Hi folks

I'm trying to create a circle plot in ggbio that shows links between different regions of the genome. I've been working through the vignette, but I find that I cannot even replicate all of the examples in the vignette. Specifically, the "rectangle" segments designed to show the positions of variants are completely absent from the plot when running the code below (taken directly from the package vignette):

​library(ggbio)
​data("CRC", package = "biovizBase")
head(mut.gr)
p <- ggbio() + circle(mut.gr, geom = "rect", color = "steelblue") +
    circle(hg19sub, geom = "ideo", fill = "gray70") +
    circle(hg19sub, geom = "scale", size = 2) +
    circle(hg19sub, geom = "text", aes(label = seqnames), vjust = 0, size = 3)
p

Does anyone have any advice? What am I doing wrong here?

I notice the package also currently has a build error (http://www.bioconductor.org/packages/devel/bioc/html/ggbio.html). I was unable to 

Session info:

> sessionInfo()
R Under development (unstable) (2016-01-24 r69993)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.4 (El Capitan)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] ggbio_1.19.10       ggplot2_2.1.0       BiocGenerics_0.17.3
[4] biovizBase_1.19.4

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.1.22  reshape2_1.4.1
 [3] VariantAnnotation_1.17.18    splines_3.3.0
 [5] lattice_0.20-33              colorspace_1.2-6
 [7] htmltools_0.3                stats4_3.3.0
 [9] rtracklayer_1.31.7           GenomicFeatures_1.23.25
[11] RBGL_1.47.0                  interactiveDisplayBase_1.9.0
[13] survival_2.38-3              XML_3.98-1.4
[15] foreign_0.8-66               DBI_0.3.1
[17] ensembldb_1.3.18             BiocParallel_1.5.20
[19] RColorBrewer_1.1-2           plyr_1.8.3
[21] stringr_1.0.0                zlibbioc_1.17.0
[23] Biostrings_2.39.12           munsell_0.4.3
[25] gtable_0.2.0                 OrganismDbi_1.13.5
[27] labeling_0.3                 latticeExtra_0.6-28
[29] Biobase_2.31.3               GGally_1.0.1
[31] IRanges_2.5.40               biomaRt_2.27.2
[33] httpuv_1.3.3                 GenomeInfoDb_1.7.6
[35] BiocInstaller_1.21.4         AnnotationDbi_1.33.7
[37] Rcpp_0.12.3                  acepack_1.3-3.3
[39] xtable_1.8-2                 scales_0.4.0
[41] BSgenome_1.39.4              S4Vectors_0.9.42
[43] graph_1.49.1                 Hmisc_3.17-2
[45] XVector_0.11.7               mime_0.4
[47] Rsamtools_1.23.3             gridExtra_2.2.1
[49] AnnotationHub_2.3.14         digest_0.6.9
[51] stringi_1.0-1                shiny_0.13.1
[53] GenomicRanges_1.23.24        grid_3.3.0
[55] tools_3.3.0                  bitops_1.0-6
[57] magrittr_1.5                 RCurl_1.95-4.8
[59] RSQLite_1.0.0                dichromat_2.0-0
[61] Formula_1.2-1                cluster_2.0.3
[63] reshape_0.8.5                httr_1.1.0
[65] R6_2.1.2                     rpart_4.1-10
[67] GenomicAlignments_1.7.20     nnet_7.3-12
>

Any help much appreciated! Alternative solutions to the problem of producing a circle plot from a GRanges object with links between regions of the genome also most welcome.

Davis

Thanks, should be fixed in ggbio 1.19.12.