Hi,
I am trying to plot mutations from multiple individuals on the same track of circular plot.
I have GRanges object that looks like this:
GRanges object with 26 ranges and 4 metadata columns:
seqnames ranges strand | id var val buu
| 
[1] 1 [32417, 32427] * | jcf7180000862659 A 1 32417
[2] 1 [58621, 58631] * | jcf7180000753913 B 1 58621
[3] 2 [25622, 25632] * | jcf7180000860774 C 1 25622
[4] 2 [44180, 44190] * | jcf7180001643718 D 1 44180
[5] 2 [66003, 66013] * | jcf7180001638671 E 1 66003

I would like to color mutations by var. I am able to plot them as points but not as rect.
cols <- RColorBrewer::brewer.pal(6,"Paired")
names(cols) <- c("A,"B","C","D", "E", "F")
p <- p + circle(lost, geom = "point", aes(fill=var, color=var, shape=0)) + scale_color_manual(values = cols) + scale_fill_manual(values = cols) + scale_shape_identity()

That works for geom point, but I would like geom rect. If I change geom to rect and use aes(fill=var, color=var​), all lines are black. It looks like it does not accept the color assignment.

Also, does not work with autoplot(lost, layout="circle", aes(fill=var, color=var)),

layout_circle(lost, aes(fill=var, color=var)) 

But works with autoplot(lost, layout="karyogram", aes(fill=var, color=var)) and

layout_karyogram(lost, aes(fill=var, color=var)) 

Is that a bug by any chance or am I doing something wrong?

Best wishes,

Agnieszka

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252    

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

other attached packages:
[1] GenomicRanges_1.18.4 GenomeInfoDb_1.2.4   IRanges_2.0.1        S4Vectors_0.4.0      ggbio_1.14.0        
[6] BiocGenerics_0.12.1  ggplot2_1.0.0       

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3          AnnotationDbi_1.28.1     base64enc_0.1-2          BatchJobs_1.5           
 [5] BBmisc_1.9               Biobase_2.26.0           BiocParallel_1.0.3       biomaRt_2.22.0          
 [9] Biostrings_2.34.1        biovizBase_1.14.1        bitops_1.0-6             brew_1.0-6              
[13] BSgenome_1.34.1          checkmate_1.5.1          cluster_1.15.3           codetools_0.2-9         
[17] colorspace_1.2-4         DBI_0.3.1                dichromat_2.0-0          digest_0.6.8            
[21] fail_1.2                 foreach_1.4.2            foreign_0.8-61           Formula_1.2-0           
[25] GenomicAlignments_1.2.1  GenomicFeatures_1.18.3   GGally_0.5.0             graph_1.44.1            
[29] grid_3.1.2               gridExtra_0.9.1          gtable_0.1.2             Hmisc_3.15-0            
[33] iterators_1.0.7          labeling_0.3             lattice_0.20-29          latticeExtra_0.6-26     
[37] MASS_7.3-35              munsell_0.4.2            nnet_7.3-8               OrganismDbi_1.8.0       
[41] plyr_1.8.1               proto_0.3-10             RBGL_1.42.0              RColorBrewer_1.1-2      
[45] Rcpp_0.11.4              RCurl_1.95-4.5           reshape_0.8.5            reshape2_1.4.1          
[49] rpart_4.1-8              Rsamtools_1.18.2         RSQLite_1.0.0            rtracklayer_1.26.2      
[53] scales_0.2.4             sendmailR_1.2-1          splines_3.1.2            stringr_0.6.2           
[57] survival_2.37-7          tools_3.1.2              VariantAnnotation_1.12.9 XML_3.98-1.1            
[61] XVector_0.6.0            zlibbioc_1.12.0         
>