xlim not working for me

[victorvvong]

Hello, Thanks for your attention

I followed the manual and try the track plot. The "xlim" is not working well for me. It does not zoom into the defined region.
Would you be able to advise me if I missed something?

Many Thanks
Victor

#

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

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] BiocInstaller_1.22.3 Hmisc_3.17-4
[3] Formula_1.2-1 survival_2.39-5
[5] lattice_0.20-33 VariantAnnotation_1.18.6
[7] Homo.sapiens_1.3.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[9] org.Hs.eg.db_3.3.0 GO.db_3.3.0
[11] OrganismDbi_1.14.1 GenomicAlignments_1.8.4
[13] Rsamtools_1.24.0 SummarizedExperiment_1.2.3
[15] ensembldb_1.4.7 GenomicFeatures_1.24.5
[17] BSgenome_1.40.1 rtracklayer_1.32.2
[19] Biostrings_2.40.2 XVector_0.12.1
[21] GenomicRanges_1.24.2 GenomeInfoDb_1.8.3
[23] biovizBase_1.20.0 AnnotationHub_2.4.2
[25] AnnotationDbi_1.34.4 IRanges_2.6.1
[27] S4Vectors_0.10.2 Biobase_2.32.0
[29] ggbio_1.20.2 ggplot2_2.1.0
[31] BiocGenerics_0.18.0

[zx8754]

@victorvvong you seem to get opposite of my results, i.e.: zoom doesn't work, but x tick labels get updated.

For me, I think xlim is working, but x ticks labels are not updating, example:

library(ggbio) # ggbio_1.20.2; ggplot2_2.1.0; BiocGenerics_0.18.0

df1 <- data.frame(time = 1:100, score = sin((1:100)/20)*10)
p1 <- qplot(data = df1, x = time, y = score, geom = "line")
df2 <- data.frame(time = 30:120, score = sin((30:120)/20)*10, value = rnorm(120-30 + 1))
p2 <- ggplot(data = df2, aes(x = time, y = score)) + 
  geom_line() + geom_point(size = 4, aes(color = value))

## binding
tracks(p1, p2, title = "No xlim")
tracks(p1, p2, xlim = c(1, 40), title = "xlim = c(1, 40)")

sessionInfo()
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 Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] ggbio_1.20.2        ggplot2_2.1.0       BiocGenerics_0.18.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7                   biovizBase_1.20.0            
 [3] lattice_0.20-34               Rsamtools_1.24.0             
 [5] Biostrings_2.40.2             digest_0.6.10                
 [7] mime_0.5                      R6_2.2.0                     
 [9] GenomeInfoDb_1.8.7            plyr_1.8.4                   
[11] chron_2.3-47                  acepack_1.3-3.3              
[13] stats4_3.3.1                  RSQLite_1.0.0                
[15] httr_1.2.1                    BiocInstaller_1.22.3         
[17] zlibbioc_1.18.0               GenomicFeatures_1.24.5       
[19] data.table_1.9.6              S4Vectors_0.10.3             
[21] rpart_4.1-10                  Matrix_1.2-7.1               
[23] labeling_0.3                  splines_3.3.1                
[25] BiocParallel_1.6.6            AnnotationHub_2.4.2          
[27] stringr_1.1.0                 foreign_0.8-67               
[29] RCurl_1.95-4.8                biomaRt_2.28.0               
[31] munsell_0.4.3                 shiny_0.14.1                 
[33] httpuv_1.3.3                  rtracklayer_1.32.2           
[35] htmltools_0.3.5               nnet_7.3-12                  
[37] SummarizedExperiment_1.2.3    gridExtra_2.2.1              
[39] interactiveDisplayBase_1.10.3 Hmisc_3.17-4                 
[41] IRanges_2.6.1                 XML_3.98-1.4                 
[43] reshape_0.8.5                 GenomicAlignments_1.8.4      
[45] bitops_1.0-6                  RBGL_1.48.1                  
[47] grid_3.3.1                    xtable_1.8-2                 
[49] GGally_1.2.0                  gtable_0.2.0                 
[51] DBI_0.5-1                     magrittr_1.5                 
[53] scales_0.4.0                  graph_1.50.0                 
[55] stringi_1.1.2                 XVector_0.12.1               
[57] reshape2_1.4.1                latticeExtra_0.6-28          
[59] Formula_1.2-1                 RColorBrewer_1.1-2           
[61] ensembldb_1.4.7               tools_3.3.1                  
[63] dichromat_2.0-0               OrganismDbi_1.14.1           
[65] BSgenome_1.40.1               Biobase_2.32.0               
[67] survival_2.39-5               AnnotationDbi_1.34.4         
[69] colorspace_1.2-7              cluster_2.0.5                
[71] GenomicRanges_1.24.3          VariantAnnotation_1.18.7 

[zx8754]

Also, tried using development version ggbio_1.21.7, same issue.

[lawremi]

Please try 1.23.1.

[zx8754]

@lawremi How do we install ggbio_1.23.1 ?

I installed development version of R:

R Under development (unstable) (2016-10-18 r71535)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Then tried below:

source("http://bioconductor.org/biocLite.R")
# Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
# Bioconductor does not yet support R version 3.4.0

biocLite("ggbio")

After lots of warnings and errors, install failed.

Edit:
Posted on forum, too:
https://support.bioconductor.org/p/88485/