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Question: [Gviz Error] Issue with plotTracks plotting ideogram track
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gravatar for cristianrohr768
8 months ago by
cristianrohr7680 wrote:

Hello,

I have an R code working OK, until today. It plot's a DataTrack a IdeogramTrack and a GenomeAxisTrack

If i only plot the DataTrack and the GenomeAxisTrack it works OK, the problem is the IdeogramTrack

This is the code:

 

    dtrack <- DataTrack(
      range = plotear,
      type = "polygon",
      genome = 'hg19',
      name = "z-score binned",
      baseline = baseline_usar,
      lty.baseline = "dashed", #dashed, dotted, solid
      col.baseline = "red",
      fill.mountain= col_usar,
      col.mountain = "black"
    )
    plotTracks(
      list(dtrack),
      from = st, to = en
    )
    itrack <- IdeogramTrack(
      genome = "hg19", chromosome = thechr, showId=FALSE
    )
    gtrack <- GenomeAxisTrack()
    png(filename = paste(nombre_graficos,"_zscore_binned_chr13.png",sep=""), units="px", width=2000, height=1000, res=300)
    plotTracks(
      list(itrack, gtrack, dtrack),
      from = st, to = en
    )
    dev.off()

the traceback of the error:

13: c(x0, y)
12: reduce(c(x0, y), drop.empty.ranges = TRUE)
11: .local(x, y, ...)
10: union(gaps(x, start = start, end = end), y)
9: union(gaps(x, start = start, end = end), y)
8: gaps(union(gaps(x, start = start, end = end), y), start = start,
       end = end)
7: .local(x, y, ...)
6: setdiff(IRanges(0, max(end(range(GdObject)))), range(GdObject))
5: setdiff(IRanges(0, max(end(range(GdObject)))), range(GdObject))
4: .local(GdObject, ...)
3: drawGD(expandedTrackList[[i]], minBase = ranges["from"], maxBase = ranges["to"],
       prepare = TRUE, subset = FALSE)
2: drawGD(expandedTrackList[[i]], minBase = ranges["from"], maxBase = ranges["to"],
       prepare = TRUE, subset = FALSE)
1: plotTracks(list(gtrack, dtrack, itrack), from = st, to = en)

 

 

and the sessionInfo

 

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04 LTS

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

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

other attached packages:
 [1] NIPTeR_1.0.2         gridExtra_2.2.1      Gviz_1.18.1          data.table_1.10.4    ggplot2_2.2.1        zoo_1.7-14           Rsamtools_1.24.0    
 [8] Biostrings_2.40.2    XVector_0.12.1       GenomicRanges_1.24.3 GenomeInfoDb_1.8.7   IRanges_2.6.1        S4Vectors_0.10.3     BiocGenerics_0.18.0 

loaded via a namespace (and not attached):
 [1] Biobase_2.32.0                httr_1.2.1                    AnnotationHub_2.4.2           splines_3.3.3                
 [5] Formula_1.2-1                 shiny_1.0.0                   assertthat_0.1                interactiveDisplayBase_1.10.3
 [9] latticeExtra_0.6-28           BSgenome_1.40.1               RSQLite_1.1-2                 backports_1.0.5              
[13] lattice_0.20-34               biovizBase_1.20.0             digest_0.6.12                 RColorBrewer_1.1-2           
[17] checkmate_1.8.2               colorspace_1.3-2              htmltools_0.3.5               httpuv_1.3.3                 
[21] Matrix_1.2-8                  plyr_1.8.4                    XML_3.98-1.5                  biomaRt_2.28.0               
[25] zlibbioc_1.18.0               xtable_1.8-2                  scales_0.4.1                  BiocParallel_1.6.6           
[29] htmlTable_1.9                 tibble_1.2                    SummarizedExperiment_1.2.3    GenomicFeatures_1.24.5       
[33] nnet_7.3-12                   lazyeval_0.2.0                survival_2.40-1               magrittr_1.5                 
[37] mime_0.5                      memoise_1.0.0                 foreign_0.8-67                BiocInstaller_1.22.3         
[41] tools_3.3.3                   matrixStats_0.51.0            stringr_1.2.0                 munsell_0.4.3                
[45] cluster_2.0.5                 AnnotationDbi_1.34.4          ensembldb_1.4.7               RCurl_1.95-4.8               
[49] dichromat_2.0-0               VariantAnnotation_1.18.7      htmlwidgets_0.8               labeling_0.3                 
[53] bitops_1.0-6                  base64enc_0.1-3               gtable_0.2.0                  sets_1.0-17                  
[57] DBI_0.5-1                     reshape2_1.4.2                R6_2.2.0                      GenomicAlignments_1.8.4      
[61] knitr_1.15.1                  rtracklayer_1.34.2            Hmisc_4.0-2                   stringi_1.1.2                
[65] Rcpp_0.12.9                   rpart_4.1-10                  acepack_1.4.1      
ADD COMMENTlink written 8 months ago by cristianrohr7680
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