Hi there,

I am trying to make volcano plot using EnhancedVolcano to mark the gene label (using selectLab function) in different colours, but fail to do so. I have also looked into the suggestion in https://github.com/kevinblighe/EnhancedVolcano#highlighting-key-variables-via-custom-point-sizes, but with no luck.

I found out some functionality (e.g labCol, subtitle, caption, shape, pointSize, boxedlabels, drawConnectors, widthConnectors) in my session did not work, and return the below:

Error in EnhancedVolcano(res.annotA, lab = gene_nameAV, x = "log2FoldChange",  : 
  unused argument (labCol = "blue"), etc

Not sure if it is a version (1.0.1) problem... How could I upgrade the version? as the BiocManager::install('EnhancedVolcano') only install this older version for my R Packrat.

========================================================

Though I can still plot the basic function with the following functionalities:

EnhancedVolcano(res.annotA,
    lab = gene_nameA,
    x = 'log2FoldChange',
    y = 'padj',
    selectLab = gene_nameA_selected,   
    xlim = c(-3, 11),
    ylim = c(-1, 35),
    xlab = bquote(~Log[2]~ 'fold change'),
    ylab = bquote(~-Log[10]~adjusted~italic(P)),
    title = 'XXX',
    pCutoff = 0.05,
    FCcutoff = 1.0,
    transcriptPointSize = 1.5,
    transcriptLabSize = 4.0,
    col=c('black', 'orange', 'red3', 'green'),
    colAlpha = 1,
    cutoffLineType = 'dotted',
    cutoffLineCol = 'grey50',
    cutoffLineWidth = 0.8,
    legend=c("Not significant","Log|Fold Change|>1","adj-p<0.05","adj-p<0.05 & Log|Fold Change|>1"),
    legendPosition = 'bottom',
    legendLabSize = 13,
    legendIconSize = 2.0,
    colConnectors = 'grey30'
    )

Any idea on how to highlight certain gene label/point (in different shape/colour) would be very much appreciated :)

====================

Here is my sessionInfo()

R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] dplyr_0.8.3           EnhancedVolcano_1.0.1 ggrepel_0.8.1        
 [4] ggplot2_3.2.1         biomaRt_2.38.0        GenomicRanges_1.34.0 
 [7] GenomeInfoDb_1.18.2   IRanges_2.16.0        S4Vectors_0.20.1     
[10] BiocGenerics_0.28.0  

loaded via a namespace (and not attached):
 [1] httr_1.4.1                  Biobase_2.42.0             
 [3] bit64_0.9-7                 splines_3.5.2              
 [5] Formula_1.2-3               assertthat_0.2.1           
 [7] BiocManager_1.30.4          latticeExtra_0.6-28        
 [9] blob_1.2.0                  GenomeInfoDbData_1.2.0     
[11] yaml_2.2.0                  progress_1.2.2             
[13] pillar_1.4.2                RSQLite_2.1.2              
[15] backports_1.1.4             lattice_0.20-38            
[17] glue_1.3.1                  digest_0.6.20              
[19] RColorBrewer_1.1-2          XVector_0.22.0             
[21] checkmate_1.9.4             colorspace_1.4-1           
[23] htmltools_0.3.6             Matrix_1.2-17              
[25] DESeq2_1.22.2               XML_3.98-1.20              
[27] pkgconfig_2.0.2             genefilter_1.64.0          
[29] zlibbioc_1.28.0             purrr_0.3.2                
[31] xtable_1.8-4                scales_1.0.0               
[33] BiocParallel_1.16.6         htmlTable_1.13.1           
[35] tibble_2.1.3                annotate_1.60.1            
[37] withr_2.1.2                 SummarizedExperiment_1.12.0
[39] nnet_7.3-12                 lazyeval_0.2.2             
[41] survival_2.43-3             magrittr_1.5               
[43] crayon_1.3.4                evaluate_0.14              
[45] memoise_1.1.0               foreign_0.8-71             
[47] prettyunits_1.0.2           tools_3.5.2                
[49] data.table_1.12.2           hms_0.5.1                  
[51] matrixStats_0.54.0          stringr_1.4.0              
[53] locfit_1.5-9.1              munsell_0.5.0              
[55] cluster_2.0.7-1             DelayedArray_0.8.0         
[57] AnnotationDbi_1.44.0        packrat_0.5.0              
[59] compiler_3.5.2              rlang_0.4.0                
[61] grid_3.5.2                  RCurl_1.95-4.12            
[63] rstudioapi_0.10             htmlwidgets_1.3            
[65] rmarkdown_1.15              bitops_1.0-6               
[67] base64enc_0.1-3             gtable_0.3.0               
[69] DBI_1.0.0                   R6_2.4.0                   
[71] gridExtra_2.3               knitr_1.24                 
[73] bit_1.1-14                  zeallot_0.1.0              
[75] Hmisc_4.2-0                 stringi_1.4.3              
[77] Rcpp_1.0.2                  vctrs_0.2.0                
[79] geneplotter_1.60.0          rpart_4.1-13               
[81] acepack_1.4.1               tidyselect_0.2.5           
[83] xfun_0.9