Package: iSEEtree 1.1.3
Giulio Benedetti
iSEEtree: Interactive visualisation for microbiome data
iSEEtree is an extension of iSEE for the TreeSummarizedExperiment. It leverages the functionality from the miaViz package for microbiome data visualisation to create panels that are specific for TreeSummarizedExperiment objects. Not surprisingly, it also depends on the generic panels from iSEE.
Authors:
iSEEtree_1.1.3.tar.gz
iSEEtree_1.1.3.zip(r-4.5)iSEEtree_1.1.3.zip(r-4.4)
iSEEtree_1.1.3.tgz(r-4.5-any)iSEEtree_1.1.3.tgz(r-4.4-any)
iSEEtree_1.1.3.tar.gz(r-4.5-noble)iSEEtree_1.1.3.tar.gz(r-4.4-noble)
iSEEtree_1.1.3.tgz(r-4.4-emscripten)
iSEEtree.pdf |iSEEtree.html✨
iSEEtree/json (API)
NEWS
| # Install 'iSEEtree' in R: |
| install.packages('iSEEtree', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/microbiome/iseetree/issues
On BioConductor:iSEEtree-1.1.2(bioc 3.21)iSEEtree-1.0.0(bioc 3.20)
microbiomesoftwarevisualizationguishinyappsdataimportshiny-appsvisualisation
Last updated 11 hours agofrom:c2698eac54. Checks:1 OK, 6 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 11 2025 |
| R-4.5-win | NOTE | Mar 11 2025 |
| R-4.5-mac | NOTE | Mar 11 2025 |
| R-4.5-linux | NOTE | Mar 11 2025 |
| R-4.4-win | NOTE | Mar 11 2025 |
| R-4.4-mac | NOTE | Mar 11 2025 |
| R-4.4-linux | NOTE | Mar 11 2025 |
Exports:AbundanceDensityPlotAbundancePlotColumnGraphPlotColumnTreePlotiSEELoadingPlotRDAPlotRowGraphPlotRowTreePlotScreePlot
Dependencies:abindapeaplotaskpassassortheadbase64encbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsbitbit64blusterbslibcachemCairocellrangercirclizeclicliprclueclustercodetoolscolorspacecolourpickercommonmarkComplexHeatmapcpp11crayoncrosstalkcurlDBIDECIPHERdecontamDelayedArrayDelayedMatrixStatsdigestDirichletMultinomialdoParalleldplyrdqrngDTemmeansestimabilityevaluatefansifarverfastmapfillpatternFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggbeeswarmggforceggfunggnewscaleggplot2ggplotifyggraphggrastrggrepelggtextggtreeGlobalOptionsgluegraphlayoutsgridExtragridGraphicsgridtextgtablehighrhmshtmltoolshtmlwidgetshttpuvhttrigraphIRangesirlbaiSEEisobanditeratorsjaneaustenrjpegjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelistviewermagrittrmarkdownMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmiamiaVizmimeminiUIMultiAssayExperimentmunsellmvtnormnlmenumDerivopensslparallellypatchworkpermutepheatmappillarpkgconfigplyrpngpolyclipprettyunitsprogresspromisespurrrR6raggrappdirsrbiomRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressreadrreadxlrematchreshape2rintrojsrjsonrlangrmarkdownRSpectrarsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscuttleshapeshinyshinyAceshinydashboardshinyjsshinyWidgetsSingleCellExperimentsitmoslamsnowSnowballCsourcetoolsSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidygraphtidyrtidyselecttidytexttidytreetinytextokenizerstreeioTreeSummarizedExperimenttweenrtzdbUCSC.utilsutf8uwotvctrsveganviporviridisviridisLitevroomwithrxfunxml2xtableXVectoryamlyulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Abundance density plot | AbundanceDensityPlot AbundanceDensityPlot-class |
| Abundance plot | AbundancePlot AbundancePlot-class |
| Column graph plot | ColumnGraphPlot ColumnGraphPlot-class |
| Column tree plot | ColumnTreePlot ColumnTreePlot-class |
| Graph plot | GraphPlot GraphPlot-class |
| iSEE layout for TreeSE | iSEE iSEE,TreeSummarizedExperiment-method |
| Loading plot | LoadingPlot LoadingPlot-class |
| RDA plot | RDAPlot RDAPlot-class |
| Row graph plot | RowGraphPlot RowGraphPlot-class |
| Row tree plot | RowTreePlot RowTreePlot-class |
| Scree plot | ScreePlot ScreePlot-class |
| Tree plot | TreePlot TreePlot-class |
