Updating iSEEnrich & iSEEinit

.github/workflows/R-CMD-check.yaml

@@ -67,11 +67,10 @@ jobs:
         if: runner.os == 'Linux'
         env:
           RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
-          sudo apt-get update && sudo apt-get -y install libcurl4-openssl-dev libglpk-dev libharfbuzz-dev libfribidi-dev
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          pak-version: devel
 
       - name: Install system dependencies (macOS)
         if: runner.os == 'macOS'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: iSEEfier
 Title: Streamlining the creation of initial states for starting an iSEE instance
-Version: 1.1.1
+Version: 1.1.2
 Authors@R:
     c(
     person(given = "Najla", family = "Abassi", role = c("aut", "cre"),

NAMESPACE

@@ -24,8 +24,6 @@ importFrom(ggplot2,scale_fill_manual)
 importFrom(ggplot2,scale_y_discrete)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_void)
-importFrom(iSEE,RowDataTable)
-importFrom(iSEEu,FeatureSetTable)
 importFrom(iSEEu,createGeneSetCommands)
 importFrom(iSEEu,registerFeatureSetCommands)
 importFrom(igraph,"V<-")

NEWS.md

@@ -2,6 +2,8 @@
 
 * Adding in a new function `iSEEmarker()`, more focused on finding marker genes
 * A new `iSEEinit()` version without the `DynamicMarkerTable` panel
+* Expanding the input of `iSEEinit()` to accept features as `data.frame` in addition to `vector`
+* Adding visualization plots to `iSEEnrich()`
 
 # iSEEfier 1.0.0
 

R/iSEEinit.R

@@ -6,15 +6,19 @@
 #' list in a single view.
 #'
 #' @param sce SingleCellExperiment object
-#' @param features A character vector containing a list of genes
+#' @param features A character vector or a data.frame containing a list of genes.
+#' If `features` is a data.frame, the column containing the gene names must be named "id"
 #' @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 gene_id A character string containing the name of the column name containing
+#'  gene names/ids, when 'features' is a data.frame
 #' @param add_markdown_panel A logical indicating whether or not to include the
 #'   MarkdownBoard panel in the initial configuration
+
 #'
 #' @return A list of "Panel" objects specifying the initial state of iSEE
 #'   instance
@@ -48,21 +52,22 @@ iSEEinit <- function(sce,
                      reddim_type = "TSNE",
                      clusters = colnames(colData(sce))[1],
                      groups = colnames(colData(sce))[1],
+                     gene_id="id",
                      add_markdown_panel = FALSE) {
 
   ## Checks on arguments
   if (!is(sce, "SingleCellExperiment"))
     stop("Please provide a SingleCellExperiment as input!")
 
-  stopifnot(is.character(features), length(features) > 0)
-
   stopifnot(isScalarCharacter(reddim_type))
 
   stopifnot(isScalarCharacter(clusters))
 
   stopifnot(isScalarCharacter(groups))
 
   stopifnot(isTRUEorFALSE(add_markdown_panel))
+
+  stopifnot(isScalarCharacter(gene_id))
 
 
   if (!(reddim_type %in% reducedDimNames(sce))) {
@@ -71,6 +76,23 @@ iSEEinit <- function(sce,
          "Please select one of these: ",
          paste(available_reddims, collapse = ", "))
   }
+
+  if (is.data.frame(features)) {
+    if ((gene_id %in% colnames(features))) {
+
+      features <- as.character(features[[gene_id]])
+    } else {
+      stop("The column name '", gene_id,"' does not exist in the 'features' data.frame!")
+    }
+  }
+
+  else if (is.vector(features)) {
+    features <- as.character(features)
+  } else {
+    stop("Unsupported feature type. Must be a character vector, or data.frame!")
+    }
+
+  stopifnot(is.character(features), NROW(features) > 0)
 
   if (!all(features %in% rownames(sce))) {
     not_available_features <- features[!features %in% rownames(sce)]
@@ -79,7 +101,7 @@ iSEEinit <- function(sce,
             paste(not_available_features, collapse = ", "))
 
     features <- features[features %in% rownames(sce)]
-    if (length(features) == 0)
+    if (NROW(features) == 0)
       stop("No features available!")
   }
 
@@ -104,57 +126,60 @@ iSEEinit <- function(sce,
     message("colData column not found for the `groups` parameter, defaulting to ",
             fallback_groups)
   }
-
-
+
 
 
   initial <- list()
 
 
-  for (j in features) {
-    initial[[paste0("ReducedDimensionPlot", which(features == j))]] <- new(
+  for (j in 1:NROW(features)) {
+    feature_name <- if (is.data.frame(features)) features[j, ] else features[[j]]
+    initial[[paste0("ReducedDimensionPlot", j)]] <- new(
       "ReducedDimensionPlot",
       Type = reddim_type,
       ColorBy = "Feature name",
-      ColorByFeatureName = j,
-      ColorByFeatureSource = paste0("RowDataTable", which(features == j)),
+      ColorByFeatureName = feature_name,
+      ColorByFeatureSource = paste0("RowDataTable", j),
       ColumnSelectionSource = "ColumnDataPlot1",
       SelectionAlpha = 0.05
     )
-    
-    initial[[paste0("FeatureAssayPlot", which(features == j))]] <- new(
+
+    initial[[paste0("FeatureAssayPlot", j)]] <- new(
       "FeatureAssayPlot",
       XAxis = "Column data",
       XAxisColumnData = clusters,
-      YAxisFeatureName = j,
-      YAxisFeatureSource = paste0("RowDataTable", which(features == j)),
+      YAxisFeatureName = feature_name,
+      YAxisFeatureSource = paste0("RowDataTable", j),
       ColorBy = "Column data",
       ColorByColumnData = clusters
     )
 
-    initial[[paste0("RowDataTable", which(features == j))]] <- new(
+    initial[[paste0("RowDataTable", j)]] <- new(
       "RowDataTable",
-      Selected = j,
-      Search = j
+      Selected = feature_name,
+      Search = feature_name
     )
   }
 
-  if (length(features) > 1) {
-    initial[[paste0("FeatureAssayPlot", length(features) + 1)]] <- new(
+  if (NROW(features) > 1) {
+    feature1 <- if (is.data.frame(features)) features[1, ] else features[[1]]
+    feature2 <- if (is.data.frame(features)) features[2, ] else features[[2]]
+
+    initial[[paste0("FeatureAssayPlot", NROW(features) + 1)]] <- new(
       "FeatureAssayPlot",
       XAxis = "Feature name",
-      XAxisFeatureName = features[[1]],
-      YAxisFeatureName = features[[2]]
+      XAxisFeatureName = feature1,
+      YAxisFeatureName = feature2
     )
   }
 
   if (add_markdown_panel == TRUE) {
-    initial[[paste0("ReducedDimensionPlot", length(features) + 1)]] <- new(
+    initial[[paste0("ReducedDimensionPlot", NROW(features) + 1)]] <- new(
       "ReducedDimensionPlot",
       Type = reddim_type,
       ColorByColumnData = clusters,
       ColorBy = "Column data",
-      ColumnSelectionSource = paste0("FeatureAssayPlot", length(features) + 1),
+      ColumnSelectionSource = paste0("FeatureAssayPlot", NROW(features) + 1),
       FacetColumnBy = "Column data",
       FacetColumnByColData = groups,
       SelectionAlpha = 0.05
@@ -165,12 +190,12 @@ iSEEinit <- function(sce,
       Content = "# Placeholder\n\nFill me with text!",
       PanelWidth = 4L)
   } else {
-    initial[[paste0("ReducedDimensionPlot", length(features) + 1)]] <- new(
+    initial[[paste0("ReducedDimensionPlot", NROW(features) + 1)]] <- new(
       "ReducedDimensionPlot",
       Type = reddim_type,
       ColorByColumnData = clusters,
       ColorBy = "Column data",
-      ColumnSelectionSource = paste0("FeatureAssayPlot", length(features) + 1),
+      ColumnSelectionSource = paste0("FeatureAssayPlot", NROW(features) + 1),
       FacetColumnBy = "Column data",
       FacetColumnByColData = groups,
       SelectionAlpha = 0.05,
@@ -196,5 +221,6 @@ iSEEinit <- function(sce,
 
 
   return(initial)
+
 
 }

R/iSEEnrich.R

@@ -11,14 +11,22 @@
 #'   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 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 reddim_type A string vector containing the dimensionality reduction
+#'   type
+#'   
+#'   
 #' @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
 #'
 #'
@@ -29,15 +37,24 @@
 #' GO_collection <- "GO"
 #' Mm_organism <- "org.Mm.eg.db"
 #' gene_id <- "SYMBOL"
+#' clusters <- "stimulus"
+#' groups <- "single cell quality"
+#' reddim_type <- "PCA"
 #' results <- iSEEnrich(sce = sce,
 #'                      collection = GO_collection,
 #'                      organism = Mm_organism,
-#'                      gene_identifier = gene_id)
+#'                      gene_identifier = gene_id,
+#'                      clusters = clusters,
+#'                      groups = groups,
+#'                      reddim_type = reddim_type)
 #' 
 iSEEnrich <- function(sce,
                       collection = c("GO", "KEGG"),
                       organism = "org.Hs.eg.db",
-                      gene_identifier = "ENTREZID") {
+                      gene_identifier = "ENTREZID",
+                      clusters = colnames(colData(sce))[1],
+                      groups = colnames(colData(sce))[1],
+                      reddim_type = "PCA") {
 
   ## Checks on arguments
   if (!is(sce, "SingleCellExperiment"))
@@ -50,7 +67,40 @@ iSEEnrich <- function(sce,
   stopifnot(isScalarCharacter(organism))
 
   stopifnot(isScalarCharacter(gene_identifier))
-
+
+  stopifnot(isScalarCharacter(clusters))
+
+  stopifnot(isScalarCharacter(groups))
+
+  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)
+  }
+
+  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 (!requireNamespace(organism, quietly = TRUE))
     stop("Please check the value of the provided orgDb package ",
          "(the package needs to be installed)...",
@@ -64,11 +114,46 @@ iSEEnrich <- function(sce,
                                 organism = organism,
                                 identifier = gene_identifier)
   sce1 <- registerFeatureSetCommands(sce, cmds)
-
-  initial[["FeatureSetTable1"]] <- FeatureSetTable()
-
-  initial[["RowDataTable1"]] <- RowDataTable(
-    RowSelectionSource = "FeatureSetTable1")
+
+  initial[["FeatureSetTable1"]] <- new(
+    "FeatureSetTable", Collection = collection)
+
+  initial[["RowDataTable1"]] <- new(
+    "RowDataTable", RowSelectionSource = "FeatureSetTable1")
+
+  initial[["FeatureAssayPlot1"]] <- new(
+    "FeatureAssayPlot",
+    XAxis = "Column data",
+    XAxisColumnData = groups,
+    YAxisFeatureSource = "RowDataTable1",
+    ColorBy = "Column data",
+    ColorByColumnData = groups,
+    ColumnSelectionSource = "ColumnDataPlot1")
+
+  initial[["ColumnDataPlot1"]] <- new(
+    "ColumnDataPlot",
+    XAxis = "Column data",
+    YAxis = clusters,
+    XAxisColumnData = groups,
+    ColorByColumnData = clusters,
+    ColorBy = "Column data"
+
+  )
+
+  initial[["ReducedDimensionPlot1"]] <- new(
+    "ReducedDimensionPlot",
+    Type = reddim_type,
+    FacetColumnByColData = groups,
+    FacetColumnBy = "Column data",
+    ColorBy = "Feature name",
+    ColorByFeatureSource = "RowDataTable1",
+    ColumnSelectionSource = "ColumnDataPlot1"
+  )
+
+  initial[["MarkdownBoard1"]] <- new(
+    "MarkdownBoard",
+    Content = "# Placeholder\n\nFill me with genes, or anything!")
+
 
   return(
     list(