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Issue with plot_gene #60

@gnarlygoat12

Description

@gnarlygoat12

Recently when running plot_gene our methylation probability graph is stuck in greyscale for me (on a Mac) and not generating for my coworker (on a PC). Additionally, the isoform annotation figure is not generating. We cannot figure out what is causing this problem and would appreciate any insight. An example image is below. Thank you in advance for your help, session information is below.

Image

R version 4.5.0 (2025-04-11)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.6.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1

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

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] BiocParallel_1.42.1 RColorBrewer_1.1-3 wesanderson_0.3.7 NanoMethViz_3.4.0
[5] plyranges_1.28.0 lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1
[9] dplyr_1.1.4 purrr_1.1.0 readr_2.1.5 tidyr_1.3.1
[13] tibble_3.3.0 ggplot2_3.5.2 tidyverse_2.0.0 dmrseq_1.28.0
[17] bsseq_1.44.1 SummarizedExperiment_1.38.1 Biobase_2.68.0 MatrixGenerics_1.20.0
[21] matrixStats_1.5.0 GenomicRanges_1.60.0 GenomeInfoDb_1.44.1 IRanges_2.42.0
[25] S4Vectors_0.46.0 BiocGenerics_0.54.0 generics_0.1.4

loaded via a namespace (and not attached):
[1] splines_4.5.0 BiocIO_1.18.0 bitops_1.0-9 filelock_1.0.3
[5] R.oo_1.27.1 XML_3.99-0.18 lifecycle_1.0.4 lattice_0.22-7
[9] magrittr_2.0.3 sass_0.4.10 limma_3.64.3 rmarkdown_2.29
[13] jquerylib_0.1.4 yaml_2.3.10 doRNG_1.8.6.2 DBI_1.2.3
[17] abind_1.4-8 R.utils_2.13.0 RCurl_1.98-1.17 rappdirs_0.3.3
[21] cpp11_0.5.2 GenomeInfoDbData_1.2.14 irlba_2.3.5.1 permute_0.9-8
[25] DelayedMatrixStats_1.30.0 codetools_0.2-20 DelayedArray_0.34.1 tidyselect_1.2.1
[29] outliers_0.15 UCSC.utils_1.4.0 farver_2.1.2 ScaledMatrix_1.16.0
[33] BiocFileCache_2.16.1 GenomicAlignments_1.44.0 jsonlite_2.0.0 annotatr_1.34.0
[37] e1071_1.7-16 iterators_1.0.14 foreach_1.5.2 dbscan_1.2.2
[41] tools_4.5.0 Rcpp_1.1.0 glue_1.8.0 SparseArray_1.8.1
[45] xfun_0.52 HDF5Array_1.36.0 withr_3.0.2 BiocManager_1.30.26
[49] fastmap_1.2.0 rhdf5filters_1.20.0 digest_0.6.37 rsvd_1.0.5
[53] timechange_0.3.0 R6_2.6.1 colorspace_2.1-1 gtools_3.9.5
[57] RSQLite_2.4.2 R.methodsS3_1.8.2 h5mread_1.0.1 data.table_1.17.8
[61] rtracklayer_1.68.0 class_7.3-23 httr_1.4.7 S4Arrays_1.8.1
[65] regioneR_1.40.1 pkgconfig_2.0.3 gtable_0.3.6 blob_1.2.4
[69] XVector_0.48.0 htmltools_0.5.8.1 scales_1.4.0 png_0.1-8
[73] knitr_1.50 rstudioapi_0.17.1 tzdb_0.5.0 reshape2_1.4.4
[77] rjson_0.2.23 nlme_3.1-168 curl_6.4.0 bumphunter_1.50.0
[81] proxy_0.4-27 cachem_1.1.0 rhdf5_2.52.1 BiocVersion_3.21.1
[85] parallel_4.5.0 vipor_0.4.7 AnnotationDbi_1.70.0 ggrastr_1.0.2
[89] restfulr_0.0.16 pillar_1.11.0 grid_4.5.0 vctrs_0.6.5
[93] BiocSingular_1.24.0 dbplyr_2.5.0 beachmat_2.24.0 beeswarm_0.4.0
[97] evaluate_1.0.4 GenomicFeatures_1.60.0 cli_3.6.5 locfit_1.5-9.12
[101] compiler_4.5.0 Rsamtools_2.24.0 rlang_1.1.6 crayon_1.5.3
[105] rngtools_1.5.2 labeling_0.4.3 plyr_1.8.9 fs_1.6.6
[109] ggbeeswarm_0.7.2 stringi_1.8.7 assertthat_0.2.1 Biostrings_2.76.0
[113] Matrix_1.7-3 BSgenome_1.76.0 hms_1.1.3 patchwork_1.3.1
[117] sparseMatrixStats_1.20.0 bit64_4.6.0-1 Rhdf5lib_1.30.0 KEGGREST_1.48.1
[121] statmod_1.5.0 AnnotationHub_3.16.1 memoise_2.0.1 bslib_0.9.0
[125] bit_4.6.0

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