I encountered a problem regard to coordinate transformation when using tracks function in ggbio package. An example is here:

# Create a GRanges and plot it normally

library(ggbio）
gr = GRanges('chr2', IRanges(start = 50, end = 100))
p = ggplot(gr) + geom_rect()
p

# However, when it is wrapped into tracks, the coordinate are not matched with the rectangular. 

tracks(p)

# Using  GRanges as xlim will fix this, however, using IRanges or numeric will make the coordinate even weird.

tracks(p, xlim = c(1,100))

tracks(p, xlim = IRanges(start = 1, end = 100))

# Also, the  + method for adding  xlim seems not working correctly.

tracks(p) + xlim(gr)

As the ggbio manual stated: 

xlim    

limits on x. could be IRanges, GRanges, numeric value

I would like to know, 

1. Could anyone reproduce these problems?

2. Is this a known bug or something?

Session Info:

R version 3.3.1 (2016-06-21)
Platform: i686-pc-linux-gnu (32-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] 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   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] ggbio_1.20.2         ggplot2_2.1.0        GenomicRanges_1.24.2
[4] GenomeInfoDb_1.8.3   IRanges_2.6.1        S4Vectors_0.10.2    
[7] BiocGenerics_0.18.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.6                   Formula_1.2-1                
 [3] AnnotationHub_2.4.2           XVector_0.12.1               
 [5] magrittr_1.5                  cluster_2.0.4                
 [7] GenomicAlignments_1.8.4       splines_3.3.1                
 [9] zlibbioc_1.18.0               xtable_1.8-2                 
[11] colorspace_1.2-6              biovizBase_1.20.0            
[13] lattice_0.20-33               BSgenome_1.40.1              
[15] R6_2.1.3                      latticeExtra_0.6-28          
[17] htmltools_0.3.5               digest_0.6.10                
[19] interactiveDisplayBase_1.10.3 Matrix_1.2-6                 
[21] shiny_0.13.2                  acepack_1.3-3.3              
[23] RCurl_1.95-4.8                BiocInstaller_1.22.3         
[25] scales_0.4.0                  Hmisc_3.17-4                 
[27] Biostrings_2.40.2             Rsamtools_1.24.0             
[29] GenomicFeatures_1.24.5        reshape_0.8.5                
[31] httpuv_1.3.3                  graph_1.50.0                 
[33] AnnotationDbi_1.34.4          OrganismDbi_1.14.1           
[35] GGally_1.2.0                  munsell_0.4.3                
[37] BiocParallel_1.6.3            httr_1.2.1                   
[39] plyr_1.8.4                    stringr_1.1.0                
[41] ensembldb_1.4.7               tools_3.3.1                  
[43] grid_3.3.1                    nnet_7.3-12                  
[45] dichromat_2.0-0               SummarizedExperiment_1.2.3   
[47] Biobase_2.32.0                data.table_1.9.6             
[49] gtable_0.2.0                  DBI_0.5                      
[51] RBGL_1.48.1                   survival_2.39-5              
[53] gridExtra_2.2.1               rtracklayer_1.32.2           
[55] reshape2_1.4.1                RColorBrewer_1.1-2           
[57] bitops_1.0-6                  biomaRt_2.28.0               
[59] rpart_4.1-10                  RSQLite_1.0.0                
[61] mime_0.5                      labeling_0.3                 
[63] stringi_1.1.1                 XML_3.98-1.4                 
[65] VariantAnnotation_1.18.6      foreign_0.8-66               
[67] chron_2.3-47                 

Thanks in advance !

I would like to remove this answer, but I have no privileges to do it.

It was not an answer for the question at all.

I had the same problem. Try to do this:

library(ggbio）
        gr = GRanges('chr2', IRanges(start = 50, end = 100))
        p = ggplot(gr) + geom_rect()
        p
fixed (p) <- TRUE

tracks(p)

You need to fix the x axis of your single plots in order for them to be combined with the right x scale.

Best,