default_session: Create a default session for a custom JBrowse view

In JBrowseR: An R Interface to the JBrowse 2 Genome Browser

Create a default session for a custom JBrowse view

Description

Creates the necessary configuration string for a default session for your browser. A default session is the set of tracks that are displayed when your browser is first displayed.

Usage

default_session(assembly, displayed_tracks, display_assembly = TRUE)

Arguments

assembly	the config string generated by assembly
displayed_tracks	a vector of tracks generated by a track_* command.
display_assembly	a boolean determining whether the reference sequence is visible or not. TRUE by default.

Value

a character vector of stringified JSON configuration for the defaultSession to be used by the browser when first loaded

Examples

# create the assembly configuration
assembly <- assembly("https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", bgzip = TRUE)

# create variant and wiggle tracks
variant <- track_variant(
 "clinvar.vcf.gz",
 assembly
)
wiggle <- track_wiggle(
 "read-cov.bw",
 assembly
)

# create a default session with those tracks open by default
default_session <- default_session(
 assembly,
 c(variant, wiggle)
)

JBrowseR documentation built on May 29, 2024, 11:26 a.m.