Column names not showing up in plotGroupedHeatmap()

[ycl6]

Hi,

Testing the latest scater from bioconductor in R-4.3.1 and found the column names have disappeared when using plotGroupedHeatmap(). I've also tried passing show_colnames = T (which is the default setting in pheatmap) but it has no effect either.

• R version 4.3.1
• scater_1.28.0
• pheatmap_1.0.12

    library(scater)
    #> 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':
    #> 
    #>     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    #>     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    #>     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    #>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    #>     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
    #>     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':
    #> 
    #>     expand.grid, I, 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
    #> Loading required package: scuttle
    #> Loading required package: ggplot2
    example_sce <- mockSCE()
    example_sce <- logNormCounts(example_sce)
    example_sce$Group <- paste0(example_sce$Treatment, "+", example_sce$Mutation_Status)

    plotGroupedHeatmap(example_sce, features=rownames(example_sce)[1:10], group="Group")

^{Created on 2023-07-19 with reprex v2.0.2}

[shimin-chen]

I have the same question. Does anyone have a solution to this?

[alanocallaghan]

Sorry I must've missed this while on hols. There's no setting that'll fix it because summarizeAssayByGroup is returning an object with no colnames. Will get this fixed ASAP

[shimin-chen]

Thank you!