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igvr's Introduction

igvR

igvR is an R package providing interactive connections to igv.js (the Integrative Genomics Viewer) running in a web browser.

alttag I am grateful to Jim Robinson, Helga Thorvaldsdóttir, Douglass Turner and colleagues for their fine work in igv.js, and their unfailing responsiveness to all requests and questions.

igvR is based upon the Bioconductor R package BrowserViz - of which it is a subclass. It offers easy interactive visual exploration of genomic data from R, including

  • Bed (annotation) and BedGraph (quantitative) tracks can be created out of R data.frames and GenomicRanges objects.
  • Aligment data from bam files via GAlignments objects offered by the GenomicAlignments class
  • variant data from VCF files via VCF objects offered by the VariantAnnotation class.
  • GWAS
  • any tabular data with genomic coordinates and a bed-like format

This work is motivated by our belief that contemporary web browsers, supporting HTML5 and Canvas, and running increasingly powerful Javascript libraries (Three.js, d3, igv.js and cytoscape.js) have become the best setting in which to develop interactive graphics for exploratory data analysis.

This package has a first cousin, igvShiny.
RStudio may at some point release a version of Shiny which, when launched, leaves the R console open for interactive commands. When that feature is available, I will merge igvR and igvShiny.

The package is fully documented here, with full function reference and many examples in vignettes (see the Articles menu).

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nathanweeks

igvr's Issues

Error with status 0 when following example from vignette

Hi!
I am trying to automate plotting of many seg files in IGV using R and trying out your package. Thank you for developing this tool!
I tried to follow the Introduction: a simple demo vignette found here, and encountered an error when running displayTrack(igv, track). Please see the screenshot. I am not sure what it refers to or where to start troubleshooting.
The exact code I was executing is:

library(igvR)
igv <- igvR()
setBrowserWindowTitle(igv, "simple igvR demo")
setGenome(igv, "hg38")
showGenomicRegion(igv, "MYC")
loc <- getGenomicRegion(igv)

tbl.bed <- data.frame(chrom=loc$chrom, start=loc$start + 2000, end=loc$end-2000,
                      name="simple.example", stringsAsFactors=FALSE)

track <- DataFrameAnnotationTrack("simple bed", tbl.bed, color="random")
displayTrack(igv, track)

I am connected to RStudio on remote server through ssh with X11 forwarding enabled. I am also attaching the session info - am I missing any dependencies to run the igvR package?

image

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-centos7-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /gsc/software/linux-x86_64-centos7/R-3.6.3/lib64/R/lib/libRblas.so
LAPACK: /gsc/software/linux-x86_64-centos7/R-3.6.3/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] igvR_1.6.1                  BrowserViz_2.8.0            httpuv_1.5.4                jsonlite_1.7.1             
 [5] GenomicAlignments_1.22.1    Rsamtools_2.2.3             Biostrings_2.54.0           XVector_0.26.0             
 [9] SummarizedExperiment_1.16.1 DelayedArray_0.12.3         BiocParallel_1.20.1         matrixStats_0.59.0         
[13] Biobase_2.46.0              GenomicRanges_1.38.0        GenomeInfoDb_1.22.1         IRanges_2.20.2             
[17] S4Vectors_0.24.4            BiocGenerics_0.32.0         ggthemes_4.2.4              forcats_0.5.1              
[21] stringr_1.4.0               dplyr_1.0.5                 purrr_0.3.4                 readr_1.4.0                
[25] tidyr_1.1.2                 tibble_3.0.4                ggplot2_3.3.2               tidyverse_1.3.0     

loaded via a namespace (and not attached):
 [1] bitops_1.0-6             fs_1.5.0                 lubridate_1.7.9.2        bit64_4.0.5             
 [5] progress_1.2.2           httr_1.4.2               tools_3.6.3              backports_1.1.9         
 [9] R6_2.5.0                 seqLogo_1.52.0           DBI_1.1.0                splitstackshape_1.4.8   
[13] colorspace_2.0-1         withr_2.3.0              prettyunits_1.1.1        tidyselect_1.1.0        
[17] curl_4.3                 bit_4.0.4                compiler_3.6.3           cli_2.5.0               
[21] rvest_0.3.6              xml2_1.3.2               rtracklayer_1.46.0       scales_1.1.1            
[25] askpass_1.1              rappdirs_0.3.1           digest_0.6.27            pkgconfig_2.0.3         
[29] BSgenome_1.54.0          dbplyr_2.0.0             rlang_0.4.10             readxl_1.3.1            
[33] rstudioapi_0.13          RSQLite_2.2.1            generics_0.1.0           VariantAnnotation_1.32.0
[37] RCurl_1.98-1.2           magrittr_2.0.1           GenomeInfoDbData_1.2.2   Matrix_1.2-18           
[41] Rcpp_1.0.5               munsell_0.5.0            lifecycle_1.0.0          stringi_1.5.3           
[45] zlibbioc_1.32.0          Rtsne_0.15               BiocFileCache_1.10.2     grid_3.6.3              
[49] blob_1.2.1               randomcoloR_1.1.0.1      promises_1.1.1           crayon_1.4.1            
[53] lattice_0.20-41          haven_2.3.1              GenomicFeatures_1.38.2   hms_0.5.3               
[57] pillar_1.4.7             biomaRt_2.42.1           reprex_0.3.0             XML_3.99-0.3            
[61] glue_1.4.2               V8_3.4.2                 data.table_1.13.2        BiocManager_1.30.10     
[65] modelr_0.1.8             vctrs_0.3.7              cellranger_1.1.0         openssl_1.4.3           
[69] gtable_0.3.0             assertthat_0.2.1         broom_0.7.2              later_1.1.0.1           
[73] MotifDb_1.28.0           AnnotationDbi_1.48.0     memoise_1.1.0            cluster_2.1.0           
[77] ellipsis_0.3.1

Is there a way to use setCustomGenome without URL?

Hi,

My reference files and index files both sit on the server I am working on. I was wondering if there is a way for me to use them without giving url but instead giving path to the file which contains the reference fasta. How do I go about it for igvR?

Thank you
Saad

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