Can someone assist me with making a DEXSeq plot from plotDEXSeq not in the logarithmic scale?

Thanks!

Code should be placed in three backticks as shown below

# include your problematic code here with any corresponding output 

```    dxd = estimateSizeFactors( dxd )
    dxd = estimateDispersions(dxd,BPPARAM=BPPARAM)
    dxd = testForDEU( dxd ,fullModel = design(dxd),reducedModel = ~exon)
    dxd = estimateExonFoldChanges( dxd, fitExpToVar="Genotype")
    dxr1 = DEXSeqResults( dxd )
    dxr1=dxr1[order(dxr1$featureID),]
    gene="X"
    name=annot[gene,7]
    plotDEXSeq( dxr1,  gene, legend=TRUE, cex.axis=1, cex=1, lwd=2 ,fitExpToVar="Genotype")

please also include the results of running the following in an R session

sessionInfo( )

```

R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 26100)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] WriteXLS_6.7.0              scales_1.3.0                DEXSeq_1.46.0               RColorBrewer_1.1-3          AnnotationDbi_1.62.2        BiocParallel_1.34.2        
 [7] DESeq2_1.40.2               SummarizedExperiment_1.30.2 Biobase_2.60.0              MatrixGenerics_1.12.3       matrixStats_1.5.0           ggtranscript_1.0.0         
[13] lubridate_1.9.4             forcats_1.0.0               stringr_1.5.1               dplyr_1.1.2                 purrr_1.0.4                 readr_2.1.5                
[19] tidyr_1.3.1                 tibble_3.2.1                tidyverse_2.0.0             ggplot2_3.5.1               rtracklayer_1.60.1          GenomicRanges_1.52.1       
[25] GenomeInfoDb_1.36.4         IRanges_2.34.1              S4Vectors_0.38.2            BiocGenerics_0.46.0        

loaded via a namespace (and not attached):
 [1] DBI_1.2.3                bitops_1.0-9             biomaRt_2.56.1           rlang_1.1.1              magrittr_2.0.3           compiler_4.3.0          
 [7] RSQLite_2.3.9            png_0.1-8                vctrs_0.6.5              pkgconfig_2.0.3          crayon_1.5.3             fastmap_1.2.0           
[13] dbplyr_2.5.0             XVector_0.40.0           labeling_0.4.3           Rsamtools_2.16.0         tzdb_0.4.0               bit_4.6.0               
[19] zlibbioc_1.46.0          cachem_1.1.0             progress_1.2.3           blob_1.2.4               DelayedArray_0.26.7      parallel_4.3.0          
[25] prettyunits_1.2.0        R6_2.6.1                 stringi_1.8.4            genefilter_1.82.1        pkgload_1.4.0            Rcpp_1.0.14             
[31] Matrix_1.6-5             splines_4.3.0            timechange_0.3.0         tidyselect_1.2.1         rstudioapi_0.17.1        abind_1.4-8             
[37] yaml_2.3.10              codetools_0.2-20         hwriter_1.3.2.1          curl_6.2.2               lattice_0.22-6           withr_3.0.2             
[43] KEGGREST_1.40.1          survival_3.8-3           BiocFileCache_2.8.0      xml2_1.3.8               Biostrings_2.68.1        pillar_1.10.2           
[49] filelock_1.0.3           generics_0.1.3           RCurl_1.98-1.17          hms_1.1.3                munsell_0.5.1            xtable_1.8-4            
[55] glue_1.6.2               tools_4.3.0              BiocIO_1.10.0            annotate_1.78.0          locfit_1.5-9.12          GenomicAlignments_1.36.0
[61] XML_3.99-0.18            grid_4.3.0               colorspace_2.1-0         GenomeInfoDbData_1.2.10  restfulr_0.0.15          cli_3.6.1               
[67] rappdirs_0.3.3           S4Arrays_1.0.6           gtable_0.3.6             digest_0.6.37            ggrepel_0.9.6            geneplotter_1.78.0      
[73] rjson_0.2.23             farver_2.1.2             memoise_2.0.1            lifecycle_1.0.4          httr_1.4.7               statmod_1.5.0           
[79] bit64_4.6.0-1           

It's hard coded, so you will not be able to change the vertical axis of the top plot without getting the code and modifying. You can simply use git clone to get the repo, make changes, and then build/check/install the local repo.