Hi,

I am trying to plot a volcano plot using custom colors and I'd like to use legend labels containing subscript e.g. log2.

When I use colCustom argument, legendLabels argument does not work and use of expression function in named vector is not supported.

1. Do you know if there is a way to replace the names of keyvals by legend labels in order to be able to use the expression function and add subscripts to legend text?
2. Is it possible to hide/remove the legend completely from the plot?

I used the following code to create custom colors and plot:

# create custom key-value pairs for 'high', 'low', 'mid' expression by fold-change
# this can be achieved with nested ifelse statements
keyvals <- ifelse(res$pvalue <= 0.05, 
                  ifelse(res$log2FoldChange < -1, 
                         'dodgerblue',
                         ifelse(res$log2FoldChange > 1, 
                                'firebrick3',
                                'grey')),
                  ifelse(res$log2FoldChange < -1, 
                         'black',
                         ifelse(res$log2FoldChange > 1, 
                                'black',
                                'black'))
)

keyvals[is.na(keyvals)] <- 'grey'
names(keyvals)[keyvals == 'dodgerblue'] <- "p-value and log2 FC Down"
names(keyvals)[keyvals == 'grey'] <- 'p-value'
names(keyvals)[keyvals == 'firebrick3'] <- "p-value and log2 FC Up"
names(keyvals)[keyvals == 'black'] <- "NS" #'low & non sign'
names(keyvals)[keyvals == 'black'] <- "NS" #'mid & non sign'
names(keyvals)[keyvals == 'black'] <- "NS" #'high & non sign'

x = EnhancedVolcano(res,
                    lab = res$Genes,
                    x = 'log2FoldChange',
                    y = 'pvalue',
                    selectLab = genes_to_draw,
                    FCcutoff = 1, 
                    pCutoff = 0.05,
                    colCustom = keyvals,
                    # col = c("yellow", "green", "grey", "firebrick3"), # non-sign/nonFC, non-sign/FC, sign/nonFC, sign/FC
                    drawConnectors = TRUE,
                    arrowheads = FALSE,
                    widthConnectors = 1, 
                    lengthConnectors =  unit(1, "cm"),
                    boxedLabels = TRUE,
                    # legend = c("NS", "p-value", "p-value and log2 FC Down", "p-value and log2 FC Up"),
                    # legendLabels = c('NS', 'p-value', expression(p-value~and~Log[2]~FC), expression(p-value~and~Log[2]~FC)),
                    legendLabSize = 15,
                    title = NULL, subtitle = NULL, caption = NULL)
print(x)

sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=Greek_Greece.1253  LC_CTYPE=Greek_Greece.1253    LC_MONETARY=Greek_Greece.1253 LC_NUMERIC=C                  LC_TIME=Greek_Greece.1253    
system code page: 1252

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

other attached packages:
[1] EnhancedVolcano_1.12.0 ggrepel_0.9.1          ggplot2_3.3.6         

loaded via a namespace (and not attached):
  [1] ggbeeswarm_0.6.0      colorspace_2.0-3      rjson_0.2.21          deldir_1.0-6          ellipsis_0.3.2        circlize_0.4.15       htmlTable_2.4.1      
  [8] GlobalOptions_0.1.2   base64enc_0.1-3       fs_1.5.2              clue_0.3-61           rstudioapi_0.14       farver_2.1.1          remotes_2.4.2        
 [15] fansi_1.0.3           codetools_0.2-18      splines_4.1.2         extrafont_0.18        doParallel_1.0.17     cachem_1.0.6          knitr_1.40           
 [22] pkgload_1.3.0         Formula_1.2-4         Rttf2pt1_1.3.11       cluster_2.1.2         png_0.1-7             shiny_1.7.2           compiler_4.1.2       
 [29] backports_1.4.1       assertthat_0.2.1      Matrix_1.5-1          fastmap_1.1.0         cli_3.4.1             later_1.3.0           htmltools_0.5.3      
 [36] prettyunits_1.1.1     tools_4.1.2           gtable_0.3.1          glue_1.6.2            dplyr_1.0.10          maps_3.4.0            Rcpp_1.0.9           
 [43] cellranger_1.1.0      vctrs_0.4.2           ggalt_0.4.0           extrafontdb_1.0       iterators_1.0.14      xfun_0.33             stringr_1.4.1        
 [50] ps_1.7.1              openxlsx_4.2.5        mime_0.12             miniUI_0.1.1.1        lifecycle_1.0.3       devtools_2.4.5        MASS_7.3-54          
 [57] scales_1.2.1          promises_1.2.0.1      parallel_4.1.2        proj4_1.0-11          RColorBrewer_1.1-3    ComplexHeatmap_2.13.1 memoise_2.0.1        
 [64] gridExtra_2.3         ggrastr_1.0.1         rpart_4.1-15          latticeExtra_0.6-30   stringi_1.7.8         S4Vectors_0.32.4      corrplot_0.92        
 [71] foreach_1.5.2         checkmate_2.1.0       BiocGenerics_0.40.0   pkgbuild_1.3.1        zip_2.2.1             shape_1.4.6           rlang_1.0.6          
 [78] pkgconfig_2.0.3       matrixStats_0.62.0    lattice_0.20-45       purrr_0.3.5           labeling_0.4.2        htmlwidgets_1.5.4     processx_3.7.0       
 [85] tidyselect_1.2.0      magrittr_2.0.3        R6_2.5.1              IRanges_2.28.0        generics_0.1.3        Hmisc_4.7-1           profvis_0.3.7        
 [92] DBI_1.1.3             pillar_1.8.1          foreign_0.8-81        withr_2.5.0           survival_3.2-13       nnet_7.3-16           ash_1.0-15           
 [99] tibble_3.1.8          crayon_1.5.2          interp_1.1-3          KernSmooth_2.23-20    utf8_1.2.2            urlchecker_1.0.1      jpeg_0.1-9           
[106] GetoptLong_1.0.5      usethis_2.1.6         grid_4.1.2            readxl_1.4.1          data.table_1.14.4     callr_3.7.2           digest_0.6.29        
[113] xtable_1.8-4          httpuv_1.6.6          stats4_4.1.2          munsell_0.5.0         beeswarm_0.4.0        vipor_0.4.5           sessioninfo_1.2.2

Hey,

That looks like a nice volcano plot.

Firstly, to hide the legend, just use legendPosition = 'none'.

Regarding the other issue, I have tried to be as methodical / comprehensive as possible to cater for every eventuality down which a user may go, and I believe an obscure parameter may help you here: parseLabels. By default, parseLabels = FALSE, but you need to set it to TRUE and then try to pass the new labels as, I believe:

keyvals[is.na(keyvals)] <- 'grey'
names(keyvals)[keyvals == 'dodgerblue'] <- "expression(p-value~and~Log[2]~FC~Down)"
names(keyvals)[keyvals == 'grey'] <- 'p-value'
names(keyvals)[keyvals == 'firebrick3'] <- "expression(p-value~and~Log[2]~FC~Up)"
names(keyvals)[keyvals == 'black'] <- "NS"

, or use:

keyvals[is.na(keyvals)] <- 'grey'
names(keyvals)[keyvals == 'dodgerblue'] <- "p-value and Log[2] FC Down"
names(keyvals)[keyvals == 'grey'] <- 'p-value'
names(keyvals)[keyvals == 'firebrick3'] <- "p-value and Log[2] FC Up"
names(keyvals)[keyvals == 'black'] <- "NS"

   EnhancedVolcano(
     ...
     legend = c("NS", "p-value", "p-value and log2 FC Down", "p-value and log2 FC Up"),
     legendLabels = c('NS', 'p-value', expression(p-value~and~Log[2]~FC~Down), expression(p-value~and~Log[2]~FC~Up)),
     ...)

Kind regards,

Kevin