kpAddBaseNumbers issue on plot.type=2

[freddymonteiro]

Hi guys, I stumbled upon the impossibility to add Base Numbers to a Type 2 ideogram. A few months ago I was able to generate a KaryoPlot of type 2 with custom cytobands and custom annotations without any issues. I tried to correct one annotation recycling my code and stumbled upon the impossibility to add base numbers. Here is an example using the shipped datasets:

> kp <- plotKaryotype(genome="hg19",plot.type=2)
> kpAddBaseNumbers(kp)

Error in ccf(chr = rep(chr.name, length(tick.pos)), x = tick.pos) : 
  In coordChangeFunction: data.panel is required

Providing data.panel attribute to kpAddBaseNumbers does not help.

Is this only happening to me, or is it a bug? Thanks in advance for looking into this.

[bernatgel]

That's a bug. I'll try to fix it as soon as I get to a computer. Thanks for reporting it.

El mié., 14 nov. 2018 10:25, Freddy Monteiro notifications@github.com escribió:

Hi guys, I stumbled upon the impossibility to add Base Numbers to a Type 2 ideogram. A few months ago I was able to generate a KaryoPlot of type 2 with custom cytobands and custom annotations without any issues. I tried to correct one annotation recycling my code and stumbled upon the impossibility to add base numbers. Here is an example using the shipped datasets:

kp <- plotKaryotype(genome="hg19",plot.type=2) kpAddBaseNumbers(kp)

Error in ccf(chr = rep(chr.name, length(tick.pos)), x = tick.pos) : In coordChangeFunction: data.panel is required

Is this only happening to me, or is it a bug? Thanks in advance for looking into this.

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[bernatgel]

Hi @freddymonteiro

I thought it was a bug but I think I actually fixed it in a previous version. Could you provide the output of sessionInfo()? Code works for me in latest release version (1.8.2) and latest devel version (1.9.3)

Could you update to the latest version and check if you still see the error?

Bernat

[freddymonteiro]

The issue persists, despite I seem to be running on the last version....

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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

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

other attached packages:
[1] karyoploteR_1.8.2    regioneR_1.14.0      GenomicRanges_1.34.0
[4] GenomeInfoDb_1.18.1  IRanges_2.16.0       S4Vectors_0.20.1    
[7] BiocGenerics_0.28.0 

loaded via a namespace (and not attached):
 [1] Biobase_2.42.0              httr_1.3.1                 
 [3] bit64_0.9-7                 splines_3.5.1              
 [5] Formula_1.2-3               assertthat_0.2.0           
 [7] latticeExtra_0.6-28         blob_1.1.1                 
 [9] BSgenome_1.50.0             GenomeInfoDbData_1.2.0     
[11] Rsamtools_1.34.0            progress_1.2.0             
[13] pillar_1.3.0                RSQLite_2.1.1              
[15] backports_1.1.2             lattice_0.20-38            
[17] biovizBase_1.30.0           digest_0.6.18              
[19] RColorBrewer_1.1-2          XVector_0.22.0             
[21] checkmate_1.8.5             colorspace_1.3-2           
[23] htmltools_0.3.6             Matrix_1.2-15              
[25] plyr_1.8.4                  XML_3.98-1.16              
[27] pkgconfig_2.0.2             biomaRt_2.38.0             
[29] zlibbioc_1.28.0             scales_1.0.0               
[31] BiocParallel_1.16.0         tibble_1.4.2               
[33] htmlTable_1.12              AnnotationFilter_1.6.0     
[35] ggplot2_3.1.0               SummarizedExperiment_1.12.0
[37] GenomicFeatures_1.34.1      nnet_7.3-12                
[39] lazyeval_0.2.1              survival_2.43-1            
[41] magrittr_1.5                crayon_1.3.4               
[43] memoise_1.1.0               foreign_0.8-71             
[45] data.table_1.11.8           tools_3.5.1                
[47] prettyunits_1.0.2           hms_0.4.2                  
[49] matrixStats_0.54.0          stringr_1.3.1              
[51] munsell_0.5.0               bamsignals_1.14.0          
[53] cluster_2.0.7-1             DelayedArray_0.8.0         
[55] ensembldb_2.6.1             AnnotationDbi_1.44.0       
[57] Biostrings_2.50.1           compiler_3.5.1             
[59] bezier_1.1                  rlang_0.3.0.1              
[61] grid_3.5.1                  RCurl_1.95-4.11            
[63] dichromat_2.0-0             rstudioapi_0.8             
[65] VariantAnnotation_1.28.1    htmlwidgets_1.3            
[67] bitops_1.0-6                base64enc_0.1-3            
[69] gtable_0.2.0                curl_3.2                   
[71] DBI_1.0.0                   R6_2.3.0                   
[73] GenomicAlignments_1.18.0    gridExtra_2.3              
[75] knitr_1.20                  rtracklayer_1.42.0         
[77] bit_1.1-14                  Hmisc_4.1-1                
[79] ProtGenerics_1.14.0         stringi_1.2.4              
[81] Rcpp_1.0.0                  rpart_4.1-13               
[83] acepack_1.4.1      

Base numbers are not a strictly necessary. I just found the behavior strange given my previous experience producing these plots without any major issue. Sorry for the trouble. Freddy

[bernatgel]

Hi @freddymonteiro

You are totally correct. The bug was still there. Should be fixed in 1.8.4 (and devel 1.9.5). Available in Bioconductor in a couple of days and right now in github.

Thanks for the bug report.

Bernat

[freddymonteiro]

Thank you for following this up @bernatgel !! Glad this report is useful and the bug can be fixed soon. Have a great week ahead. Freddy