Can we align all the names of the transcripts (GeneRegionTrack) in the plotTracks() output?
Entering edit mode
Vaibhav • 0
Last seen 10 months ago

While visualizing the gene along with its transcripts, I found that different transcripts started from different genomic coordinates because of the difference in their exons.

For example, for the gene ENSG00000000419 (DPM1), ENST00000413082 (DPM1-204) starts from the right of the other three protein-coding transcripts. As a result, its annotation is also slightly to the right of the other three transcripts.

Example plot

Without manual intervention, how can I ensure that the annotation for the transcript ENST00000413082 is also along with the other three transcript annotations in this plot? Is there any function argument I can use?


sessionInfo( ) -

R version 4.0.1 (2020-06-06) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale: 1 LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252

attached base packages: 1 grid stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: 1 ensembldb_2.12.1 AnnotationFilter_1.12.0 GenomicFeatures_1.40.1 AnnotationDbi_1.50.3
[5] Biobase_2.48.0 Gviz_1.32.0 GenomicRanges_1.40.0 GenomeInfoDb_1.24.2
[9] IRanges_2.22.2 S4Vectors_0.26.1 AnnotationHub_2.20.2 BiocFileCache_1.12.1
[13] dbplyr_1.4.4 BiocGenerics_0.34.0

loaded via a namespace (and not attached): 1 ProtGenerics_1.20.0 bitops_1.0-6 matrixStats_0.56.0
[4] bit64_4.0.5 RColorBrewer_1.1-2 progress_1.2.2
[7] httr_1.4.2 backports_1.1.7 tools_4.0.1
[10] R6_2.4.1 rpart_4.1-15 lazyeval_0.2.2
[13] Hmisc_4.4-1 DBI_1.1.0 colorspace_1.4-1
[16] nnet_7.3-14 gridExtra_2.3 tidyselect_1.1.0
[19] prettyunits_1.1.1 bit_4.0.4 curl_4.3
[22] compiler_4.0.1 htmlTable_2.1.0 xml2_1.3.2
[25] DelayedArray_0.14.1 rtracklayer_1.48.0 checkmate_2.0.0
[28] scales_1.1.1 askpass_1.1 rappdirs_0.3.1
[31] stringr_1.4.0 digest_0.6.25 Rsamtools_2.4.0
[34] foreign_0.8-80 XVector_0.28.0 dichromat_2.0-0
[37] base64enc_0.1-3 jpeg_0.1-8.1 pkgconfig_2.0.3
[40] htmltools_0.5.0 fastmap_1.0.1 BSgenome_1.56.0
[43] htmlwidgets_1.5.1 rlang_0.4.7 rstudioapi_0.11
[46] RSQLite_2.2.1 shiny_1.5.0 generics_0.0.2
[49] BiocParallel_1.22.0 dplyr_1.0.0 VariantAnnotation_1.34.0
[52] RCurl_1.98-1.2 magrittr_1.5 GenomeInfoDbData_1.2.3
[55] Formula_1.2-4 Matrix_1.2-18 Rcpp_1.0.5
[58] munsell_0.5.0 lifecycle_0.2.0 stringi_1.4.6
[61] yaml_2.2.1 SummarizedExperiment_1.18.2 zlibbioc_1.34.0
[64] blob_1.2.1 promises_1.1.1 crayon_1.3.4
[67] lattice_0.20-41 Biostrings_2.56.0 splines_4.0.1
[70] hms_0.5.3 knitr_1.29 pillar_1.4.6
[73] biomaRt_2.44.4 XML_3.99-0.5 glue_1.4.1
[76] BiocVersion_3.11.1 biovizBase_1.36.0 latticeExtra_0.6-29
[79] data.table_1.12.8 BiocManager_1.30.10 vctrs_0.3.2
[82] png_0.1-7 httpuv_1.5.4 gtable_0.3.0
[85] openssl_1.4.2 purrr_0.3.4 assertthat_0.2.1
[88] ggplot2_3.3.2 xfun_0.15 mime_0.9
[91] xtable_1.8-4 later_1.1.0.1 survival_3.1-12
[94] tibble_3.0.3 GenomicAlignments_1.24.0 tinytex_0.25
[97] memoise_1.1.0 cluster_2.1.0 ellipsis_0.3.1
[100] interactiveDisplayBase_1.26.3

Annotation Alignment Gviz • 242 views
Entering edit mode
Robert Ivanek ▴ 690
Last seen 3 days ago


What about putting the annotation to the end? They seem to be aligned :)

Unfortunately, I believe there is no way how to achieve it in Gviz without a manual intervention. The names are aligned based on the feature coordinates.

I guess the easiest might be to add some white space in to the name of the last transcript, if you really want to have them aligned.

Best, Robert

Entering edit mode

Hello Robert,

Thank you for your input. I also could not find any way to achieve what I wanted without any manual intervention.

Nevertheless, please do let me know if you come across any way to do this without any manual intervention.



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