Question: Arrange Gviz plotTracks() figure and basic R plot on a canvas
gravatar for izzy.yichao.cai
14 months ago by
izzy.yichao.cai10 wrote:


I am trying to put Gviz output and a basic R plot on the same canvas.

The figures I have:

1) A basic R plot recorded with recordPlot()

2) A bunch of Gviz tracks

Attempts I took:

I tried to grab the Gviz output using grid::grid.grabExp() and use cowplot::plot_grid() to put them on the same canvas.

tp <- grid.grabExpr(plotTracks(list(gtrack,ht),from = chrstart, to=chrend, chromosome = chrm, add = TRUE))

# >Warning message:

# >In grabDL(warn, wrap, ...) :

# >one of more grobs overwritten (grab WILL not be faithful; try 'wrap = TRUE')

figure <- plot_grid(basic_R, tp)

The final figure did no 100% replicate what I saw with plotTracks(). Some (NOT ALL!) data tracks in "polygon" style lost their color fill in mountains. I could still see the colored line but the fill between colored peaks and baseline was totally lost.

Adding the 'wrap = TRUE' would not solve this problem and the error still occured.

How could I properly arrange them on the same canvas?

Thank you so much for your help!




R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/
LAPACK: /usr/lib/lapack/

[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_SG.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_SG.UTF-8  
[6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_SG.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C           

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

other attached packages:
[1] gridGraphics_0.3-0                      gdtools_0.1.7                           bindrcpp_0.2                          
[4]                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.30.3                
[7] AnnotationDbi_1.40.0                    Biobase_2.38.0                          Gviz_1.22.3                           
[10] GenomicRanges_1.30.3                    GenomeInfoDb_1.14.0                     IRanges_2.12.0                        
[13] S4Vectors_0.16.0                        BiocGenerics_0.24.0                     optparse_1.4.4                        
[16] Sushi_1.16.0                            biomaRt_2.34.2                          zoo_1.8-1                             
[19] forcats_0.3.0                           stringr_1.3.0                           tidyr_0.8.0                           
[22] tibble_1.4.2                            tidyverse_1.2.1                         RColorBrewer_1.1-2                    
[25] cowplot_0.9.2                           gridExtra_2.3                           ggpubr_0.1.6.999                      
[28] magrittr_1.5                            svglite_1.2.1                           scales_0.5.0.9000                     
[31] ggrepel_0.7.3                           ggplot2_2.2.1.9000                      purrr_0.2.4                           
[34] readr_1.1.1                             dplyr_0.7.4                             here_0.1                               

loaded via a namespace (and not attached):
[1] colorspace_1.3-2              rprojroot_1.3-2               biovizBase_1.26.0             htmlTable_1.11.2            
[5] XVector_0.18.0                base64enc_0.1-3               dichromat_2.0-0               rstudioapi_0.7              
[9] getopt_1.20.2                 bit64_0.9-7                   interactiveDisplayBase_1.16.0 lubridate_1.7.4             
[13] xml2_1.2.0                    splines_3.4.4                 mnormt_1.5-5                  knitr_1.20                  
[17] Formula_1.2-2                 jsonlite_1.5                  Rsamtools_1.30.0              broom_0.4.3                 
[21] cluster_2.0.7-1               shiny_1.0.5                   compiler_3.4.4                httr_1.3.1                  
[25] backports_1.1.2               assertthat_0.2.0              Matrix_1.2-14                 lazyeval_0.2.1              
[29] cli_1.0.0                     acepack_1.4.1                 htmltools_0.3.6               prettyunits_1.0.2           
[33] tools_3.4.4                   gtable_0.2.0                  glue_1.2.0                    GenomeInfoDbData_1.0.0      
[37] reshape2_1.4.3                Rcpp_0.12.16                  cellranger_1.1.0              Biostrings_2.46.0           
[41] nlme_3.1-137                  rtracklayer_1.38.3            psych_1.7.8                   rvest_0.3.2                 
[45] mime_0.5                      ensembldb_2.2.2               XML_3.98-1.10                 AnnotationHub_2.10.1        
[49] zlibbioc_1.24.0               BSgenome_1.46.0               BiocInstaller_1.28.0          VariantAnnotation_1.24.5    
[53] ProtGenerics_1.10.0           hms_0.4.2                     SummarizedExperiment_1.8.1    AnnotationFilter_1.2.0      
[57] curl_3.1                      yaml_2.1.18                   memoise_1.1.0                 rpart_4.1-13                
[61] latticeExtra_0.6-28           stringi_1.1.7                 RSQLite_2.0                   RMySQL_0.10.14              
[65] checkmate_1.8.5               BiocParallel_1.12.0           rlang_0.2.0.9001              pkgconfig_2.0.1             
[69] bitops_1.0-6                  matrixStats_0.53.1            lattice_0.20-35               bindr_0.1.1                 
[73] labeling_0.3                  GenomicAlignments_1.14.1      htmlwidgets_1.0               bit_1.1-12                  
[77] plyr_1.8.4                    R6_2.2.2                      Hmisc_4.1-1                   DelayedArray_0.4.1          
[81] DBI_0.8                       pillar_1.2.2                  haven_1.1.1                   foreign_0.8-70              
[85] withr_2.1.2                   survival_2.42-3               RCurl_1.95-4.10               nnet_7.3-12                 
[89] modelr_0.1.1                  crayon_1.3.4                  progress_1.1.2                readxl_1.1.0                
[93] data.table_1.10.4-3           blob_1.1.0                    digest_0.6.15                 xtable_1.8-2                
[97] httpuv_1.3.6.2                munsell_0.4.3                
gviz gviz-package • 282 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by izzy.yichao.cai10
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