Merge pull request #37 from microbiome/coltree&loadings

Added LoadingPlot and ColumnTreePlot panels
microbiome · Oct 16, 2024 · e1ecd98 · e1ecd98
2 parents 6914429 + bcf80b0
commit e1ecd98
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -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 = "[email protected]",
@@ -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:

diff --git a/NAMESPACE b/NAMESPACE
@@ -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)
@@ -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)

diff --git a/NEWS b/NEWS
@@ -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
diff --git a/R/LoadingPlotNA.pdf b/R/LoadingPlotNA.pdf
diff --git a/R/class-AbundanceDensityPlot.R b/R/class-AbundanceDensityPlot.R
@@ -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.