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library('pasilla')
#> Loading required package: DEXSeq
#> Loading required package: BiocParallel
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#> Welcome to Bioconductor
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#> Loading required package: IRanges
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#> Loading required package: DESeq2
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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

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
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#> 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
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#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
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#> time zone: America/Chicago
#> tzcode source: internal
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#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
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#>  [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

example('renderReport', 'regionReport', ask=FALSE)