Can anyone identify whether I am doing something wrong or if there is a bug in the recent ggbio version?  There seems to be no color support for Granges objects with the autoplot function.  The vignette example in the ggbio does not produce the desired color for the gene model :

library('ggbio')
library('Homo.sapiens')

data(genesymbol, package = "biovizBase")
wh <- genesymbol[c("BRCA1", "NBR1")]
wh <- range(wh, ignore.strand = TRUE)

autoplot(Homo.sapiens, which  = wh, label.color = "black", color = "brown", fill = "brown")

sessionInfo()

R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.1 (El Capitan)

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

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

other attached packages:
 [1] Homo.sapiens_1.3.1                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [3] org.Hs.eg.db_3.2.3                      GO.db_3.2.2                            
 [5] RSQLite_1.0.0                           DBI_0.3.1                              
 [7] OrganismDbi_1.12.1                      GenomicFeatures_1.22.8                 
 [9] GenomicRanges_1.22.3                    GenomeInfoDb_1.6.2                     
[11] AnnotationDbi_1.32.3                    IRanges_2.4.6                          
[13] S4Vectors_0.8.7                         Biobase_2.30.0                         
[15] ggbio_1.18.3                            ggplot2_2.0.0                          
[17] BiocGenerics_0.16.1                    

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.0.2 VariantAnnotation_1.16.4   reshape2_1.4.1             splines_3.2.3             
 [5] lattice_0.20-33            colorspace_1.2-6           rtracklayer_1.30.1         RBGL_1.46.0               
 [9] survival_2.38-3            XML_3.98-1.3               foreign_0.8-66             BiocParallel_1.4.3        
[13] RColorBrewer_1.1-2         lambda.r_1.1.7             plyr_1.8.3                 stringr_1.0.0             
[17] zlibbioc_1.16.0            Biostrings_2.38.3          munsell_0.4.2              gtable_0.1.2              
[21] futile.logger_1.4.1        labeling_0.3               latticeExtra_0.6-26        GGally_1.0.1              
[25] biomaRt_2.26.1             BiocInstaller_1.20.1       Rcpp_0.12.3                acepack_1.3-3.3           
[29] scales_0.3.0               BSgenome_1.38.0            graph_1.48.0               Hmisc_3.17-1              
[33] XVector_0.10.0             Rsamtools_1.22.0           gridExtra_2.0.0            stringi_1.0-1             
[37] biovizBase_1.18.0          grid_3.2.3                 tools_3.2.3                bitops_1.0-6              
[41] magrittr_1.5               RCurl_1.95-4.7             dichromat_2.0-0            Formula_1.2-1             
[45] cluster_2.0.3              futile.options_1.0.0       reshape_0.8.5              rpart_4.1-10              
[49] GenomicAlignments_1.6.3    nnet_7.3-11             

Hi Timothy,

Looks like a bug causing ggbio to silently drop those arguments. The vignette even contains several figures that ignored the color argument.

You can workaround this issue by mapping colors to color and fill within aes() and using identity scales. For example:

autoplot(Homo.sapiens, aes(fill = "brown", color = "brown"), which = wh) + 
  scale_fill_identity() + 
  scale_color_identity()