Error in graphics::par

[renee9904]

Hi, I have run into this problem while ploting my custom genome, the figure plotted only in white and black which is not consistent with the tutorial.

Could you please help me to solve it?

[bernatgel]

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

[renee9904]

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:

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.

[bernatgel]

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