Hi,

I generated this beautiful plot using EnhancedVolcano. However, I would like the labels to be on the sides of the graph with arrows pointing to the DEG. I know I can use ggrepel with EnhancedVolcano but I am having trouble figuring out the code to go about that. What I want is to plot all the points but only label a select few and have them away from the plot. Can anyone help me?

Thanks in advance.

vplot <- EnhancedVolcano(myTopHits.df,
                lab = myTopHits.df$geneID,
                selectLab = allgenes,
                labFace = 'bold',
                boxedLabels = TRUE,
                labSize = 4,
                typeConnectors = "closed",
                drawConnectors = TRUE,
                widthConnectors = 0.75,
                colConnectors = 'black',
                lengthConnectors = unit(0.01, "npc"),
                maxoverlapsConnectors = 6,
                title = 'title',
                x = 'logFC',
                y = 'adj.P.Val',
                xlim = c(-7,7),
                ylim = c(0, 7),
                axisLabSize = 12,
                FCcutoff = 2,
                pCutoff = 0.05,
                cutoffLineType = 'longdash',
                colAlpha = 1,
                cutoffLineWidth = 1,
                legendPosition = 'bottom',
                legendLabSize = 10,
                legendIconSize = 3.0,
                gridlines.major = FALSE,
                gridlines.minor = FALSE,
                border = 'full',
                borderWidth = 0.5,
                raster = FALSE)

include your problematic code here with any corresponding output

vplot + geom_label_repel(mapping = aes(myTopHits.df[c(8,516,1381,1811,210, 528), ]))

Output:

nolabel + geom_label_repel(mapping = aes(myTopHits.df[c(8,516,1381,1811,210, 528), ]))
Error: Aesthetics must be either length 1 or the same as the data (2115): x

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

sessionInfo( )

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4

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

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

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

other attached packages:
 [1] EnhancedVolcano_1.10.0 ggrepel_0.9.1          gt_0.3.0              
 [4] DT_0.18                forcats_0.5.1          stringr_1.4.0         
 [7] dplyr_1.0.7            purrr_0.3.4            readr_1.4.0           
[10] tidyr_1.1.3            tibble_3.1.2           ggplot2_3.3.5         
[13] tidyverse_1.3.1        edgeR_3.34.0           limma_3.48.1          

loaded via a namespace (and not attached):
 [1] fs_1.5.0            usethis_2.0.1       lubridate_1.7.10   
 [4] devtools_2.4.2      ash_1.0-15          RColorBrewer_1.1-2 
 [7] httr_1.4.2          rprojroot_2.0.2     tools_4.1.0        
[10] backports_1.2.1     utf8_1.2.1          R6_2.5.0           
[13] KernSmooth_2.23-20  vipor_0.4.5         DBI_1.1.1          
[16] colorspace_2.0-2    withr_2.4.2         tidyselect_1.1.1   
[19] prettyunits_1.1.1   ggrastr_0.2.3       processx_3.5.2     
[22] ggalt_0.4.0         compiler_4.1.0      extrafontdb_1.0    
[25] cli_3.0.0           rvest_1.0.0         xml2_1.3.2         
[28] desc_1.3.0          scales_1.1.1        proj4_1.0-10.1     
[31] callr_3.7.0         digest_0.6.27       pkgconfig_2.0.3    
[34] htmltools_0.5.1.1   extrafont_0.17      sessioninfo_1.1.1  
[37] dbplyr_2.1.1        fastmap_1.1.0       maps_3.3.0         
[40] htmlwidgets_1.5.3   rlang_0.4.11        readxl_1.3.1       
[43] rstudioapi_0.13     generics_0.1.0      jsonlite_1.7.2     
[46] magrittr_2.0.1      Rcpp_1.0.7          ggbeeswarm_0.6.0   
[49] munsell_0.5.0       fansi_0.5.0         lifecycle_1.0.0    
[52] stringi_1.6.2       MASS_7.3-54         pkgbuild_1.2.0     
[55] grid_4.1.0          crayon_1.4.1        lattice_0.20-44    
[58] haven_2.4.1         hms_1.1.0           locfit_1.5-9.4     
[61] ps_1.6.0            pillar_1.6.1        pkgload_1.2.1      
[64] reprex_2.0.0        glue_1.4.2          remotes_2.4.0      
[67] BiocManager_1.30.16 modelr_0.1.8        vctrs_0.3.8        
[70] testthat_3.0.4      Rttf2pt1_1.3.8      cellranger_1.1.0   
[73] gtable_0.3.0        assertthat_0.2.1    cachem_1.0.5       
[76] broom_0.7.8         beeswarm_0.4.0      memoise_2.0.0      
[79] ellipsis_0.3.2

EnhancedVolcano already uses geom_text_repel for you, and there is an argument called 'selectLab' that you can use to select only those that you want to have labels for. See the vignette, particularly section 4.8