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bernatgel avatar bernatgel commented on August 28, 2024

ok, that's strange.

Do the cytobands have a color specified using the standard cytobands colors?

Could you give me a failing genomeA object/file and the cytobands? And also the output of sessionInfo()

Thanks

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renee9904 avatar renee9904 commented on August 28, 2024

No, they don't have any color.

And the genomeA is the SARS-CoV-2 genome that I was trying to plot. The code is :
genomeA <- toGRanges(data.frame(chr="A", start=1, end=29903))

I used mycytobands.txt to create cytobands which are:
Screen Shot 2023-06-09 at 10 23 10 AM

And the sessionInfo() is:

R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] Gviz_1.42.1          karyoploteR_1.24.0   regioneR_1.30.0      GenomicRanges_1.50.2
 [5] GenomeInfoDb_1.34.9  IRanges_2.32.0       S4Vectors_0.36.2     BiocGenerics_0.44.0 
 [9] gridExtra_2.3        reshape2_1.4.4       stringr_1.5.0        ggpubr_0.6.0        
[13] dplyr_1.1.2          tidyr_1.3.0          ggplot2_3.4.2       

loaded via a namespace (and not attached):
  [1] backports_1.4.1             Hmisc_5.1-0                 BiocFileCache_2.6.1        
  [4] plyr_1.8.8                  lazyeval_0.2.2              BiocParallel_1.32.6        
  [7] usethis_2.1.6               digest_0.6.31               ensembldb_2.22.0           
 [10] htmltools_0.5.5             fansi_1.0.4                 magrittr_2.0.3             
 [13] checkmate_2.2.0             memoise_2.0.1               BSgenome_1.66.3            
 [16] cluster_2.1.4               remotes_2.4.2               Biostrings_2.66.0          
 [19] matrixStats_0.63.0          prettyunits_1.1.1           jpeg_0.1-10                
 [22] colorspace_2.1-0            blob_1.2.4                  rappdirs_0.3.3             
 [25] xfun_0.39                   callr_3.7.3                 crayon_1.5.2               
 [28] RCurl_1.98-1.12             VariantAnnotation_1.44.1    glue_1.6.2                 
 [31] gtable_0.3.3                zlibbioc_1.44.0             XVector_0.38.0             
 [34] DelayedArray_0.24.0         car_3.1-2                   pkgbuild_1.4.0             
 [37] abind_1.4-5                 scales_1.2.1                bezier_1.1.2               
 [40] DBI_1.1.3                   rstatix_0.7.2               miniUI_0.1.1.1             
 [43] Rcpp_1.0.10                 xtable_1.8-4                progress_1.2.2             
 [46] htmlTable_2.4.1             foreign_0.8-84              bit_4.0.5                  
 [49] Formula_1.2-5               profvis_0.3.8               htmlwidgets_1.6.2          
 [52] httr_1.4.6                  RColorBrewer_1.1-3          ellipsis_0.3.2             
 [55] farver_2.1.1                urlchecker_1.0.1            pkgconfig_2.0.3            
 [58] XML_3.99-0.14               deldir_1.0-6                nnet_7.3-19                
 [61] dbplyr_2.3.2                utf8_1.2.3                  labeling_0.4.2             
 [64] tidyselect_1.2.0            rlang_1.1.1                 later_1.3.1                
 [67] AnnotationDbi_1.60.2        munsell_0.5.0               tools_4.2.2                
 [70] cachem_1.0.8                cli_3.6.1                   generics_0.1.3             
 [73] RSQLite_2.3.1               devtools_2.4.5              broom_1.0.4                
 [76] evaluate_0.21               fastmap_1.1.1               yaml_2.3.7                 
 [79] processx_3.8.1              knitr_1.42                  bit64_4.0.5                
 [82] fs_1.6.2                    purrr_1.0.1                 KEGGREST_1.38.0            
 [85] AnnotationFilter_1.22.0     mime_0.12                   xml2_1.3.4                 
 [88] biomaRt_2.54.1              compiler_4.2.2              rstudioapi_0.14            
 [91] filelock_1.0.2              curl_5.0.0                  png_0.1-8                  
 [94] ggsignif_0.6.4              tibble_3.2.1                stringi_1.7.12             
 [97] ps_1.7.5                    GenomicFeatures_1.50.4      lattice_0.21-8             
[100] ProtGenerics_1.30.0         Matrix_1.5-4                vctrs_0.6.2                
[103] pillar_1.9.0                lifecycle_1.0.3             BiocManager_1.30.20        
[106] data.table_1.14.8           bitops_1.0-7                httpuv_1.6.11              
[109] rtracklayer_1.58.0          latticeExtra_0.6-30         R6_2.5.1                   
[112] BiocIO_1.8.0                promises_1.2.0.1            sessioninfo_1.2.2          
[115] codetools_0.2-19            dichromat_2.0-0.1           pkgload_1.3.2              
[118] SummarizedExperiment_1.28.0 rjson_0.2.21                withr_2.5.0                
[121] GenomicAlignments_1.34.1    Rsamtools_2.14.0            GenomeInfoDbData_1.2.9     
[124] parallel_4.2.2              hms_1.1.3                   rpart_4.1.19               
[127] bamsignals_1.30.0           rmarkdown_2.21              MatrixGenerics_1.10.0      
[130] carData_3.0-5               biovizBase_1.46.0           Biobase_2.58.0             
[133] shiny_1.7.4                 base64enc_0.1-3             interp_1.1-4               
[136] restfulr_0.0.15            

Thank you for your help.

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bernatgel avatar bernatgel commented on August 28, 2024

Hi @renee9904

The problem with black and white is simply because you are using the gieStain column with values unkown to karyoploteR. karyoploteR will understand only the standard values used in UCSC:

gneg gpos25 gpos33 gpos50 gpos66 gpos75 gpos100 gpos stalk acen gvar

but you are using ORF, S, M... changing these values should make it work

Hope this helps

Bernat

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