rGenomeTracks

rGenomeTracks package leverages the power of pyGenomeTracks software with the interactivity of R. pyGenomeTracks is a python software that offers robust method for visualizing epigenetic data files like narrowPeak, Hic matrix, TADs and arcs, however though, here is no way currently to use it within R interactive session. rGenomeTracks wrapped the whole functionality of pyGenomeTracks with additional utilites to make to more pleasant for R users.

# loading the rGenomeTracks
library(rGenomeTracks)
# loading example data
#library(rGenomeTracksData)

Installing PyGenomeTracks

You should have pyGenomeTracks installed on R’s loading environment. To avoid dependency clash, we highly recommend using install_pyGenomeTracks(). That way, you ensure using the tested pyGenomeTracks version with the current release. rGenomeTracks is supposed to automatically prompt you to install this dependency after running plot_gtracks(). If this step failed, you can manually install pyGenomeTracks with install_pyGenomeTracks()

install_pyGenomeTracks()

Principle

rGenomeTracks deals creates tracks in a class genome_track. Currently, there are 14 tracks available: 1. track_bed() 2. track_bedgraph() 3. track_bedgraph_matrix() 4. track_gtf() 5. track_hlines() 6. track_vlines() 7. track_spacer() 8. track_bigwig() 9. track_epilogos() 10. track_narrowPeak() 11. track_domains() 12. track_hic_matrix() 13. track_links() 14. track_scalebar() 15. track_x_axis()

Please refer to the help page for each one of them for details and examples.

We will download .h5 matrix and store the location in temporary directory for demonstration.

# Download h5 example
ah <- AnnotationHub()
query(ah, "rGenomeTracksData")
h5_dir <-  ah[["AH95901"]]

 # Create HiC track from HiC matrix
 h5 <- track_hic_matrix(
   file = h5_dir, depth = 250000, min_value = 5, max_value = 200,
   transform = "log1p", show_masked_bins = FALSE
 )

Other demonstration for TADS, arcs and bigwig data will be loaded from the built-in package example data.

 # Load other examples
 tads_dir <- system.file("extdata", "tad_classification.bed", package = "rGenomeTracks")
 arcs_dir <- system.file("extdata", "links2.links", package = "rGenomeTracks")
 bw_dir <- system.file("extdata", "bigwig2_X_2.5e6_3.5e6.bw", package = "rGenomeTracks")
 
 # Create TADS track
 tads <- track_domains(
   file = tads_dir, border_color = "black",
   color = "none", height = 5,
   line_width = 5,
   show_data_range = FALSE,
   overlay_previous = "share-y"
 )

 # Create arcs track
 arcs <- track_links(
   file = arcs_dir, links_type = "triangles",
   line_style = "dashed",
   overlay_previous = "share-y",
   color = "darkred",
   line_width = 3,
   show_data_range = FALSE
 )

 # Create bigwig track
 bw <- track_bigwig(
   file = bw_dir, color = "red",
   max_value = 50,
   min_value = 0,
   height = 4,
   overlay_previous = "no",
   show_data_range = FALSE
 )

genome_track objects can be added together using + function.

 # Create one object from HiC, arcs and bigwid
 tracks <- tads + arcs + bw

The track(s) to be plotted is to be passed to plot_gtracks() for the generation of the plot. Additionally, plot_gtracks() requires the genomic region to be plotted. Optionally, you can set plot title, dpi, width, height, fontsize, track-to-label fraction, label alignment position, and directory to save the plot.

 # Plot the tracks
## Note to verify installing miniconda if not installed.

 layout(matrix(c(1,1,2,3,4,4), nrow = 3, ncol = 2, byrow = TRUE))
 plot_gtracks(tracks, chr = "X", start = 25 * 10^5, end = 31 * 10^5)

# Plot HiC, TADS and bigwig tracks
 plot_gtracks(h5 + tads + bw, chr = "X", start = 25 * 10^5, end = 31 * 10^5)

Tips

Quickly create multiple tracks

If you have tracks with the same format, you can import them quickly by using lapply() and reduce() functions.

You can repeat this process for tracks of same category then pass the tracks to plot_gtracks()

Create complex layout figures

You may choose create a complex figure using layout() and split.screen() function then save the device.

Note that you cannot make use of dir argument in plot_gtracks() if you used this method as it is passed to pyGenomeTracks. So, you have to capture R’s graphic device and save it manually.

Session Information

sessionInfo()
#> R version 4.2.0 RC (2022-04-21 r82226)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.4 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
#> LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB              LC_COLLATE=C              
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] rGenomeTracks_1.3.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] igraph_1.3.1             Rcpp_1.0.8.3             rGenomeTracksData_0.99.0
#>  [4] knitr_1.38               magrittr_2.0.3           lattice_0.20-45         
#>  [7] R6_2.5.1                 jpeg_0.1-9               rlang_1.0.2             
#> [10] fastmap_1.1.0            highr_0.9                stringr_1.4.0           
#> [13] tools_4.2.0              grid_4.2.0               xfun_0.30               
#> [16] png_0.1-7                cli_3.3.0                jquerylib_0.1.4         
#> [19] htmltools_0.5.2          yaml_2.3.5               digest_0.6.29           
#> [22] Matrix_1.4-1             bmp_0.3                  purrr_0.3.4             
#> [25] sass_0.4.1               evaluate_0.15            tiff_0.1-11             
#> [28] rmarkdown_2.14           readbitmap_0.1.5         stringi_1.7.6           
#> [31] compiler_4.2.0           bslib_0.3.1              imager_0.42.13          
#> [34] reticulate_1.24          jsonlite_1.8.0           pkgconfig_2.0.3