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 