Question: tracks () function from ggbio does not allow italic expression in the title
0
gravatar for oswaldo.lorenzo
3.1 years ago by
oswaldo.lorenzo10 wrote:

I'm trying to combine plain text with italic text in the title of a combined tracks() plot generated by ggbio, but I can not include the part of the title that I want in italic fonts.

Here you have several examples of titles that allow italics using expression(italic(x)) and the last one is the one that does not work for me.

library(ggbio)
library(grDevices)

This is the title that I want to use: "Variation in AAAA gene"

I can get it with this code:

plot_title <- expression(paste("Variation in ", italic("AAAA"), " gene"))

It works for me in this first example using the plot()

x <- c(2*5)
y <- c(2^5)
plot(x,y, main = plot_title)

It also works for me in the second example using the autoplot()

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

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

This is the plot that I would like to have with the title including the AAAA in italics

combined_tracks <-   tracks(t_a, t_b, title = "Variation in AAAA gene") + xlim (100, 200)    
combined_tracks

When I use the tracks() and I try to use the plot_title to generate the final plot, R crashes

combined_tracks2 <-   tracks(t_a, t_b, title = plot_title) + xlim (100, 200)    
combined_tracks2

I get the following error:

Error in validObject(.Object) :
  invalid class "Tracks" object: invalid object for slot "main" in class "Tracks": got class "expression", should be or extend class "characterORNULL"

Does anybody how to get around this error,

I have looked on the Internet, but I haven't found an answer for this specific tracks() function.

Thank you very much,

Best,

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   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] Homo.sapiens_1.3.1                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [3] org.Hs.eg.db_3.3.0                      GO.db_3.3.0                            
 [5] OrganismDbi_1.14.1                      GenomicFeatures_1.24.5                 
 [7] AnnotationDbi_1.34.4                    Biobase_2.32.0                         
 [9] GenomicRanges_1.24.3                    GenomeInfoDb_1.8.7                     
[11] IRanges_2.6.1                           S4Vectors_0.10.3                       
[13] biovizBase_1.20.0                       ggbio_1.20.2                           
[15] ggplot2_2.1.0                           BiocGenerics_0.18.0                    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7                   lattice_0.20-34               Rsamtools_1.24.0             
 [4] Biostrings_2.40.2             digest_0.6.10                 mime_0.5                     
 [7] R6_2.1.3                      plyr_1.8.4                    chron_2.3-47                 
[10] acepack_1.3-3.3               RSQLite_1.0.0                 httr_1.2.1                   
[13] BiocInstaller_1.22.3          zlibbioc_1.18.0               data.table_1.9.6             
[16] rpart_4.1-10                  Matrix_1.2-7.1                labeling_0.3                 
[19] splines_3.3.1                 BiocParallel_1.6.6            AnnotationHub_2.4.2          
[22] stringr_1.1.0                 foreign_0.8-67                RCurl_1.95-4.8               
[25] biomaRt_2.28.0                munsell_0.4.3                 shiny_0.14                   
[28] httpuv_1.3.3                  rtracklayer_1.32.2            htmltools_0.3.5              
[31] nnet_7.3-12                   SummarizedExperiment_1.2.3    gridExtra_2.2.1              
[34] interactiveDisplayBase_1.10.3 Hmisc_3.17-4                  XML_3.98-1.4                 
[37] reshape_0.8.5                 GenomicAlignments_1.8.4       bitops_1.0-6                 
[40] RBGL_1.48.1                   grid_3.3.1                    xtable_1.8-2                 
[43] GGally_1.2.0                  gtable_0.2.0                  DBI_0.5-1                    
[46] magrittr_1.5                  scales_0.4.0                  graph_1.50.0                 
[49] stringi_1.1.1                 XVector_0.12.1                reshape2_1.4.1               
[52] latticeExtra_0.6-28           Formula_1.2-1                 RColorBrewer_1.1-2           
[55] ensembldb_1.4.7               tools_3.3.1                   dichromat_2.0-0              
[58] BSgenome_1.40.1               survival_2.39-5               colorspace_1.2-6             
[61] cluster_2.0.4                 VariantAnnotation_1.18.7     
 
 

 

ggbio ggplot2 title typography • 583 views
ADD COMMENTlink modified 2.8 years ago • written 3.1 years ago by oswaldo.lorenzo10

This issue was solved by Michael Lawrence in ggbio 1.21.6 version.

Thanks

ADD REPLYlink written 3.1 years ago by oswaldo.lorenzo10

Dear Michael Lawrence,

I posted this comment as a new question. It was really long.

Thanks,

Oswaldo

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by oswaldo.lorenzo10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 338 users visited in the last hour