Bioc review

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: iSEEfier
 Title: Streamlining the creation of initial states for starting an iSEE instance
-Version: 0.99.1
+Version: 0.99.2
 Authors@R:
     c(
     person(given = "Najla", family = "Abassi", role = c("aut", "cre"),
@@ -33,7 +33,8 @@ Imports:
     stats,
     SummarizedExperiment,
     SingleCellExperiment,
-    visNetwork
+    visNetwork,
+    BiocBaseUtils
 Suggests:
     knitr,
     rmarkdown,

NAMESPACE

@@ -11,6 +11,9 @@ importClassesFrom(iSEE,FeatureAssayPlot)
 importClassesFrom(iSEE,ReducedDimensionPlot)
 importClassesFrom(iSEE,RowDataTable)
 importClassesFrom(iSEEu,MarkdownBoard)
+importFrom(BiocBaseUtils,isCharacter)
+importFrom(BiocBaseUtils,isScalarCharacter)
+importFrom(BiocBaseUtils,isTRUEorFALSE)
 importFrom(SingleCellExperiment,reducedDimNames)
 importFrom(SummarizedExperiment,colData)
 importFrom(ggplot2,aes)

NEWS.md

@@ -1,3 +1,9 @@
+# iSEEfier 0.99.2
+
+* Addressing the points raised in the Bioc review
+* Better checks of the arguments - more compact and robust
+* Explicitly suggesting the instructions to install potentially missing packages for `iSEEnrich()`
+
 # iSEEfier 0.99.1
 
 * Ready for Bioconductor review

R/iSEEinit.R

@@ -1,16 +1,26 @@
-#' iSEEinit: Create an initial state of an iSEE instance for gene expression visualization
+#' 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.
+#' `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
 #' @param features A character vector containing a list of genes
-#' @param reddim_type A string vector containing the dimensionality reduction type
-#' @param clusters A character string containing the name of the clusters/cell-type/state...(as listed in the colData of the sce)
-#' @param groups A character string of the groups/conditions...(as it appears in the colData of the sce)
-#' @param add_markdown_panel A logical indicating whether or not to include the MarkdownBoard panel in the initial configuration
-#' @param add_dynamicTable_panel A logical indicating whether or not the DynamicMarkerTable and linked panels should be included in the initial configuration
+#' @param reddim_type A string vector containing the dimensionality reduction
+#'   type
+#' @param clusters A character string containing the name of the
+#'   clusters/cell-type/state...(as listed in the colData of the sce)
+#' @param groups A character string of the groups/conditions...(as it appears in
+#'   the colData of the sce)
+#' @param add_markdown_panel A logical indicating whether or not to include the
+#'   MarkdownBoard panel in the initial configuration
+#' @param add_dynamicTable_panel A logical indicating whether or not the
+#'   DynamicMarkerTable and linked panels should be included in the initial
+#'   configuration
 #'
-#' @return A list of "Panel" objects specifying the initial state of iSEE instance
+#' @return A list of "Panel" objects specifying the initial state of iSEE
+#'   instance
 #' @export
 #' @importFrom methods new
 #' @importFrom SummarizedExperiment colData
@@ -22,14 +32,17 @@
 #' @importClassesFrom iSEE RowDataTable
 #' @importClassesFrom iSEE ComplexHeatmapPlot
 #' @importClassesFrom iSEEu MarkdownBoard
+#' @importFrom BiocBaseUtils isCharacter isScalarCharacter isTRUEorFALSE
 #'
 #'
 #' @examples
 #' sce <- scRNAseq::RichardTCellData()
 #' sce <- scuttle::logNormCounts(sce)
 #' sce <- scater::runPCA(sce)
 #' sce <- scater::runTSNE(sce)
-#' gene_list <- c("ENSMUSG00000026581", "ENSMUSG00000005087", "ENSMUSG00000015437")
+#' gene_list <- c("ENSMUSG00000026581",
+#'                "ENSMUSG00000005087",
+#'                "ENSMUSG00000015437")
 #' cluster <- "stimulus"
 #' group <- "single cell quality"
 #' initial <- iSEEinit(sce = sce, features = gene_list, clusters = cluster, groups = group)
@@ -45,22 +58,17 @@ iSEEinit <- function(sce,
   if (!is(sce, "SingleCellExperiment"))
     stop("Please provide a SingleCellExperiment as input!")
 
-  stopifnot(is.character(features))
-  stopifnot(length(features) > 0)
+  stopifnot(is.character(features), length(features) > 0)
 
-  stopifnot(is.character(reddim_type))
-  stopifnot(length(reddim_type) == 1)
+  stopifnot(isScalarCharacter(reddim_type))
 
-  stopifnot(is.character(clusters))
-  stopifnot(length(clusters) == 1)
+  stopifnot(isScalarCharacter(clusters))
 
-  stopifnot(is.character(groups))
-  stopifnot(length(groups) == 1)
+  stopifnot(isScalarCharacter(groups))
 
-  stopifnot(is.logical(add_markdown_panel))
-  stopifnot(length(add_markdown_panel) == 1)
-  stopifnot(is.logical(add_dynamicTable_panel))
-  stopifnot(length(add_dynamicTable_panel) == 1)
+  stopifnot(isTRUEorFALSE(add_markdown_panel))
+
+  stopifnot(isTRUEorFALSE(add_dynamicTable_panel))
 
   if (!(reddim_type %in% reducedDimNames(sce))) {
     available_reddims <- reducedDimNames(sce)
@@ -179,21 +187,21 @@ iSEEinit <- function(sce,
       PanelWidth = 4L)
   }
 
-  if(add_dynamicTable_panel == TRUE) {
-    initial[[paste0("ReducedDimensionPlot",length(features)+2)]] <- new(
+  if (add_dynamicTable_panel == TRUE) {
+    initial[[paste0("ReducedDimensionPlot",length(features) + 2)]] <- new(
       "ReducedDimensionPlot",
       Type = reddim_type,
       ColorByColumnData = clusters,
       ColorBy = "Column data",
       SelectionAlpha = 0.05,
-      ColumnSelectionSource = paste0("FeatureAssayPlot",length(features)+2))
+      ColumnSelectionSource = paste0("FeatureAssayPlot",length(features) + 2))
 
 
     initial[["DynamicMarkerTable1"]] <- new(
       "DynamicMarkerTable",
-      ColumnSelectionSource = paste0("ReducedDimensionPlot",length(features)+2))
+      ColumnSelectionSource = paste0("ReducedDimensionPlot",length(features) + 2))
 
-    initial[[paste0("FeatureAssayPlot",length(features)+2)]] <- new(
+    initial[[paste0("FeatureAssayPlot",length(features) + 2)]] <- new(
       "FeatureAssayPlot",
       XAxis = "Column data",
       XAxisColumnData = groups,

R/iSEEnrich.R

@@ -1,19 +1,25 @@
 #' iSEEnrich
 #'
-#' `iSEEnrich()` creates an initial state of an iSEE instance for interactive exploration of feature sets extracted from GO and KEGG database,
-#' displaying all associated genes in a `RowDataTable` panel.
+#' `iSEEnrich()` creates an initial state of an iSEE instance for interactive
+#' exploration of feature sets extracted from GO and KEGG database, displaying
+#' all associated genes in a `RowDataTable` panel.
 #'
 #' @param sce SingleCellExperiment object
-#' @param collection A character vector specifying the gene set collections of interest (GO,KEGG)
-#' @param organism A character string of the org.*.eg.db package to use to extract mappings of gene sets to gene IDs.
-#' @param gene_identifier A character string specifying the identifier to use to extract gene IDs for the organism package
+#' @param collection A character vector specifying the gene set collections of
+#'   interest (GO,KEGG)
+#' @param organism A character string of the org.*.eg.db package to use to
+#'   extract mappings of gene sets to gene IDs.
+#' @param gene_identifier A character string specifying the identifier to use to
+#'   extract gene IDs for the organism package
 #'
-#' @return A list of "Panel" objects specifying the initial state of iSEE instance
+#' @return A list of "Panel" objects specifying the initial state of iSEE
+#'   instance
 #' @export iSEEnrich
 #' @importFrom iSEE RowDataTable
 #' @importFrom iSEEu createGeneSetCommands
 #' @importFrom iSEEu registerFeatureSetCommands
 #' @importFrom iSEEu FeatureSetTable
+#' @importFrom BiocBaseUtils isScalarCharacter
 #'
 #'
 #' @examples
@@ -27,7 +33,7 @@
 #'                      collection = GO_collection,
 #'                      organism = Mm_organism,
 #'                      gene_identifier = gene_id)
-#'
+#' 
 iSEEnrich <- function(sce,
                       collection = c("GO", "KEGG"),
                       organism = "org.Hs.eg.db",
@@ -37,20 +43,19 @@ iSEEnrich <- function(sce,
   if (!is(sce, "SingleCellExperiment"))
     stop("Please provide a SingleCellExperiment as input!")
 
-  stopifnot(is.character(collection))
-  stopifnot(length(collection) == 1)
+  stopifnot(isScalarCharacter(collection))
 
   collection <- match.arg(collection, c("GO", "KEGG"))
 
-  stopifnot(is.character(organism))
-  stopifnot(length(organism) == 1)
+  stopifnot(isScalarCharacter(organism))
 
-  stopifnot(is.character(gene_identifier))
-  stopifnot(length(gene_identifier) == 1)
+  stopifnot(isScalarCharacter(gene_identifier))
 
   if (!requireNamespace(organism, quietly = TRUE))
     stop("Please check the value of the provided orgDb package ",
-         "(it needs to be installed)...")
+         "(the package needs to be installed)...",
+         "If you want to install it run the following line:\n",
+         "BiocManager::install('", organism,"')")
 
 
   initial <- list()
@@ -62,7 +67,8 @@ iSEEnrich <- function(sce,
 
   initial[["FeatureSetTable1"]] <- FeatureSetTable()
 
-  initial[["RowDataTable1"]] <- RowDataTable(RowSelectionSource="FeatureSetTable1")
+  initial[["RowDataTable1"]] <- RowDataTable(
+    RowSelectionSource = "FeatureSetTable1")
 
   return(
     list(

R/utils.R

@@ -26,6 +26,7 @@
 #' @importFrom ggplot2 ggplot aes geom_tile scale_fill_manual scale_y_discrete
 #' theme theme_void
 #' @importFrom rlang .data
+#' @importFrom BiocBaseUtils isCharacter
 #'
 #' @seealso [view_initial_network()]
 #'
@@ -36,7 +37,9 @@
 #' sce <- scater::runPCA(sce)
 #' sce <- scater::runTSNE(sce)
 #' ## Select some features and aspects to focus on
-#' gene_list <- c("ENSMUSG00000026581", "ENSMUSG00000005087", "ENSMUSG00000015437")
+#' gene_list <- c("ENSMUSG00000026581",
+#'                "ENSMUSG00000005087",
+#'                "ENSMUSG00000015437")
 #' cluster <- "stimulus"
 #' group <- "single cell quality"
 #' initial <- iSEEinit(sce = sce,
@@ -73,7 +76,7 @@ view_initial_tiles <- function(initial) {
   cur_row <- 1
 
   # fill in the tiles vector "with the rule of 12"
-  for(i in seq_len(length(initial))) {
+  for (i in seq_len(length(initial))) {
     this_width <- panel_widths[i]
     this_paneltype <- panel_types[i]
     this_color <- iSEE_panel_colors[this_paneltype]
@@ -133,7 +136,7 @@ view_initial_tiles <- function(initial) {
       name = "iSEE Panel type",
       values = iSEE_panel_colors
     ) +
-    theme(legend.position="bottom")
+    theme(legend.position = "bottom")
 
   return(p)
 }
@@ -328,7 +331,7 @@ glue_initials <- function(...,
   allowed_panels <- names(iSEE_panel_colors)
 
   if (!is.null(custom_panels_allowed)) {
-    stopifnot(is.character(custom_panels_allowed))
+    stopifnot(isCharacter(custom_panels_allowed))
     allowed_panels <- c(allowed_panels, custom_panels_allowed)
   }