diff --git a/DESCRIPTION b/DESCRIPTION index c8134bb..3b673f2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -66,6 +66,6 @@ biocViews: ImmunoOncology, SingleCell, RNASeq, QualityControl, Preprocessing, No GeneExpression, Sequencing, Software, DataImport, DataRepresentation, Infrastructure, Coverage Encoding: UTF-8 -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 URL: http://bioconductor.org/packages/scater/ BugReports: https://support.bioconductor.org/ diff --git a/NAMESPACE b/NAMESPACE index 7bc9a3e..7d0186c 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -212,9 +212,35 @@ importFrom(ggrepel,geom_text_repel) importFrom(methods,as) importFrom(rlang,as_label) importFrom(scuttle,.bpNotSharedOrUp) +importFrom(scuttle,addPerCellQC) +importFrom(scuttle,addPerFeatureQC) +importFrom(scuttle,aggregateAcrossCells) +importFrom(scuttle,aggregateAcrossFeatures) +importFrom(scuttle,calculateAverage) +importFrom(scuttle,calculateCPM) +importFrom(scuttle,calculateFPKM) +importFrom(scuttle,calculateTPM) +importFrom(scuttle,computeLibraryFactors) +importFrom(scuttle,computeMedianFactors) importFrom(scuttle,fitLinearModel) +importFrom(scuttle,isOutlier) +importFrom(scuttle,librarySizeFactors) +importFrom(scuttle,logNormCounts) +importFrom(scuttle,makePerCellDF) +importFrom(scuttle,makePerFeatureDF) +importFrom(scuttle,medianSizeFactors) +importFrom(scuttle,mockSCE) +importFrom(scuttle,normalizeCounts) +importFrom(scuttle,numDetectedAcrossCells) +importFrom(scuttle,numDetectedAcrossFeatures) importFrom(scuttle,perCellQCMetrics) +importFrom(scuttle,perFeatureQCMetrics) +importFrom(scuttle,quickPerCellQC) +importFrom(scuttle,readSparseCounts) +importFrom(scuttle,sumCountsAcrossCells) +importFrom(scuttle,sumCountsAcrossFeatures) importFrom(scuttle,summarizeAssayByGroup) +importFrom(scuttle,uniquifyFeatureNames) importFrom(stats,cmdscale) importFrom(stats,dist) importFrom(stats,median) diff --git a/man/plot_reddim.Rd b/man/plot_reddim.Rd index 77b9ccb..0807319 100644 --- a/man/plot_reddim.Rd +++ b/man/plot_reddim.Rd @@ -12,19 +12,19 @@ \alias{plotPCA} \title{Plot specific reduced dimensions} \usage{ -plotPCASCE(object, ..., ncomponents = 2) +plotPCASCE(object, ..., ncomponents = 2, dimred = "PCA") -plotTSNE(object, ..., ncomponents = 2) +plotTSNE(object, ..., ncomponents = 2, dimred = "TSNE") -plotUMAP(object, ..., ncomponents = 2) +plotUMAP(object, ..., ncomponents = 2, dimred = "UMAP") -plotDiffusionMap(object, ..., ncomponents = 2) +plotDiffusionMap(object, ..., ncomponents = 2, dimred = "DiffusionMap") -plotMDS(object, ..., ncomponents = 2) +plotMDS(object, ..., ncomponents = 2, dimred = "MDS") -plotNMF(object, ..., ncomponents = 2) +plotNMF(object, ..., ncomponents = 2, dimred = "NMF") -\S4method{plotPCA}{SingleCellExperiment}(object, ..., ncomponents = 2) +\S4method{plotPCA}{SingleCellExperiment}(object, ..., ncomponents = 2, dimred = "PCA") } \arguments{ \item{object}{A SingleCellExperiment object.}