具有发光效果的基因组

时间:2018-10-12 10:09:59

标签: r shiny

我正在尝试构建一个利用 rtracklayer 在Genome Browser中创建自定义轨道的Shiny应用程序。代码本身非常简单-我创建了一个范围,一个轨道,一个会话,然后调用browserGenome。

#Coords is simply a table of coordinates 
targetRanges <- IRanges(coords$start, coords$end)
targetTrack <- with(coords,GRangesForUCSCGenome("hg38", chromosome_name, targetRanges, strand,name, gene))


session <- browserSession("UCSC")

track(session, "custom_1") <- targetTrack

geneRange <- subset(coords,gene==geneName)

grange <- as(paste(geneRange$chromosome_name[1],':',geneRange$start_position[1],'-',geneRange$end_position[1],sep=''),"GRanges")

browseGenome(targetTrack, range = grange,name="custom_1",viewParams=list(full=c("custom_1")))

这封装在我的Shiny应用程序的服务器部分中。当我在RStudio的Mac上本地运行该应用程序时,它运行得很好。但是,当我在Shiny Server的Ubuntu 16.04.4 LTS上运行它时,它失败并显示以下错误。

Listening on http://127.0.0.1:33958
/usr/bin/xdg-open: 778: /usr/bin/xdg-open: www-browser: not found
/usr/bin/xdg-open: 778: /usr/bin/xdg-open: links2: not found
/usr/bin/xdg-open: 778: /usr/bin/xdg-open: elinks: not found
/usr/bin/xdg-open: 778: /usr/bin/xdg-open: links: not found
/usr/bin/xdg-open: 778: /usr/bin/xdg-open: lynx: not found
/usr/bin/xdg-open: 778: /usr/bin/xdg-open: w3m: not found
xdg-open: no method available for opening 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr1%3a43978943-43991170&ct_cust$

现在,我了解它正在尝试打开新的浏览器窗口,但未能在服务器端打开。我不明白的是如何直接将其打开客户端浏览器窗口。

或者,我正在研究是否可以某种方式访问​​ browseGenome 生成的URL(使用正确的 hgsid ),我可以设置 view = FALSE 并创建我自己的链接供客户端点击。但是经过大量检查和搜索后,我无法在任何数据对象中找到URL。

任何完成这些事情的指针将不胜感激。

谢谢!

Vivek

> sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

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

other attached packages:
 [1] seqinr_3.4-5         rtracklayer_1.38.3   GenomicRanges_1.30.3 GenomeInfoDb_1.14.0  IRanges_2.12.0       S4Vectors_0.16.0    
 [7] BiocGenerics_0.24.0  biomaRt_2.37.8       openxlsx_4.1.0       shinyjs_1.0          shiny_1.1.0          tidyr_0.8.1         
[13] gplots_3.0.1         dplyr_0.7.6          epivizrChart_1.3.3  

loaded via a namespace (and not attached):
  [1] backports_1.1.2               Hmisc_4.1-1                   AnnotationHub_2.10.1          plyr_1.8.4                   
  [5] lazyeval_0.2.1                splines_3.5.1                 BiocParallel_1.12.0           ggplot2_3.0.0                
  [9] digest_0.6.17                 BiocInstaller_1.28.0          ensembldb_2.2.2               htmltools_0.3.6              
 [13] gdata_2.18.0                  magrittr_1.5                  checkmate_1.8.5               memoise_1.1.0                
 [17] cluster_2.0.7-1               Biostrings_2.46.0             matrixStats_0.54.0            prettyunits_1.0.2            
 [21] epivizrServer_1.6.0           colorspace_1.3-2              blob_1.1.1                    crayon_1.3.4                 
 [25] RCurl_1.95-4.11               jsonlite_1.5                  graph_1.56.0                  bindr_0.1.1                  
 [29] survival_2.42-6               glue_1.3.0                    gtable_0.2.0                  zlibbioc_1.24.0              
 [33] XVector_0.18.0                DelayedArray_0.4.1            scales_1.0.0                  DBI_1.0.0                    
 [37] Rcpp_0.12.19                  viridisLite_0.3.0             xtable_1.8-3                  progress_1.2.0               
 [41] htmlTable_1.12                foreign_0.8-71                bit_1.1-14                    OrganismDbi_1.20.0           
 [45] Formula_1.2-3                 sqldf_0.4-11                  htmlwidgets_1.3               httr_1.3.1                   
 [49] RColorBrewer_1.1-2            acepack_1.4.1                 pkgconfig_2.0.2               XML_3.98-1.16                
 [53] nnet_7.3-12                   tidyselect_0.2.4              rlang_0.2.2                   later_0.7.5                  
 [57] AnnotationDbi_1.40.0          munsell_0.5.0                 tools_3.5.1                   gsubfn_0.7                   
 [61] RSQLite_2.1.1                 ade4_1.7-13                   stringr_1.3.1                 yaml_2.2.0                   
 [65] knitr_1.20                    bit64_0.9-7                   zip_1.0.0                     caTools_1.17.1.1             
 [69] purrr_0.2.5                   AnnotationFilter_1.2.0        bindrcpp_0.2.2                RBGL_1.54.0                  
 [73] mime_0.5                      compiler_3.5.1                rstudioapi_0.7                curl_3.2                     
 [77] png_0.1-7                     interactiveDisplayBase_1.16.0 tibble_1.4.2                  stringi_1.2.4                
 [81] GenomicFeatures_1.30.3        lattice_0.20-35               ProtGenerics_1.10.0           Matrix_1.2-14                
 [85] pillar_1.3.0                  data.table_1.11.8             bitops_1.0-6                  httpuv_1.4.5.9000            
 [89] R6_2.2.2                      latticeExtra_0.6-28           epivizrData_1.6.0             RMySQL_0.10.15               
 [93] promises_1.0.1                KernSmooth_2.23-15            gridExtra_2.3                 MASS_7.3-50                  
 [97] gtools_3.8.1                  assertthat_0.2.0              chron_2.3-53                  SummarizedExperiment_1.8.1   
[101] proto_1.0.0                   rjson_0.2.20                  withr_2.1.2                   GenomicAlignments_1.14.2     
[105] Rsamtools_1.30.0              GenomeInfoDbData_1.0.0        hms_0.4.2                     grid_3.5.1                   
[109] rpart_4.1-13                  Biobase_2.38.0                base64enc_0.1-3 

0 个答案:

没有答案