diff --git a/DESCRIPTION b/DESCRIPTION index 4ed9077..81a68f3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -73,6 +73,6 @@ BugReports: https://github.com/iSEE/iSEEu/issues biocViews: ImmunoOncology, Visualization, GUI, DimensionReduction, FeatureExtraction, Clustering, Transcription, GeneExpression, Transcriptomics, SingleCell, CellBasedAssays -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Roxygen: list(markdown = TRUE) VignetteBuilder: knitr diff --git a/NAMESPACE b/NAMESPACE index 730c304..c50606c 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -84,6 +84,7 @@ exportMethods(.multiSelectionClear) exportMethods(.multiSelectionCommands) exportMethods(.multiSelectionDimension) exportMethods(.multiSelectionInvalidated) +exportMethods(.multiSelectionResponsive) exportMethods(.panelColor) exportMethods(.prioritizeDotPlotData) exportMethods(.refineParameters) diff --git a/man/AggregatedDotPlot.Rd b/man/AggregatedDotPlot.Rd index dba0903..93527ac 100644 --- a/man/AggregatedDotPlot.Rd +++ b/man/AggregatedDotPlot.Rd @@ -18,6 +18,7 @@ \alias{.definePanelTour,AggregatedDotPlot-method} \alias{.createObservers,AggregatedDotPlot-method} \alias{.refineParameters,AggregatedDotPlot-method} +\alias{.multiSelectResponsive,AggregateDotPlot-method} \alias{initialize,AggregatedDotPlot-method} \title{The AggregatedDotPlot class} \description{ @@ -37,6 +38,12 @@ Defaults to \code{TRUE}. typically corresponding to the row names of the \linkS4class{SummarizedExperiment}. Names should be new-line separated within this string. Defaults to the name of the first row in the SummarizedExperiment. +\item \code{CapMaxRows}, a logical scalar indicating whether to cap the number of features to be shown on the plot. +This ensures that the \pkg{iSEE} application does not freeze when asked to cluster a very large selection of rows. +Defaults to \code{TRUE}, in which case a notification will be raised if the cap needs to be enforced. +\item \code{MaxRows}, an integer specifying the cap on the number of features to be shown on the plot. +Only used if \code{CapMaxRows} is set to \code{TRUE}. +Defaults to 50. } The following slots control the specification of groups: @@ -74,6 +81,19 @@ Defaults to \code{FALSE}. Defaults to \code{FALSE}. } +The following slots control the clustering of rows: +\itemize{ +\item \code{ClusterRows}, a logical scalar indicating whether clustering of the rows should be performed, +so as to group genes that have more similar average expression profiles across groups. +Defaults to \code{FALSE}. +\item \code{ClusterRowsDistance}, string specifying the distance metric to use. +This can be any one of \code{"euclidean"}, \code{"maximum"}, \code{"manhattan"}, \code{"canberra"}, \code{"binary"}, \code{"minkowski"}, \code{"pearson"}, \code{"spearman"}, or \code{"kendall"}. +Defaults to \code{"euclidean"}. +\item \code{ClusterRowsMethod}, string specifying a linkage method to use. +This can be any one of \code{"ward.D"}, \code{"ward.D2"}, \code{"single"}, \code{"complete"}, \code{"average"}, \code{"mcquitty"}, \code{"median"}, or \code{"centroid"}. +Defaults to \code{"ward.D2"}. +} + The following slots control the color: \itemize{ \item \code{UseCustomColormap}, a logical scalar indicating whether to use a custom color scale.