Hello,

For some reason my previously working code to set the y and x limits for Enhanced Volcano are no longer working. The vignette was updated 8/19/2021, but it looks like the syntax for adjusting the y and x limits was not changed. Can someone please help me figure out what I am doing wrong? Also, apologies in advance if I forgot something or didn't post this correctly; it is my first post here. Thank you!

Thank you!

> EnhancedVolcano(res.pt.celline, 
+                 lab = rownames(res.pt.celline), 
+                 x="log2FoldChange", 
+                 y="padj", 
+                 FCcutoff = 1.0, 
+                 pCutoff =0.1,
+                 pointSize = 1.5, 
+                 labSize = 3.0, 
+                 ylim = c(0,6), 
+                 xlim = c(-3,3),
+                 colAlpha=1)
Warning message:
Ignoring unknown parameters: xlim, ylim

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows >= 8 (build 9200)

Matrix products: default


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

other attached packages:
 [1] RColorBrewer_1.1-2          EnhancedVolcano_1.10.0      ggrepel_0.9.1               pca3d_0.10.2               
 [5] apeglm_1.14.0               vsn_3.60.0                  limma_3.48.3                DESeq2_1.32.0              
 [9] SummarizedExperiment_1.22.0 Biobase_2.52.0              MatrixGenerics_1.4.2        matrixStats_0.60.0         
[13] GenomicRanges_1.44.0        GenomeInfoDb_1.28.1         IRanges_2.26.0              S4Vectors_0.30.0           
[17] BiocGenerics_0.38.0         devtools_2.4.2              usethis_2.0.1               ggplot2_3.3.5              
[21] BiocManager_1.30.16         rlang_0.4.11               

loaded via a namespace (and not attached):
  [1] ggbeeswarm_0.6.0       colorspace_2.0-2       ellipsis_0.3.2         rprojroot_2.0.2        XVector_0.32.0        
  [6] fs_1.5.0               rstudioapi_0.13        farver_2.1.0           remotes_2.4.0          affyio_1.62.0         
 [11] bit64_4.0.5            AnnotationDbi_1.54.1   fansi_0.5.0            mvtnorm_1.1-2          splines_4.1.0         
 [16] extrafont_0.17         cachem_1.0.5           geneplotter_1.70.0     knitr_1.33             pkgload_1.2.1         
 [21] jsonlite_1.7.2         Rttf2pt1_1.3.9         annotate_1.70.0        png_0.1-7              compiler_4.1.0        
 [26] httr_1.4.2             Matrix_1.3-3           fastmap_1.1.0          cli_3.0.1              htmltools_0.5.1.1     
 [31] prettyunits_1.1.1      tools_4.1.0            coda_0.19-4            gtable_0.3.0           glue_1.4.2            
 [36] GenomeInfoDbData_1.2.6 affy_1.70.0            dplyr_1.0.7            maps_3.3.0             Rcpp_1.0.7            
 [41] bbmle_1.0.24           vctrs_0.3.8            Biostrings_2.60.2      ggalt_0.4.0            preprocessCore_1.54.0 
 [46] extrafontdb_1.0        crosstalk_1.1.1        xfun_0.25              ps_1.6.0               testthat_3.0.4        
 [51] lifecycle_1.0.0        XML_3.99-0.7           zlibbioc_1.38.0        MASS_7.3-54            scales_1.1.1          
 [56] proj4_1.0-10.1         memoise_2.0.0          ggrastr_0.2.3          emdbook_1.3.12         bdsmatrix_1.3-4       
 [61] RSQLite_2.2.7          genefilter_1.74.0      desc_1.3.0             pkgbuild_1.2.0         BiocParallel_1.26.1   
 [66] pkgconfig_2.0.3        bitops_1.0-7           rgl_0.107.10           lattice_0.20-44        purrr_0.3.4           
 [71] labeling_0.4.2         htmlwidgets_1.5.3      bit_4.0.4              processx_3.5.2         tidyselect_1.1.1      
 [76] plyr_1.8.6             magrittr_2.0.1         R6_2.5.1               generics_0.1.0         DelayedArray_0.18.0   
 [81] DBI_1.1.1              pillar_1.6.2           withr_2.4.2            survival_3.2-11        KEGGREST_1.32.0       
 [86] RCurl_1.98-1.4         ash_1.0-15             tibble_3.1.3           crayon_1.4.1           KernSmooth_2.23-20    
 [91] utf8_1.2.2             ellipse_0.4.2          locfit_1.5-9.4         grid_4.1.0             blob_1.2.2            
 [96] callr_3.7.0            digest_0.6.27          xtable_1.8-4           numDeriv_2016.8-1.1    munsell_0.5.0         
[101] beeswarm_0.4.0         vipor_0.4.5            sessioninfo_1.1.1     
>  

sessionInfo( )

Hi Rachel,

I am the EnhancedVolcano main developer. There have been some 'significant' changes in one of the packages used by EnhancedVolcano, which has greatly affected the usability of it [affected the usability of EnhancedVolcano] - I have had to implement various code changes.

For now, could you try to install the development version from GitHub and test that?

remotes::install_github('kevinblighe/EnhancedVolcano')

or:

devtools::install_github('kevinblighe/EnhancedVolcano')

This GitHub version is definitely working:

It will be released in the next Bioconductor cycle, which is early next month (I think).

Kevin