library(scuttle)
+#> Loading required package: SingleCellExperiment
+#> Loading required package: SummarizedExperiment
+#> Loading required package: MatrixGenerics
+#> Loading required package: matrixStats
+#>
+#> Attaching package: ‘MatrixGenerics’
+#> The following objects are masked from ‘package:matrixStats’:
+#>
+#> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
+#> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
+#> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
+#> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
+#> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
+#> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
+#> colWeightedMeans, colWeightedMedians, colWeightedSds,
+#> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
+#> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
+#> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
+#> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
+#> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
+#> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
+#> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
+#> rowWeightedSds, rowWeightedVars
+#> Loading required package: GenomicRanges
+#> Loading required package: stats4
+#> Loading required package: BiocGenerics
+#>
+#> Attaching package: ‘BiocGenerics’
+#> The following objects are masked from ‘package:stats’:
+#>
+#> IQR, mad, sd, var, xtabs
+#> The following objects are masked from ‘package:base’:
+#>
+#> Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
+#> as.data.frame, basename, cbind, colnames, dirname, do.call,
+#> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
+#> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
+#> pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
+#> union, unique, unsplit, which.max, which.min
+#> Loading required package: S4Vectors
+#>
+#> Attaching package: ‘S4Vectors’
+#> The following object is masked from ‘package:utils’:
+#>
+#> findMatches
+#> The following objects are masked from ‘package:base’:
+#>
+#> I, expand.grid, unname
+#> Loading required package: IRanges
+#> Loading required package: GenomeInfoDb
+#> Loading required package: Biobase
+#> Welcome to Bioconductor
+#>
+#> Vignettes contain introductory material; view with
+#> 'browseVignettes()'. To cite Bioconductor, see
+#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
+#>
+#> Attaching package: ‘Biobase’
+#> The following object is masked from ‘package:MatrixGenerics’:
+#>
+#> rowMedians
+#> The following objects are masked from ‘package:matrixStats’:
+#>
+#> anyMissing, rowMedians
+library(scater)
+#> Loading required package: ggplot2
+library(scran)
+library(ggplot2)
+sce <- mockSCE()
+sce <- logNormCounts(sce)
+clusters <- clusterCells(sce, assay.type = 'logcounts')
+colLabels(sce) <- clusters
+sce <- runUMAP(sce, assay.type = 'logcounts')
+#> Found more than one class "dist" in cache; using the first, from namespace 'spam'
+#> Also defined by ‘BiocGenerics’
+#> Found more than one class "dist" in cache; using the first, from namespace 'spam'
+#> Also defined by ‘BiocGenerics’
+#> Found more than one class "dist" in cache; using the first, from namespace 'spam'
+#> Also defined by ‘BiocGenerics’
+p <- sc_dim(sce, reduction = 'UMAP')
+p1 <- sc_dim_count(p)
+