来自ggbio的tracks()函数不允许在标题中使用斜体表达式

时间:2016-09-22 17:01:54

标签: r ggplot2 title typography bioconductor

我正在尝试将纯文本与斜体文本组合在由ggbio生成的组合曲目()图表的标题中,但我不能在斜体字体中包含我想要的标题部分。

这里有几个标题的例子,它们允许使用表达式斜体(斜体(x)),最后一个是不适用于我的标题。

library(ggbio)
library(grDevices)

这是我想要使用的标题:“ AAAA 基因的变异”

我可以使用此代码获取它:

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

在第一个例子中使用plot()

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

在使用autoplot()

的第二个示例中,它也适用于我
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

这是我想要的标题,包括 AAAA in italics

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

当我使用曲目()并尝试使用plot_title生成最终曲线时,R崩溃

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

我收到以下错误:

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"

有人如何解决这个错误,

我在互联网上看过,但我没有找到这个特定track()函数的答案。

非常感谢,

最佳,

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     

0 个答案:

没有答案