Question: EnhancedVolcano, selectLab highlights nothing
gravatar for FallingBabyEagle
13 months ago by
FallingBabyEagle0 wrote:

Would somebody look at my code and point me in the right direction? Without the "selectLab" line, I can label the genes but I only want to highlight a few select genes.

I installed this package today with devtools:



                lab = mydata$gene,
                x = 'log2FoldChange',
                y = 'padj',
                selectLab = c("CRNN"),
                pCutoff = 0.05,
                FCcutoff = 1.5,
                xlim = c(min(mydata[,"log2FoldChange"], na.rm=TRUE),
                         max(mydata[,"log2FoldChange"], na.rm=TRUE)),
                ylim = c(0, max(-log10(mydata[,"padj"]), na.rm=TRUE)),
                                axisLabSize = 18,
                title = 'cx vs tum',
                subtitle = '',
                legendPosition = 'right',
                legendLabSize = 12,
                legendIconSize = 4.0,
                drawConnectors = TRUE,
                widthConnectors = 0.2,
                colConnectors = 'grey30',
                transcriptPointSize = 1.0,
                transcriptLabSize = 3.5,
                transcriptLabCol = 'black',
                transcriptLabFace = 'bold',
                boxedlabels = TRUE,
                colAlpha = 4/5,
                xlab = bquote(~Log[2]~ "fold change"),
                ylab = bquote(~-Log[10]~adjusted~italic(P)),

R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/libblas/
LAPACK: /usr/lib/lapack/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 

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

other attached packages:
[1] calibrate_1.7.2       MASS_7.3-50           EnhancedVolcano_1.1.3 ggrepel_0.8.1         ggplot2_3.1.1.9000   

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1        pillar_1.3.1      compiler_3.4.4    remotes_2.0.4     prettyunits_1.0.2 tools_3.4.4      
 [7] testthat_2.1.1    digest_0.6.18     pkgbuild_1.0.3    pkgload_1.0.2     memoise_1.1.0     tibble_2.1.1     
[13] gtable_0.3.0      pkgconfig_2.0.2   rlang_0.3.4       cli_1.1.0         rstudioapi_0.10   yaml_2.2.0       
[19] withr_2.1.2       dplyr_0.8.0.1     fs_1.3.1          desc_1.2.0        devtools_2.0.2    rprojroot_1.3-2  
[25] grid_3.4.4        tidyselect_0.2.5  glue_1.3.1        R6_2.4.0          processx_3.3.1    sessioninfo_1.1.1
[31] purrr_0.3.2       callr_3.2.0       magrittr_1.5      usethis_1.5.0     scales_1.0.0      backports_1.1.4  
[37] ps_1.3.0          assertthat_0.2.1  colorspace_1.4-1  labeling_0.3      lazyeval_0.2.2    munsell_0.5.0    
[43] crayon_1.3.4
rna-seq • 535 views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 13 months ago by FallingBabyEagle0

EnhancedVolcano should have been a tag in your question. That would probably have alerted its developer, Kevin Blighe

ADD REPLYlink written 13 months ago by RamRS27k
gravatar for Kevin Blighe
13 months ago by
Kevin Blighe60k
Kevin Blighe60k wrote:

Hey, for selectLab to function correctly, CRNN has to definitely be a member of mydata$gene. Also check that mydata$gene is encoded as a character vector.

What does grepl("CRNN", mydata$gene) return? It should return the index at which CRNN resides in mydata$gene

Also, I know that I have a part in the vignette for plotting the negative log10 of the adjusted p-values, but the general practice is to plot the nominal p-values. See here:

ADD COMMENTlink modified 11 months ago • written 13 months ago by Kevin Blighe60k
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