[BUG] Error when generating a DESeq2 HTML report passing a ggplot2 theme

[hspitia]

Hello,

First, thanks a lot for this wonderful package!
I am getting an error when generating an HTML report passing a ggplot2 theme to the DESeq2Report function. The source code (regionReport/R/DESeq2Report.R) shows that the error is due to the verification in line 175. Should the function ggplot2::is.theme() be used instead of is() in this line?

I'll appreciate you taking a look into this issue.

Best,
Hector

Detailed info

All the Bioconductor packages (including regionReport) were installed via BiocManager::install() using R (v4.3.1) installed via Homebrew.

Minimally reproducible example

library('pasilla')
#> Loading required package: DEXSeq
#> Loading required package: BiocParallel
#> Loading required package: Biobase
#> 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
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#> 
#> Attaching package: 'matrixStats'
#> The following objects are masked from 'package:Biobase':
#> 
#>     anyMissing, rowMedians
#> 
#> 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
#> The following object is masked from 'package:Biobase':
#> 
#>     rowMedians
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> 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: DESeq2
#> Loading required package: AnnotationDbi
#> Loading required package: RColorBrewer
library('DESeq2')
library('ggplot2')
library('regionReport')

data("pasillaDEXSeqDataSet")

countData <- counts(dxd)
colData <- colData(dxd)[, c('condition', 'type')]

# Create DESeqDataSet object from the pasilla package
dds <- DESeqDataSetFromMatrix(countData = countData,
                              colData = colData,
                              design = ~ condition)

# Perform the differential expression analysis
dds <- DESeq(dds)
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
#> -- replacing outliers and refitting for 1 genes
#> -- DESeq argument 'minReplicatesForReplace' = 7 
#> -- original counts are preserved in counts(dds)
#> estimating dispersions
#> fitting model and testing
dir.create('DESeq2-example', showWarnings = FALSE, recursive = TRUE)

# Create the HTML report
report <- DESeq2Report(dds, project = 'DESeq2 HTML report',
                       intgroup = c('condition', 'type'), outdir = 'DESeq2-example',
                       output = 'index', theme = theme_bw())
#> Error in is(theme, c("theme", "gg")): length(class2) == 1L is not TRUE

R session info

sessionInfo()
#> R version 4.3.1 (2023-06-16)
#> Platform: x86_64-apple-darwin22.4.0 (64-bit)
#> Running under: macOS Ventura 13.4.1
#> 
#> Matrix products: default
#> BLAS:   /usr/local/Cellar/openblas/0.3.23/lib/libopenblasp-r0.3.23.dylib 
#> LAPACK: /usr/local/Cellar/r/4.3.1/lib/R/lib/libRlapack.dylib;  LAPACK version 3.11.0
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> time zone: America/Chicago
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.33     fastmap_1.1.1     xfun_0.39         glue_1.6.2       
#>  [5] knitr_1.43        htmltools_0.5.5   rmarkdown_2.23    lifecycle_1.0.3  
#>  [9] cli_3.6.1         reprex_2.0.2      withr_2.5.0       compiler_4.3.1   
#> [13] rstudioapi_0.15.0 tools_4.3.1       evaluate_0.21     yaml_2.3.7       
#> [17] rlang_1.1.1       fs_1.6.2

[hasanbmirza]

Same error for me, I have tried clearing the loaded libraries but same error. Hopefully someone will answer soon.