ggbio with facet_grid()

[JokingHero]

Hi!

I get this error lately when trying to combine ggbio archplots with facets. Could you help me to get around this?

archRanges <- data.frame(strand = c("+", "+", "+"),
                     start = c(84, 60, 66),
                     end = c(96, 172, 180),
                     frequency = c(0.375, 0.125, 0.0625),
                     cut = c(1, 2, 1),
                     seqnames = c("ID_1", "ID_3", "ID_3"))

 arch_plot_top <- ggplot() + geom_arch(data = archRanges, 
                                      aes(alpha = frequency,
                                          size = frequency,
                                          x = start,
                                          xend = end))
arch_plot_bot <- ggplot() + geom_arch(data = archRanges,
                                      aes(alpha = frequency,
                                          size = frequency,
                                          x = start,
                                          xend = end)) + 
  facet_grid(seqnames ~ .)

ggbio::tracks(arch_plot_top,
              arch_plot_bot)

Error in mapply(child_vp, vp_name = vpname(x$layout), t = x$layout$t,  : 
  zero-length inputs cannot be mixed with those of non-zero length
In addition: Warning messages:
1: In min(g$layout[idx, ]$l) :
  no non-missing arguments to min; returning Inf
2: In max(g$layout[idx, ]$r) :
  no non-missing arguments to max; returning -Inf
3: In min(g$layout[idx, ]$l) :
  no non-missing arguments to min; returning Inf
4: In max(g$layout[idx, ]$r) :
  no non-missing arguments to max; returning -Inf

My sessionInfo():

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

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

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

other attached packages:
[1] ggbio_1.22.0        ggplot2_2.2.0       BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8                   biovizBase_1.22.0             lattice_0.20-34               Rsamtools_1.26.1             
 [5] Biostrings_2.42.0             assertthat_0.1                digest_0.6.10                 mime_0.5                     
 [9] R6_2.2.0                      GenomeInfoDb_1.10.1           plyr_1.8.4                    acepack_1.4.1                
[13] stats4_3.3.1                  RSQLite_1.0.0                 BiocInstaller_1.24.0          httr_1.2.1                   
[17] zlibbioc_1.20.0               GenomicFeatures_1.26.0        lazyeval_0.2.0                data.table_1.9.8             
[21] S4Vectors_0.12.0              rpart_4.1-10                  Matrix_1.2-7.1                labeling_0.3                 
[25] splines_3.3.1                 BiocParallel_1.8.1            AnnotationHub_2.6.4           stringr_1.1.0                
[29] foreign_0.8-67                RCurl_1.95-4.8                biomaRt_2.30.0                munsell_0.4.3                
[33] shiny_0.14.2                  httpuv_1.3.3                  rtracklayer_1.34.1            htmltools_0.3.5              
[37] nnet_7.3-12                   SummarizedExperiment_1.4.0    tibble_1.2                    gridExtra_2.2.1              
[41] htmlTable_1.7                 interactiveDisplayBase_1.12.0 Hmisc_4.0-0                   IRanges_2.8.1                
[45] XML_3.98-1.5                  reshape_0.8.6                 GenomicAlignments_1.10.0      bitops_1.0-6                 
[49] RBGL_1.50.0                   grid_3.3.1                    xtable_1.8-2                  GGally_1.3.0                 
[53] gtable_0.2.0                  DBI_0.5-1                     magrittr_1.5                  scales_0.4.1                 
[57] graph_1.52.0                  stringi_1.1.2                 XVector_0.14.0                reshape2_1.4.2               
[61] latticeExtra_0.6-28           Formula_1.2-1                 RColorBrewer_1.1-2            ensembldb_1.6.2              
[65] tools_3.3.1                   dichromat_2.0-0               OrganismDbi_1.16.0            BSgenome_1.42.0              
[69] Biobase_2.34.0                yaml_2.1.14                   survival_2.40-1               AnnotationDbi_1.36.0         
[73] colorspace_1.3-1              cluster_2.0.5                 GenomicRanges_1.26.1          VariantAnnotation_1.20.1     
[77] knitr_1.15.1    

[lawremi]

This is due to recent changes in ggplot2 (renamed grobs). It was fixed in devel last week and now I've pushed it to release. Watch for version 1.22.1.

[JokingHero]

Hi Michael,

I have installed the ggbio in version 1.23 from devel, but I still get the same error. Also ggbio stable is still 1.22, when will it update?

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

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

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

other attached packages:
[1] ggbio_1.23.0        BiocGenerics_0.20.0 ggplot2_2.2.0      

loaded via a namespace (and not attached):
 [1] Biobase_2.34.0                httr_1.2.1                    AnnotationHub_2.6.4           splines_3.3.1                
 [5] Formula_1.2-1                 shiny_0.14.2                  assertthat_0.1                interactiveDisplayBase_1.12.0
 [9] stats4_3.3.1                  latticeExtra_0.6-28           RBGL_1.50.0                   BSgenome_1.42.0              
[13] Rsamtools_1.26.1              yaml_2.1.14                   RSQLite_1.1                   lattice_0.20-34              
[17] biovizBase_1.22.0             digest_0.6.10                 GenomicRanges_1.26.1          RColorBrewer_1.1-2           
[21] XVector_0.14.0                colorspace_1.3-1              htmltools_0.3.5               httpuv_1.3.3                 
[25] Matrix_1.2-7.1                plyr_1.8.4                    OrganismDbi_1.16.0            XML_3.98-1.5                 
[29] biomaRt_2.30.0                zlibbioc_1.20.0               xtable_1.8-2                  scales_0.4.1                 
[33] BiocParallel_1.8.1            htmlTable_1.7                 tibble_1.2                    IRanges_2.8.1                
[37] SummarizedExperiment_1.4.0    GenomicFeatures_1.26.0        nnet_7.3-12                   lazyeval_0.2.0               
[41] survival_2.40-1               magrittr_1.5                  mime_0.5                      memoise_1.0.0                
[45] GGally_1.3.0                  foreign_0.8-67                graph_1.52.0                  BiocInstaller_1.24.0         
[49] tools_3.3.1                   data.table_1.9.8              stringr_1.1.0                 S4Vectors_0.12.1             
[53] munsell_0.4.3                 cluster_2.0.5                 AnnotationDbi_1.36.0          ensembldb_1.6.2              
[57] Biostrings_2.42.1             GenomeInfoDb_1.10.1           grid_3.3.1                    RCurl_1.95-4.8               
[61] dichromat_2.0-0               VariantAnnotation_1.20.2      labeling_0.3                  bitops_1.0-6                 
[65] gtable_0.2.0                  DBI_0.5-1                     reshape_0.8.6                 reshape2_1.4.2               
[69] R6_2.2.0                      GenomicAlignments_1.10.0      gridExtra_2.2.1               knitr_1.15.1                 
[73] rtracklayer_1.34.1            Hmisc_4.0-0                   stringi_1.1.2                 Rcpp_0.12.8                  
[77] rpart_4.1-10                  acepack_1.4.1

[lawremi]

I don't think any of the new versions have propagated due to additional problems with the new ggplot2. Unfortunately, I have no ETA on a fix.