geom_gene() doesn't work about gggenomes HOT 5 CLOSED

Hi thackl,
When I add a column type="CDS" ,it can run normally now.
Thank you again for your timely reply.
Looking forward to the new version of gggenomes！

Best Wishes,
Kirito

from gggenomes.

Hi Kirito,

thanks for reaching out. Not sure what the problem is. I ran your code and both versions work for me. Can you share the output of sessionInfo(). Do you get any other warnings or so

p1 <- gggenomes(emale_genes) + geom_gene(aes(fill=strand), position="strand")

test2 <- emale_genes %>% dplyr::select(seq_id,start,end,strand)
p2 <- gggenomes(genes = test2 )+ geom_gene(aes(fill=strand), position="strand")

p1+p2

from gggenomes.

Thanks for your reply so fast!
Here is my sessionInfo:

sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /usr/bin/R-4.1.3/lib64/R/lib/libRblas.so
LAPACK: /usr/bin/R-4.1.3/lib64/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] gggenomes_0.9.7.9000 snakecase_0.11.0 jsonlite_1.8.3 tibble_3.1.8 thacklr_0.0.0.9000 tidyr_1.2.1 stringr_1.4.1
[8] readr_2.1.3 purrr_0.3.5 gggenes_0.4.1 vctrs_0.5.0 ggplot2_3.4.1 dplyr_1.0.10

loaded via a namespace (and not attached):
[1] bitops_1.0-7 matrixStats_0.63.0 fs_1.5.2 usethis_2.1.6 devtools_2.4.5
[6] rprojroot_2.0.3 GenomeInfoDb_1.30.1 tools_4.1.3 profvis_0.3.7 utf8_1.2.3
[11] R6_2.5.1 DBI_1.1.3 BiocGenerics_0.40.0 colorspace_2.1-0 urlchecker_1.0.1
[16] withr_2.5.0 tidyselect_1.2.0 prettyunits_1.1.1 processx_3.8.0 curl_4.3.3
[21] compiler_4.1.3 textshaping_0.3.6 cli_3.6.0 Biobase_2.54.0 desc_1.4.2
[26] DelayedArray_0.20.0 labeling_0.4.2 rtracklayer_1.54.0 scales_1.2.1 callr_3.7.3
[31] systemfonts_1.0.4 digest_0.6.30 Rsamtools_2.10.0 XVector_0.34.0 pkgconfig_2.0.3
[36] htmltools_0.5.3 sessioninfo_1.2.2 MatrixGenerics_1.6.0 fastmap_1.1.0 htmlwidgets_1.5.4
[41] rlang_1.0.6 rstudioapi_0.14 shiny_1.7.3 farver_2.1.1 BiocIO_1.4.0
[46] generics_0.1.3 BiocParallel_1.28.3 RCurl_1.98-1.9 magrittr_2.0.3 GenomeInfoDbData_1.2.7
[51] Matrix_1.5-3 Rcpp_1.0.10 munsell_0.5.0 S4Vectors_0.32.4 fansi_1.0.4
[56] ggfittext_0.9.1 lifecycle_1.0.3 stringi_1.7.8 yaml_2.3.6 SummarizedExperiment_1.24.0
[61] zlibbioc_1.40.0 pkgbuild_1.4.0 grid_4.1.3 parallel_4.1.3 promises_1.2.0.1
[66] crayon_1.5.2 miniUI_0.1.1.1 lattice_0.20-45 Biostrings_2.62.0 hms_1.1.2
[71] ps_1.7.2 pillar_1.8.1 GenomicRanges_1.46.1 rjson_0.2.21 stats4_4.1.3
[76] pkgload_1.3.2 XML_3.99-0.12 glue_1.6.2 remotes_2.4.2 tzdb_0.3.0
[81] httpuv_1.6.6 gtable_0.3.1 assertthat_0.2.1 cachem_1.0.6 mime_0.12
[86] xtable_1.8-4 restfulr_0.0.15 later_1.3.0 ragg_1.2.4 GenomicAlignments_1.30.0
[91] memoise_2.0.1 IRanges_2.28.0 ellipsis_0.3.2

from gggenomes.

OK, I think I found the problem. The easiest workaround for you right now should be to add a column type="CDS" to your data.

I'll try to fix the underlying problem in the package when I have more time.

test2 <- emale_genes %>% dplyr::transmute(seq_id,start,end,strand,type="CDS")

from gggenomes.

The latest version should now also be able again to show genes if you don't explicitly provide them with type="CDS".

from gggenomes.