Question

我一直在尝试使用ggbio中的tracks（）函数来组合几个基因组轨道，但似乎无论何时组合它们，x轴都不会保持原始比例。您可以在下面找到显示我的问题的示例的代码。如果您查看两个图的x轴，无论是combined_tracks1还是combined_tracks2，即使您指定了特定的xlim坐标，并且t_a和t_b具有正确的比例，两者都会将x轴标记在错误的位置！

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

非常感谢，

最佳，

Yatrosin

Answer 1

我对自己的问题有答案。您需要以下列方式修复x轴：

fixed(t_a) <- TRUE
fixed(t_b) <- TRUE

每个单一地块。

这样，在track（）函数生成的最终图中不会修改x轴。

最佳，

ggbio tracks（）函数在组合图时以错误的方式处理x轴

1 个答案: