I am using the great EnhancedVolcano package for creating Volcano plots and have 2 tiny questions:

1. Is it possible to put in a preselected set of labels for the argument selectLab? I have created a vector and all containing labels are in the lab argument, but it does not seem to work.
2. According to the vignette even when using selectLab only variables passing the cut offs are labeled. But in my case it lables all of them. What am I doing wrong?

Thank you very much for your help!

Checkpoints <- as.vector(list_genes$IMMUNE.CHECKPOINTS.)
Checkpoints
Checkpoints <- Checkpoints[-c(15:268)] 

EnhancedVolcano(res,
                lab = rownames(res),
                x = 'log2FoldChange',
                y = 'padj',
                selectLab = Checkpoints,
                xlab = bquote(~Log[2]~ 'fold change'),
                pCutoff = 0.05,
                pCutoffCol = 'padj',
                FCcutoff = 0.75,
                pointSize = 3.0,
                labSize = 4.0)

sessionInfo( )

R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.5.2

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8

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

other attached packages:
 [1] EnhancedVolcano_1.10.0      ggrepel_0.9.1              
 [3] pheatmap_1.0.12             ggpubr_0.4.0               
 [5] ggplot2_3.3.5               RColorBrewer_1.1-2         
 [7] DESeq2_1.32.0               SummarizedExperiment_1.22.0
 [9] Biobase_2.52.0              MatrixGenerics_1.4.3       
[11] matrixStats_0.60.1          GenomicRanges_1.44.0       
[13] GenomeInfoDb_1.28.4         IRanges_2.26.0             
[15] S4Vectors_0.30.0            BiocGenerics_0.38.0        

loaded via a namespace (and not attached):
 [1] bitops_1.0-7           bit64_4.0.5            ash_1.0-15            
 [4] httr_1.4.2             tools_4.1.1            backports_1.2.1       
 [7] utf8_1.2.2             R6_2.5.1               vipor_0.4.5           
[10] KernSmooth_2.23-20     DBI_1.1.1              colorspace_2.0-2      
[13] withr_2.4.2            ggrastr_0.2.3          tidyselect_1.1.1      
[16] ggalt_0.4.0            extrafontdb_1.0        bit_4.0.4             
[19] curl_4.3.2             compiler_4.1.1         DelayedArray_0.18.0   
[22] labeling_0.4.2         scales_1.1.1           proj4_1.0-10.1        
[25] genefilter_1.74.0      digest_0.6.27          foreign_0.8-81        
[28] rio_0.5.27             XVector_0.32.0         pkgconfig_2.0.3       
[31] extrafont_0.17         maps_3.3.0             fastmap_1.1.0         
[34] rlang_0.4.11           readxl_1.3.1           rstudioapi_0.13       
[37] RSQLite_2.2.8          generics_0.1.0         farver_2.1.0          
[40] BiocParallel_1.26.2    dplyr_1.0.7            zip_2.2.0             
[43] car_3.0-11             RCurl_1.98-1.4         magrittr_2.0.1        
[46] GenomeInfoDbData_1.2.6 Matrix_1.3-4           ggbeeswarm_0.6.0      
[49] Rcpp_1.0.7             munsell_0.5.0          fansi_0.5.0           
[52] abind_1.4-5            lifecycle_1.0.0        stringi_1.7.4         
[55] carData_3.0-4          MASS_7.3-54            zlibbioc_1.38.0       
[58] grid_4.1.1             blob_1.2.2             forcats_0.5.1         
[61] crayon_1.4.1           lattice_0.20-44        Biostrings_2.60.2     
[64] haven_2.4.3            splines_4.1.1          annotate_1.70.0       
[67] hms_1.1.0              KEGGREST_1.32.0        locfit_1.5-9.4        
[70] pillar_1.6.2           ggsignif_0.6.2         geneplotter_1.70.0    
[73] XML_3.99-0.7           glue_1.4.2             data.table_1.14.0     
[76] BiocManager_1.30.16    png_0.1-7              vctrs_0.3.8           
[79] Rttf2pt1_1.3.9         cellranger_1.1.0       gtable_0.3.0          
[82] purrr_0.3.4            tidyr_1.1.3            assertthat_0.2.1      
[85] cachem_1.0.6           openxlsx_4.2.4         xtable_1.8-4          
[88] broom_0.7.9            rstatix_0.7.0          survival_3.2-13       
[91] tibble_3.1.4           beeswarm_0.4.0         AnnotationDbi_1.54.1  
[94] memoise_2.0.0          ellipsis_0.3.2

Hi Johannes,

Is it possible to put in a preselected set of labels for the argument selectLab? I have created a vector and all containing labels are in the lab argument, but it does not seem to work.

Can you help me to better understand this problem? - how do you define "it does not seem to work"? You can show examples from rownames(res) and Checkpoints, and, also, please show the output of str(res) and str(Checkpoints).

According to the vignette even when using selectLab only variables passing the cut offs are labeled. But in my case it lables all of them. What am I doing wrong?

The default is to label everything, irrespective of statistical significance. I can see the conflicting line in the vignette that would make one think otherwise - I will modify this. Thank you

Kevin