "FeatureAssayPlot",
+      XAxis = "Column data",
+      XAxisColumnData = clusters,
+      YAxisFeatureName = j,
+      YAxisFeatureSource = paste0("RowDataTable", which(feature.list == j)),
+      ColorBy = "Column data",
+      ColorByColumnData = clusters
     )
-
-    initial[[paste0("RowDataTable", which(feature.list == j))]] <- new("RowDataTable",
-                                                                       Selected = j,
-                                                                       Search = j
+
+    initial[[paste0("RowDataTable", which(feature.list == j))]] <- new(
+      "RowDataTable",
+      Selected = j,
+      Search = j
     )
   }
-  
+
   if (length(feature.list) > 1) {
-    initial[[paste0("FeatureAssayPlot", length(feature.list) + 1)]] <- new("FeatureAssayPlot", 
-                                                                           XAxis = "Feature name", 
-                                                                           XAxisFeatureName = feature.list[[1]],
-                                                                           YAxisFeatureName = feature.list[[2]]
+    initial[[paste0("FeatureAssayPlot", length(feature.list) + 1)]] <- new(
+      "FeatureAssayPlot",
+      XAxis = "Feature name",
+      XAxisFeatureName = feature.list[[1]],
+      YAxisFeatureName = feature.list[[2]]
     )
   }
-
-  initial[[paste0("ReducedDimensionPlot", length(feature.list) + 1)]] <- new("ReducedDimensionPlot",
-                                                                             Type = reddim.type,
-                                                                             ColorByColumnData = clusters,
-                                                                             ColorBy = "Column data",
-                                                                             ColumnSelectionSource = paste0("FeatureAssayPlot", length(feature.list) + 1),
-                                                                             FacetColumnBy = "Column data",
-                                                                             FacetColumnByColData = group,
-                                                                             SelectionAlpha = 0.05
+
+  initial[[paste0("ReducedDimensionPlot", length(feature.list) + 1)]] <- new(
+    "ReducedDimensionPlot",
+    Type = reddim.type,
+    ColorByColumnData = clusters,
+    ColorBy = "Column data",
+    ColumnSelectionSource = paste0("FeatureAssayPlot", length(feature.list) + 1),
+    FacetColumnBy = "Column data",
+    FacetColumnByColData = groups,
+    SelectionAlpha = 0.05
   )
-
-
-  initial[["ComplexHeatmapPlot1"]] <- new("ComplexHeatmapPlot",
-                                          CustomRowsText = paste(feature.list, collapse = "\n"),
-                                          ColumnData = clusters
+
+
+  initial[["ComplexHeatmapPlot1"]] <- new(
+    "ComplexHeatmapPlot",
+    CustomRowsText = paste(feature.list, collapse = "\n"),
+    ColumnData = clusters
   )
-
-  initial[["ColumnDataPlot1"]] <- new("ColumnDataPlot",
-                                      YAxis = clusters,
-                                      ColorBy = "Column data",
-                                      ColorByColumnData = clusters,
-                                      PanelWidth = 6L
+
+  initial[["ColumnDataPlot1"]] <- new(
+    "ColumnDataPlot",
+    YAxis = clusters,
+    ColorBy = "Column data",
+    ColorByColumnData = clusters,
+    PanelWidth = 6L
   )
-  
+
   if (markdownboard == TRUE) {
-    initial[["MarkdownBoard1"]] <- new("MarkdownBoard",
-                                       Content = "# Placeholder\n\nFill me with text!",
-                                       PanelWidth = 4L)
+    initial[["MarkdownBoard1"]] <- new(
+      "MarkdownBoard",
+      Content = "# Placeholder\n\nFill me with text!",
+      PanelWidth = 4L)
   }
-  
+
   if(dynamicMarkerTable == TRUE) {
-    initial[[paste0("ReducedDimensionPlot",length(feature.list)+2)]] <- new("ReducedDimensionPlot",
-                                                                            Type = reddim.type,
-                                                                            ColorByColumnData = clusters,
-                                                                            ColorBy = "Column data",
-                                                                            SelectionAlpha = 0.05,
-                                                                            ColumnSelectionSource = paste0("FeatureAssayPlot",length(feature.list)+2))
-
-
-    initial[["DynamicMarkerTable1"]] <- new("DynamicMarkerTable",
-                                            ColumnSelectionSource = paste0("ReducedDimensionPlot",length(feature.list)+2))
-
-    initial[[paste0("FeatureAssayPlot",length(feature.list)+2)]] <- new("FeatureAssayPlot",
-                                                                        XAxis = "Column data",
-                                                                        XAxisColumnData = group,
-                                                                        YAxisFeatureSource = "DynamicMarkerTable1")
+    initial[[paste0("ReducedDimensionPlot",length(feature.list)+2)]] <- new(
+      "ReducedDimensionPlot",
+      Type = reddim.type,
+      ColorByColumnData = clusters,
+      ColorBy = "Column data",
+      SelectionAlpha = 0.05,
+      ColumnSelectionSource = paste0("FeatureAssayPlot",length(feature.list)+2))
+
+
+    initial[["DynamicMarkerTable1"]] <- new(
+      "DynamicMarkerTable",
+      ColumnSelectionSource = paste0("ReducedDimensionPlot",length(feature.list)+2))
+
+    initial[[paste0("FeatureAssayPlot",length(feature.list)+2)]] <- new(
+      "FeatureAssayPlot",
+      XAxis = "Column data",
+      XAxisColumnData = groups,
+      YAxisFeatureSource = "DynamicMarkerTable1")
   }
-  
+
   return(initial)
-  
-}
+
+}