Q:

ggbio tracks() function handling x axis in the wrong way when combining plots

I've been trying to use tracks() function from ggbio to combine several genomic tracks, but it seems that whenever you combine them, the x axis does not keep the original scale. Below you can find the code for an example that shows my problem. If you look at the x axis of both plots, either combined_tracks1 or combined_tracks2, both have the x axis ticks in the wrong positions even hough you specify your specific xlim coordinates and t_a and t_b have the right scales!!
library(ggbio）

test_a = GRanges('chr1', IRanges(start = 150, end = 180))
t_a <- autoplot(test_a)
t_a

test_b = GRanges('chr1', IRanges(start = 100, end = 200))
t_b <- autoplot(test_b)
t_b

## ORDER A, B
combined_tracks1 <-   tracks(t_a, t_b) + xlim (100, 200)     
combined_tracks1

## ORDER B, A
combined_tracks2 <-   tracks(t_b, t_a) + xlim (100, 200)     
combined_tracks2

R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
 [1] SNPlocs.Hsapiens.dbSNP142.GRCh37_0.99.5 VariantAnnotation_1.18.7                Rsamtools_1.24.0                       
 [4] SummarizedExperiment_1.2.3              BSgenome.Hsapiens.UCSC.hg19_1.4.0       BSgenome_1.40.1                        
 [7] Biostrings_2.40.2                       XVector_0.12.1                          rtracklayer_1.32.2                     
[10] cowplot_0.6.2                           scales_0.4.0                            plyr_1.8.4                             
[13] reshape_0.8.5                           Homo.sapiens_1.3.1                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[16] org.Hs.eg.db_3.3.0                      GO.db_3.3.0                             OrganismDbi_1.14.1                     
[19] GenomicFeatures_1.24.5                  AnnotationDbi_1.34.4                    Biobase_2.32.0                         
[22] GenomicRanges_1.24.2                    GenomeInfoDb_1.8.3                      IRanges_2.6.1                          
[25] S4Vectors_0.10.3                        biovizBase_1.20.0                       ggbio_1.20.2                           
[28] ggplot2_2.1.0                           BiocGenerics_0.18.0                    

loaded via a namespace (and not attached):
 [1] httr_1.2.1                    AnnotationHub_2.4.2           splines_3.3.1                 Formula_1.2-1                
 [5] shiny_0.13.2                  interactiveDisplayBase_1.10.3 latticeExtra_0.6-28           RBGL_1.48.1                  
 [9] RSQLite_1.0.0                 lattice_0.20-33               chron_2.3-47                  digest_0.6.10                
[13] RColorBrewer_1.1-2            colorspace_1.2-6              htmltools_0.3.5               httpuv_1.3.3                 
[17] Matrix_1.2-6                  XML_3.98-1.4                  biomaRt_2.28.0                zlibbioc_1.18.0              
[21] xtable_1.8-2                  BiocParallel_1.6.6            nnet_7.3-12                   survival_2.39-5              
[25] magrittr_1.5                  mime_0.5                      GGally_1.2.0                  foreign_0.8-66               
[29] graph_1.50.0                  BiocInstaller_1.22.3          tools_3.3.1                   data.table_1.9.6             
[33] stringr_1.1.0                 munsell_0.4.3                 cluster_2.0.4                 ensembldb_1.4.7              
[37] grid_3.3.1                    RCurl_1.95-4.8                dichromat_2.0-0               bitops_1.0-6                 
[41] labeling_0.3                  gtable_0.2.0                  DBI_0.5                       reshape2_1.4.1               
[45] R6_2.1.3                      GenomicAlignments_1.8.4       gridExtra_2.2.1               Hmisc_3.17-4                 
[49] stringi_1.1.1                 Rcpp_0.12.6                   rpart_4.1-10                  acepack_1.3-3.3          

ggpl

Thank you very much,
Best,
Yatrosin

A:

I have the answer to my own question. You need to fix the x axis in the following way:
fixed(t_a) <- TRUE
fixed(t_b) <- TRUE 

for each of your single plots.
This way, x axis won't be modified in the final plot generated by the tracks() function.
Best,

