[Gviz Error] Issue with plotTracks plotting ideogram track
0
0
Entering edit mode
@cristianrohr768-12538
Last seen 4.7 years ago

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      
gviz plottracks ideogramtrack • 617 views
ADD COMMENT

Login before adding your answer.

Traffic: 261 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6