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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 packagedds<- DESeqDataSetFromMatrix(countData=countData,
colData=colData,
design=~condition)
# Perform the differential expression analysisdds<- 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 reportreport<- 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
The text was updated successfully, but these errors were encountered:
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 functionggplot2::is.theme()
be used instead ofis()
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 viaBiocManager::install()
using R (v4.3.1) installed via Homebrew.Minimally reproducible example
R session info
The text was updated successfully, but these errors were encountered: