Merge pull request #45 from microbiome/examples

Examples

Author: RiboRings

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+export(.check_all_panels)
+export(.check_panel)
 export(AbundanceDensityPlot)
 export(AbundancePlot)
 export(ColumnGraphPlot)

R/class-AbundanceDensityPlot.R

@@ -15,7 +15,8 @@
 #' \item \code{order_descending}, a string specifying the descending order.
 #' }
 #'
-#' In addition, this class inherits all slots from its parent \linkS4class{Panel} class.
+#' In addition, this class inherits all slots from its parent class
+#' \code{\link[iSEE:Panel-class]{Panel}}.
 #'
 #' @return
 #' The \code{AbundanceDensityPlot(...)} constructor creates an instance of an

R/class-AbundancePlot.R

@@ -13,7 +13,8 @@
 #' \item \code{add_legend}, a logical indicating if the color legend should appear.
 #' }
 #'
-#' In addition, this class inherits all slots from its parent \linkS4class{Panel} class.
+#' In addition, this class inherits all slots from its parent class
+#' \code{\link[iSEE:Panel-class]{Panel}}.
 #'
 #' @return
 #' The \code{AbundancePlot(...)} constructor creates an instance of an

R/class-LoadingPlot.R

@@ -14,7 +14,8 @@
 #' \item \code{add.tree}, a logical indicating whether the tree should be shown.
 #' }
 #'
-#' In addition, this class inherits all slots from its parent \linkS4class{Panel} class.
+#' In addition, this class inherits all slots from its parent class
+#' \code{\link[iSEE:Panel-class]{Panel}}.
 #'
 #' @return
 #' The \code{LoadingPlot(...)} constructor creates an instance of an

R/class-RDAPlot.R

@@ -30,7 +30,8 @@
 #'  on the coordinate axes.
 #' }
 #'
-#' In addition, this class inherits all slots from its parent \linkS4class{Panel} class.
+#' In addition, this class inherits all slots from its parent class
+#' \code{\link[iSEE:Panel-class]{Panel}}.
 #'
 #' @return
 #' The \code{RDAPlot(...)} constructor creates an instance of a RDAPlot class,

R/class-ScreePlot.R

@@ -45,8 +45,8 @@
 #'   (Default: \code{c("eig", "varExplained")})
 #' }
 #' 
-#' In addition, this class inherits all slots from its parent
-#' \linkS4class{Panel} class.
+#' In addition, this class inherits all slots from its parent class
+#' \code{\link[iSEE:Panel-class]{Panel}}.
 #'
 #' @return
 #' The \code{ScreePlot(...)} constructor creates an instance of an ScreePlot

R/family-GraphPlot.R

@@ -35,7 +35,7 @@
 #' }
 #'
 #' In addition, this class inherits all slots from its parent class
-#' \linkS4class{Panel}.
+#' \code{\link[iSEE:Panel-class]{Panel}}.
 #' 
 #' @seealso
 #' \linkS4class{RowGraphPlot}

R/family-TreePlot.R

@@ -41,7 +41,7 @@
 #' }
 #'
 #' In addition, this class inherits all slots from its parent
-#' \linkS4class{Panel} class.
+#' \code{\link[iSEE:Panel-class]{Panel}}.
 #' 
 #' @seealso
 #' \linkS4class{RowTreePlot}

R/iSEE-default.R

@@ -51,48 +51,17 @@ setGeneric("iSEE", iSEE::iSEE)
 #' @export
 #' @importFrom iSEE createLandingPage ExperimentColorMap ReducedDimensionPlot
 #'   ComplexHeatmapPlot RowDataTable ColumnDataTable
-#' @importFrom TreeSummarizedExperiment TreeSummarizedExperiment rowLinks
-#'   colLinks
-#' @importFrom SingleCellExperiment reducedDims
-#' @importFrom S4Vectors metadata
-#' @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, "ColumnTreePlot", colLinks)
-    initial <- .check_panel(se, initial, "AbundancePlot", taxonomyRanks)
-    initial <- .check_panel(se, initial, "ReducedDimensionPlot", reducedDims)
-    initial <- .check_panel(se, initial, "LoadingPlot", reducedDims)
-    initial <- .check_panel(se, initial, "ScreePlot", reducedDims)
-    initial <- .check_panel(se, initial, "RDAPlot", reducedDims)
-    initial <- .check_panel(se, initial, "RowGraphPlot", metadata)
-    initial <- .check_panel(se, initial, "ColumnGraphPlot", metadata)
+    initial <- .check_all_panels(se, initial)
 
     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, 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)
-}
+})

R/iSEEtree-package.R

@@ -1,6 +1,6 @@
 #' iSEE extension for the TreeSummarizedExperiment container
 #'
-#' `iSEEtree` is an extension of \pkg{iSEE} that provides panels for the
+#' \code{iSEEtree} is an extension of \pkg{iSEE} that provides panels for the
 #' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-constructor]{TreeSummarizedExperiment}}
 #' container, enabling the interactive visualisation of typical microbiome data.
 #' The panel layout of iSEEtree is described in \code{\link{iSEE}}.
@@ -14,6 +14,6 @@
 #' 
 #' @docType package
 #' @keywords internal
-#' @name iSEEtree
+#' @name iSEEtree-package
 #' 
 "_PACKAGE"

R/utils.R

@@ -0,0 +1,89 @@
+#' iSEEtree utils
+#' 
+#' Utility functions to check the existence of specific elements in a
+#' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-constructor]{TreeSummarizedExperiment}}
+#' that are compulsory when using certain panels.
+#' 
+#' @param se a
+#' \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
+#' object.
+#' 
+#' @param initial \code{Panel vector}. A list of panel objects to check.
+#' 
+#' @param panel.class \code{Character vector}. A list of panel names
+#'   corresponding to panel objects in \code{initial}.
+#' 
+#' @param panel.fun \code{Function scalar}. The element of \code{se} whose
+#'   existance should be checked.
+#' 
+#' @param wtext \code{Character scalar}. Text of the warning message returned
+#'   if \code{panel.fun} does not exist or is empty.
+#' 
+#' @return
+#' \code{.check_panel} returns the input \code{initial} list of panels excluding
+#' the checked panel if \code{panel.fun} is \code{NULL} or empty.
+#' \code{.check_all_panels} applies \code{.check_panel} to multiple panels and
+#' returns the a filtered version of \code{initial}.
+#'
+#' @examples
+#' # Import libraries
+#' library(mia)
+#' library(TreeSummarizedExperiment)
+#' 
+#' # Import TreeSE
+#' data("Tengeler2020", package = "mia")
+#' tse <- Tengeler2020
+#'
+#' # Create list of panels
+#' initial <- c(RowTreePlot(), ColumnTreePlot())
+#' # If RowTreePlot is in initial, check whether rowLinks is defined
+#' initial <- .check_panel(tse, initial, "RowTreePlot", rowLinks)
+#' # If ColumnTreePlot is in initial, check whether colLinks is defined
+#' initial <- .check_panel(tse, initial, "ColumnTreePlot", colLinks)
+#' 
+#' # View filtered list of panels
+#' initial
+#' 
+#' @keywords internal
+#' @name utils
+NULL
+
+#' @rdname utils
+#' @export
+#' @importFrom TreeSummarizedExperiment TreeSummarizedExperiment rowLinks
+#'   colLinks
+#' @importFrom SingleCellExperiment reducedDims
+#' @importFrom S4Vectors metadata
+#' @importFrom SummarizedExperiment rowData colData
+#' @importFrom mia taxonomyRanks
+.check_all_panels <- function(se, initial){
+    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, "ColumnTreePlot", colLinks)
+    initial <- .check_panel(se, initial, "AbundancePlot", taxonomyRanks)
+    initial <- .check_panel(se, initial, "ReducedDimensionPlot", reducedDims)
+    initial <- .check_panel(se, initial, "LoadingPlot", reducedDims)
+    initial <- .check_panel(se, initial, "ScreePlot", reducedDims)
+    initial <- .check_panel(se, initial, "RDAPlot", reducedDims)
+    initial <- .check_panel(se, initial, "RowGraphPlot", metadata)
+    initial <- .check_panel(se, initial, "ColumnGraphPlot", metadata)
+    return(initial)
+}
+
+#' @rdname utils
+#' @export
+#' @importFrom S4Vectors isEmpty
+#' @importFrom methods is
+.check_panel <- function(se, initial, panel.class, panel.fun, wtext) {
+    
+    no_keep <- unlist(lapply(initial, function(x) is(x, panel.class)))
+
+    if( any(no_keep) && (is.null(panel.fun(se)) || isEmpty(panel.fun(se))) ){
+        initial <- initial[!no_keep]
+        warning("no valid ", as.character(substitute(panel.fun)),
+            " fields for ", panel.class, call. = FALSE)
+    }
+    
+    return(initial)
+}

inst/CITATION

@@ -0,0 +1,20 @@
+citHeader("To cite iSEEtree in publications use:")
+
+citEntry(
+  entry    = "Article",
+  title    = "iSEEtree: interactive explorer for hierarchical data",
+  author   = personList(
+      as.person("Giulio Benedetti"),
+      as.person("Ely Seraidarian"),
+      as.person("Theotime Pralas"),
+      as.person("Akewak Jeba"),
+      as.person("Tuomas Borman"),
+      as.person("Leo Lahti")
+  ),
+  journal  = "arXiv",
+  year     = "2024",
+  url      = "https://arxiv.org/abs/2412.02882",
+  textVersion = paste("Benedetti, G., Seraidarian, E., Pralas, T., Jeba, A.",
+  "Borman, T., & Lahti, L. (2024). iSEEtree: interactive explorer for",
+  "hierarchical data. arXiv. doi: https://doi.org/10.48550/arXiv.2412.02882")
+)

inst/REFERENCES.bib

@@ -0,0 +1,45 @@
+@Manual{core2024r,
+  title = {R: A Language and Environment for Statistical Computing},
+  author = {{R Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2024},
+  url = {https://www.R-project.org/},
+  }
+
+@article{rue2018isee,
+  title={{iSEE: interactive SummarizedExperiment explorer}},
+  author={Rue-Albrecht, Kevin and Marini, Federico and Soneson, Charlotte and Lun, Aaron TL},
+  journal={F1000Research},
+  volume={7},
+  year={2018},
+  publisher={Faculty of 1000 Ltd},
+  doi={10.12688/f1000research.14966.1}
+}
+
+@Manual{chang2024shiny,
+    title = {shiny: Web Application Framework for R},
+    author = {Winston Chang and Joe Cheng and JJ Allaire and Carson Sievert and Barret Schloerke and Yihui Xie and Jeff Allen and Jonathan McPherson and Alan Dipert and Barbara Borges},
+    year = {2024},
+    note = {R package version 1.9.1},
+    url = {https://CRAN.R-project.org/package=shiny},
+  }
+
+@Manual{borman2024mia,
+  title = {mia: Microbiome analysis},
+  author = {Tuomas Borman and Felix G.M. Ernst and Sudarshan A. Shetty and Leo Lahti},
+  year = {2024},
+  note = {R package version 1.14.0},
+  url = {https://bioconductor.org/packages/mia},
+  doi = {10.18129/B9.bioc.mia},
+}
+
+@article{huang2021treesummarizedexperiment,
+  title={{TreeSummarizedExperiment: a S4 class for data with hierarchical structure}},
+  author={Huang, Ruizhu and Soneson, Charlotte and Ernst, Felix GM and Rue-Albrecht, Kevin C and Yu, Guangchuang and Hicks, Stephanie C and Robinson, Mark D},
+  journal={F1000Research},
+  volume={9},
+  year={2021},
+  publisher={Faculty of 1000 Ltd},
+  doi={10.12688/f1000research.26669.2}
+}