pricelab / igvr Goto Github PK

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)

> 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