I want to italicise the gene labels for my volcano plot. The HTML from EnhancedVolcano shows that, in order to italicise, this should be done:
lab_italics <- paste0("italic('", rownames(res), "')")
However, in my volcano plot I obtain: italic('genename'). Do you know what's the problem?
Thank you very much.
My 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=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] latex2exp_0.9.4 fgsea_1.20.0 RUVSeq_1.28.0 pheatmap_1.0.12
[5] DESeq2_1.34.0 clusterProfiler_4.2.2 tweeDEseq_1.40.0 edgeR_3.36.0
[9] EnhancedVolcano_1.12.0 ggrepel_0.9.1 limma_3.50.1 ggbio_1.42.0
[13] ggplot2_3.3.5 stringr_1.4.0 EDASeq_2.28.0 ShortRead_1.52.0
[17] GenomicAlignments_1.30.0 SummarizedExperiment_1.24.0 MatrixGenerics_1.6.0 matrixStats_0.61.0
[21] Rsamtools_2.10.0 GenomicRanges_1.46.1 Biostrings_2.62.0 GenomeInfoDb_1.30.1
[25] XVector_0.34.0 IRanges_2.28.0 S4Vectors_0.32.3 BiocParallel_1.28.3
[29] Biobase_2.54.0 BiocGenerics_0.40.0 dplyr_1.0.8 biomaRt_2.50.3
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 SparseM_1.81 rtracklayer_1.54.0 GGally_2.1.2 R.methodsS3_1.8.1
[6] tidyr_1.2.0 bit64_4.0.5 knitr_1.38 aroma.light_3.24.0 DelayedArray_0.20.0
[11] R.utils_2.11.0 data.table_1.14.2 rpart_4.1-15 hwriter_1.3.2 KEGGREST_1.34.0
[16] RCurl_1.98-1.6 AnnotationFilter_1.18.0 generics_0.1.2 snow_0.4-4 GenomicFeatures_1.46.5
[21] RSQLite_2.2.10 shadowtext_0.1.1 mice_3.14.0 bit_4.0.4 tzdb_0.2.0
[26] enrichplot_1.14.2 xml2_1.3.3 quantsmooth_1.60.0 assertthat_0.2.1 viridis_0.6.2
[31] xfun_0.29 hms_1.1.1 evaluate_0.15 DNAcopy_1.68.0 fansi_1.0.2
[36] restfulr_0.0.13 progress_1.2.2 dbplyr_2.1.1 readxl_1.4.0 igraph_1.2.11
[41] DBI_1.1.2 geneplotter_1.72.0 htmlwidgets_1.5.4 reshape_0.8.8 purrr_0.3.4
[46] ellipsis_0.3.2 ggpubr_0.4.0 backports_1.4.1 annotate_1.72.0 vctrs_0.3.8
[51] Cairo_1.5-15 remotes_2.4.2 quantreg_5.88 ensembldb_2.18.4 abind_1.4-5
[56] cachem_1.0.6 withr_2.5.0 ggforce_0.3.3 BSgenome_1.62.0 checkmate_2.0.0
[61] treeio_1.18.1 prettyunits_1.1.1 cluster_2.1.2 DOSE_3.20.1 ape_5.6-2
[66] lazyeval_0.2.2 crayon_1.5.1 genefilter_1.76.0 labeling_0.4.2 pkgconfig_2.0.3
[71] tweenr_1.0.2 vipor_0.4.5 nlme_3.1-153 ProtGenerics_1.26.0 nnet_7.3-16
[76] rlang_1.0.2 lifecycle_1.0.1 MatrixModels_0.5-0 sandwich_3.0-1 downloader_0.4
[81] filelock_1.0.2 extrafontdb_1.0 BiocFileCache_2.2.1 dichromat_2.0-0 ggrastr_1.0.1
[86] cellranger_1.1.0 polyclip_1.10-0 lmtest_0.9-40 graph_1.72.0 Matrix_1.3-4
[91] aplot_0.1.3 carData_3.0-5 zoo_1.8-9 beeswarm_0.4.0 base64enc_0.1-3
[96] png_0.1-7 viridisLite_0.4.0 rjson_0.2.21 bitops_1.0-7 R.oo_1.24.0
[101] KernSmooth_2.23-20 blob_1.2.2 qvalue_2.26.0 nor1mix_1.3-0 logistf_1.24.1
[106] rstatix_0.7.0 readr_2.1.2 jpeg_0.1-9 gridGraphics_0.5-1 ggsignif_0.6.3
[111] scales_1.1.1 memoise_2.0.1 magrittr_2.0.1 plyr_1.8.6 zlibbioc_1.40.0
[116] compiler_4.1.2 scatterpie_0.1.7 factoextra_1.0.7 BiocIO_1.4.0 ash_1.0-15
[121] RColorBrewer_1.1-2 gdsfmt_1.30.0 cli_3.2.0 patchwork_1.1.1 htmlTable_2.4.0
[126] Formula_1.2-4 MASS_7.3-54 mgcv_1.8-38 tidyselect_1.1.2 stringi_1.7.6
[131] proj4_1.0-11 yaml_2.2.1 GOSemSim_2.20.0 locfit_1.5-9.5 latticeExtra_0.6-29
[136] grid_4.1.2 VariantAnnotation_1.40.0 fastmatch_1.1-3 tools_4.1.2 parallel_4.1.2
[141] rstudioapi_0.13 foreign_0.8-81 gridExtra_2.3 farver_2.1.0 ggraph_2.0.5
[146] GWASExactHW_1.01 digest_0.6.29 BiocManager_1.30.16 operator.tools_1.6.3 Rcpp_1.0.8
[151] car_3.0-12 broom_0.7.12 ggalt_0.4.0 OrganismDbi_1.36.0 httr_1.4.2
[156] AnnotationDbi_1.56.2 biovizBase_1.42.0 colorspace_2.0-3 XML_3.99-0.9 splines_4.1.2
[161] yulab.utils_0.0.4 RBGL_1.70.0 tidytree_0.3.9 GWASTools_1.40.0 graphlayouts_0.8.0
[166] ggplotify_0.1.0 xtable_1.8-4 jsonlite_1.8.0 ggtree_3.2.1 tidygraph_1.2.0
[171] ggfun_0.0.6 formula.tools_1.7.1 R6_2.5.1 Hmisc_4.6-0 pillar_1.7.0
[176] htmltools_0.5.2 glue_1.6.2 fastmap_1.1.0 maps_3.4.0 utf8_1.2.2
[181] sva_3.42.0 lattice_0.20-45 tibble_3.1.6 ggbeeswarm_0.6.0 curl_4.3.2
[186] Rttf2pt1_1.3.10 GO.db_3.14.0 survival_3.2-13 rmarkdown_2.13 munsell_0.5.0
[191] DO.db_2.9 GenomeInfoDbData_1.2.7 reshape2_1.4.4 gtable_0.3.0 cqn_1.40.0
[196] extrafont_0.17
Hi, can you compare the contents of your variable,
lab_italics, versus those of the variable (selectLab_italics) that is produced in my vignette? - https://bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html#italicise-labels-and-flip-volcano-on-its-sideThey're the same: example of the vignette: "italic('VCAM1')" and result from my data: "italic('CARS1')"
As I am running against time because of a deadline I went for ggplot, I guess it is a better option if you really want to change every little detail.
Okay, I am guessing that the problem is that you need to update the version of EnhancedVolcano to the latest version. Can you try that? The most direct route is by direct installation:
Or, you can upgrade your version of R and, after, Bioconductor packages.
Well, I couldn't reproduce the original code. Right now, with this strategy, no label is being printed. I guess I have some error around, but don't worry I just switched to ggplot. Thank you very much.
No hay de que. Nos vemos