Visualizing Files with epivizrChart

This vignette demonstrates one of the new components added to epivizrChart, Epiviz-IGV-Track. This element uses IGV.js ( to visualize tracks from files (local and remote).


Sample dataset to use for the vignette.


Lets initialize an environment element to a specific genomic location. We can add additional annotation tracks (Homo.sapiens) and a blocks track from the example datasets.

epiviz_env <- epivizEnv(chr="chr11", start=118000000, end=121000000)
genes_track <- epiviz_env$plot(Homo.sapiens)
blocks_track <- epiviz_env$plot(tcga_colon_blocks, datasource_name="450kMeth")

We will create an R/BioConductor file object for the file we would like to visualize. We currently support BedFiles, BamFiles and BigWigFiles.

file1 <- Rsamtools::BamFile("")
file2 <- rtracklayer::BEDFile("")

Finally, we will plot the file object and when we render the environment element we will now see an IGV Track on the markdown document.

Note: IGV.js has issues with the web browser embedded in R-Studio. Please open the markdown document in firefox/chrome to visualize the tracks.

epiviz_igv <- epiviz_env$plot(
                  datasource_name = "genes2",
                  chr="chr11", start=118000000, end=121000000)


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epivizrChart documentation built on Nov. 8, 2020, 8:02 p.m.