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RiboRingsRiboRings
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Merge pull request #44 from microbiome/review
Create TreePlot and GraphPlot families and add typical tree operations and ScreePlot panel.
2 parents 628462c + e005b8d commit 32b9e30

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‎.gitignore

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@@ -10,4 +10,4 @@ inst/doc
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vignettes/*.html
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vignettes/*.R
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iSEEtree.BiocCheck/
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tests/testthat/*.pdf
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*.pdf

‎DESCRIPTION

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Package: iSEEtree
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Version: 1.1.2
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Version: 1.2.0
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Authors@R:
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c(person(given = "Giulio", family = "Benedetti", role = c("aut", "cre"),
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email = "giulio.benedetti@utu.fi",
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R (>= 4.4.0),
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iSEE (>= 2.19.2)
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Imports:
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ape,
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ggplot2,
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ggtree,
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grDevices,
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methods,
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miaViz,
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purrr,
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S4Vectors,
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shiny,
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mia,
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shinyWidgets,
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SingleCellExperiment,
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SummarizedExperiment,
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tidygraph,
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TreeSummarizedExperiment,
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utils
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Suggests:

‎NAMESPACE

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22

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export(AbundanceDensityPlot)
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export(AbundancePlot)
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export(ColumnGraphPlot)
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export(ColumnTreePlot)
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export(LoadingPlot)
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export(RDAPlot)
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export(RowGraphPlot)
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export(RowTreePlot)
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export(ScreePlot)
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export(iSEE)
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exportClasses(AbundanceDensityPlot)
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exportClasses(AbundancePlot)
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exportClasses(ColumnGraphPlot)
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exportClasses(ColumnTreePlot)
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exportClasses(GraphPlot)
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exportClasses(LoadingPlot)
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exportClasses(RDAPlot)
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exportClasses(RowGraphPlot)
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exportClasses(RowTreePlot)
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exportClasses(ScreePlot)
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exportClasses(TreePlot)
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exportMethods(iSEE)
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importFrom(S4Vectors,isEmpty)
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importFrom(S4Vectors,metadata)
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importFrom(S4Vectors,setValidity2)
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importFrom(SingleCellExperiment,reducedDim)
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importFrom(SingleCellExperiment,reducedDimNames)
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importFrom(SummarizedExperiment,colData)
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importFrom(SummarizedExperiment,rowData)
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importFrom(TreeSummarizedExperiment,TreeSummarizedExperiment)
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importFrom(TreeSummarizedExperiment,colTree)
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importFrom(TreeSummarizedExperiment,rowLinks)
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importFrom(TreeSummarizedExperiment,rowTreeNames)
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importFrom(TreeSummarizedExperiment,rowTree)
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importFrom(ape,Ntip)
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importFrom(ggplot2,aes)
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importFrom(ggplot2,geom_text)
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importFrom(ggtree,collapse)
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importFrom(ggtree,geom_tiplab)
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importFrom(ggtree,rotate_tree)
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importFrom(grDevices,dev.off)
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importFrom(grDevices,pdf)
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importFrom(grDevices,rainbow)
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importFrom(iSEE,.addSpecificTour)
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importFrom(iSEE,.addTourStep)
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importFrom(iSEE,.checkboxGroupInput.iSEE)
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importFrom(iSEE,.checkboxInput.iSEE)
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importFrom(iSEE,.conditionalOnCheckGroup)
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importFrom(iSEE,.conditionalOnCheckSolo)
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importFrom(iSEE,.conditionalOnRadio)
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importFrom(iSEE,.createProtectedParameterObservers)
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importFrom(iSEE,.createUnprotectedParameterObservers)
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importFrom(iSEE,.emptyDefault)
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importFrom(iSEE,.getEncodedName)
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importFrom(iSEE,.getPanelColor)
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importFrom(iSEE,.numericInput.iSEE)
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importFrom(iSEE,.processMultiSelections)
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importFrom(iSEE,.radioButtons.iSEE)
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importFrom(iSEE,.retrieveOutput)
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importFrom(iSEE,.selectInput.iSEE)
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importFrom(iSEE,.singleStringError)
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importFrom(iSEE,.sliderInput.iSEE)
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importFrom(iSEE,.textEval)
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importFrom(iSEE,.validLogicalError)
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importFrom(iSEE,.validNumberError)
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importFrom(iSEE,ColumnDataTable)
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importFrom(iSEE,ComplexHeatmapPlot)
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importFrom(iSEE,ExperimentColorMap)
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importFrom(iSEE,ReducedDimensionPlot)
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importFrom(iSEE,RowDataTable)
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importFrom(iSEE,collapseBox)
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importFrom(iSEE,createLandingPage)
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importFrom(methods,callNextMethod)
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importFrom(methods,is)
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importFrom(methods,new)
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importFrom(methods,slot)
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importFrom(mia,taxonomyRanks)
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importFrom(miaViz,plotColGraph)
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importFrom(miaViz,plotColTree)
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importFrom(miaViz,plotLoadings)
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importFrom(miaViz,plotRowGraph)
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importFrom(miaViz,plotRowTree)
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importFrom(miaViz,plotScree)
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importFrom(purrr,reduce)
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importFrom(shiny,plotOutput)
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importFrom(shiny,renderPlot)
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importFrom(shinyWidgets,addSpinner)
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importFrom(tidygraph,activate)
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importFrom(utils,stack)
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importMethodsFrom(iSEE,.generateOutput)
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importMethodsFrom(iSEE,.panelColor)
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importMethodsFrom(iSEE,.renderOutput)

‎NEWS

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Changes in version 0.1.3
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Changes in version 0.1.X
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* Moved to microbiome org
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Changes in version 0.1.4
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* Added panel tours
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* Prepared for submission
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Changes in version 0.99.0
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Changes in version 0.99.X
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* Submitted to Bioconductor
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Changes in version 0.99.2
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* Extended data params for all panels
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* Extended viz params for RDAPlot and RowTreePlot
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Changes in version 0.99.3
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* Added .exportOutput method
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Changes in version 0.99.8
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* Added ColumnTreePlot and LoadingPlot panels
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Changes in version 1.1.1
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Changes in version 1.1.X
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* Updated .multiSelectionResponsive
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* Conformed to iSEE v2.19.2
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Changes in version 1.2.X
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* Created TreePlot family
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* Added typical tree operations
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* Created GraphPlot family
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* Added ScreePlot panel

‎R/AllClasses.R

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tree_slots <- c(layout="character", add.legend="logical",
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edge.colour.by="character", tip.colour.by="character", order.tree="logical",
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tip.size.by="character", edge.size.by="character", tip.shape.by="character",
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node.size.by="character", node.shape.by="character", collapse="character",
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node.colour.by="character", add.node.lab="logical", add.tip.lab="logical",
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open.angle="numeric", rotate.angle="numeric", branch.length="logical",
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visual_parameters="character", size_parameters="character",
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shape_parameters="character", colour_parameters="character")
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#' @rdname TreePlot
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#' @export
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setClass("TreePlot", contains=c("Panel", "VIRTUAL"), slots=tree_slots)
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#' @rdname RowTreePlot
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#' @export
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setClass("RowTreePlot", contains="TreePlot")
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#' @rdname ColumnTreePlot
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#' @export
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setClass("ColumnTreePlot", contains="TreePlot")
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graph_slots <- c(name="character", assay.type="character", layout="character",
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edge.type="character", show.label="logical", add.legend="logical",
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edge.colour.by="character", edge.size.by="character",
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node.colour.by="character", node.shape.by="character",
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node.size.by="character", visual_parameters="character",
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size_parameters="character", shape_parameters="character",
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colour_parameters="character")
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#' @rdname GraphPlot
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#' @export
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setClass("GraphPlot", contains=c("Panel", "VIRTUAL"), slots=graph_slots)
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#' @rdname RowGraphPlot
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#' @export
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setClass("RowGraphPlot", contains="GraphPlot")
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#' @rdname ColumnGraphPlot
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#' @export
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setClass("ColumnGraphPlot", contains="GraphPlot")
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setClassUnion("charlog", c("character", "logical"))
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#' @rdname RDAPlot
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#' @export
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setClass("RDAPlot", contains="Panel", slots=c(dimred="character",
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add.ellipse="charlog", colour_by="character", vec.text="logical",
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add.vectors="logical", ellipse.alpha="numeric", confidence.level="numeric",
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add.significance="logical", add.expl.var="logical", ellipse.linewidth="numeric",
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ellipse.linetype="numeric", vec.size="numeric", vec.colour="character",
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vec.linetype="numeric", arrow.size="numeric", label.colour="character",
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label.size="numeric", visual_parameters="character"))
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#' @rdname LoadingPlot
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#' @export
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setClass("LoadingPlot", contains="Panel", slots=c(dimred="character",
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layout="character", ncomponents="numeric", add.tree="logical"))
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#' @rdname ScreePlot
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#' @export
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setClass("ScreePlot", contains="Panel", slots=c(dimred="character",
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show.barplot="logical", show.points="logical", show.line="logical",
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show.labels="logical", add.proportion="logical", add.cumulative="logical",
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n="numeric", show.names="logical", eig.name="character"))
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#' @rdname AbundancePlot
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#' @export
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setClass("AbundancePlot", contains="Panel",
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slots=c(rank="character", use_relative="logical", add_legend="logical",
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order_sample_by_row="character", order_sample="character",
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decreasing="logical", order_sample_by_column="character"))
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#' @rdname AbundanceDensityPlot
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#' @export
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setClass("AbundanceDensityPlot", contains="Panel", slots=c(layout="character",
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assay.type="character", n="numeric", dots_colour="character",
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dots_colour_by="character", add_legend="logical", flipped="logical",
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order_descending="logical", dots_shape="character",
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dots_shape_by="character"))
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‎R/class-AbundanceDensityPlot.R

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#' @name AbundanceDensityPlot
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NULL
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#' @rdname AbundanceDensityPlot
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#' @export
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setClass("AbundanceDensityPlot", contains="Panel", slots=c(layout="character",
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assay.type="character", n="numeric", dots_colour="character",
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dots_colour_by="character", add_legend="logical", flipped="logical",
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order_descending="logical", dots_shape="character", dots_shape_by="character"))
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#' @importFrom iSEE .singleStringError .validNumberError .validLogicalError
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#' @importFrom S4Vectors setValidity2
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setValidity2("AbundanceDensityPlot", function(x) {
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msg <- character(0)
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TRUE
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})
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#' @importFrom iSEE .emptyDefault
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#' @importFrom methods callNextMethod
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setMethod("initialize", "AbundanceDensityPlot", function(.Object, ...) {
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args <- list(...)
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new("AbundanceDensityPlot", ...)
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}
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#' @importFrom iSEE .getEncodedName .selectInput.iSEE .numericInput.iSEE .checkboxInput.iSEE
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#' .radioButtons.iSEE .conditionalOnRadio
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#' @importFrom methods slot
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#' @importFrom SummarizedExperiment assayNames
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setMethod(".defineDataInterface", "AbundanceDensityPlot",
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list(out[1], .create_visual_box_for_abunddens_plot(x, se), out[-1])
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})
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#' @importFrom iSEE .getEncodedName .createProtectedParameterObservers
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#' .createUnprotectedParameterObservers
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setMethod(".createObservers", "AbundanceDensityPlot",
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function(x, se, input, session, pObjects, rObjects) {
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invisible(NULL)
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})
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setMethod(".fullName", "AbundanceDensityPlot",
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function(x) "Abundance density plot")
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#' @importMethodsFrom iSEE .panelColor
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setMethod(".fullName", "AbundanceDensityPlot", function(x) "Abundance density plot")
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setMethod(".panelColor", "AbundanceDensityPlot", function(x) "#8B5A2B")
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#' @importFrom iSEE .getEncodedName
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#' @importFrom shiny plotOutput
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#' @importFrom shinyWidgets addSpinner
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setMethod(".defineOutput", "AbundanceDensityPlot", function(x) {
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color=.panelColor(x))
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})
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#' @importMethodsFrom iSEE .generateOutput
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#' @importFrom iSEE .processMultiSelections .textEval
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#' @importFrom miaViz plotRowTree
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setMethod(".generateOutput", "AbundanceDensityPlot",
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function(x, se, all_memory, all_contents) {
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list(commands=all_cmds, plot=plot_out, varname=NULL, contents=NULL)
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})
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#' @importFrom iSEE .getEncodedName .retrieveOutput
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#' @importFrom shiny renderPlot
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#' @importFrom methods callNextMethod
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setMethod(".renderOutput", "AbundanceDensityPlot",
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})
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#' @importFrom methods callNextMethod
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#' @importFrom iSEE .getEncodedName .addTourStep
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setMethod(".definePanelTour", "AbundanceDensityPlot", function(x) {
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rbind(c(paste0("#", .getEncodedName(x)), sprintf(
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"The <font color=\"%s\">Abundance Density Plot</font> panel
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callNextMethod())
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})
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#' @importFrom iSEE .getEncodedName collapseBox .selectInput.iSEE
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#' .radioButtons.iSEE .conditionalOnRadio .checkboxInput.iSEE
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#' @importFrom methods slot
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#' @importFrom SummarizedExperiment colData
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.create_visual_box_for_abunddens_plot <- function(x, se) {

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