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Added LoadingPlot and ColumnTreePlot panels #37

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Merged
merged 2 commits into from
Oct 16, 2024
Merged

Added LoadingPlot and ColumnTreePlot panels #37

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37a74a7
Added LoadingPlot and ColumnTreePlot panels
RiboRings Oct 16, 2024
bcf80b0
Add new panels to vignettes
RiboRings Oct 16, 2024
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
Package: iSEEtree
Version: 0.99.7
Version: 0.99.8
Authors@R:
c(person(given = "Giulio", family = "Benedetti", role = c("aut", "cre"),
email = "giulio.benedetti@utu.fi",
Expand All @@ -17,7 +17,7 @@ Description:
visualisation to create panels that are specific for
TreeSummarizedExperiment objects. Not surprisingly, it also depends on the
generic panels from iSEE.
biocViews: Microbiome, Software, Visualization, GUI, ShinyApps
biocViews: Microbiome, Software, Visualization, GUI, ShinyApps, DataImport
License: Artistic-2.0
Encoding: UTF-8
Depends:
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7 changes: 7 additions & 0 deletions NAMESPACE
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Expand Up @@ -2,16 +2,21 @@

export(AbundanceDensityPlot)
export(AbundancePlot)
export(ColumnTreePlot)
export(LoadingPlot)
export(RDAPlot)
export(RowTreePlot)
export(iSEE)
exportClasses(AbundanceDensityPlot)
exportClasses(AbundancePlot)
exportClasses(ColumnTreePlot)
exportClasses(LoadingPlot)
exportClasses(RDAPlot)
exportClasses(RowTreePlot)
exportMethods(iSEE)
importFrom(S4Vectors,isEmpty)
importFrom(S4Vectors,setValidity2)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SummarizedExperiment,assayNames)
Expand Down Expand Up @@ -57,6 +62,8 @@ importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(mia,taxonomyRanks)
importFrom(miaViz,plotColTree)
importFrom(miaViz,plotLoadings)
importFrom(miaViz,plotRowTree)
importFrom(shiny,plotOutput)
importFrom(shiny,renderPlot)
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3 changes: 3 additions & 0 deletions NEWS
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Expand Up @@ -14,3 +14,6 @@ Changes in version 0.99.2

Changes in version 0.99.3
* Added .exportOutput method

Changes in version 0.99.8
* Added ColumnTreePlot and LoadingPlot panels
Binary file added R/LoadingPlotNA.pdf
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2 changes: 1 addition & 1 deletion R/class-AbundanceDensityPlot.R
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Expand Up @@ -6,7 +6,7 @@
#' to generate the plot.
#'
#' @section Slot overview:
#' The following slots control the thresholds used in the visualization:
#' The following slots control the thresholds used in the visualisation:
#' \itemize{
#' \item \code{layout}, a string specifying abundance layout (jitter, density or points).
#' \item \code{assay.type}, a string specifying the assay to visualize.
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