| Title: | An R Interface to the JBrowse 2 Genome Browser |
| Version: | 0.10.2 |
| Description: | Provides an R interface to the JBrowse 2 genome browser. Enables embedding a JB2 genome browser in a Shiny app or R Markdown document. The browser can also be launched from an interactive R console. The browser can be loaded with a variety of common genomics data types, and can be used with a custom theme. |
| License: | Apache License (≥ 2) |
| URL: | https://gmod.github.io/JBrowseR/ https://github.com/GMOD/JBrowseR |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.1.2 |
| Imports: | htmltools, htmlwidgets, reactR, stringr, magrittr, readr, jsonlite, httpuv, mime, cli, ids, dplyr |
| Suggests: | testthat (≥ 3.0.0), knitr, rmarkdown |
| Config/testthat/edition: | 3 |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2023-12-20 16:45:54 UTC; cdiesh |
| Author: | Elliot Hershberg 
[aut],
Colin Diesh [aut,
cre],
the JBrowse 2 Team [aut] |
| Maintainer: | Colin Diesh <colin.diesh@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2023-12-20 17:20:06 UTC |
Pipe operator
Description
See magrittr::%>% for details.
Usage
lhs %>% rhs
R interface to JBrowse 2 genome browser
Description
Embed a JBrowse 2 linear genome view in your Shiny app, Rmd document, or interactive R console.
Usage
JBrowseR(view, ..., width = NULL, height = NULL, elementId = NULL)
Arguments
view |
Which JBrowse 2 view to use. View, JsonView, ViewHg19, ViewHg38 |
... |
The parameters passed on to the view |
width |
The width of the htmlwidget |
height |
The height of the htmlwidget |
elementId |
The elementId of the htmlwidget |
Value
an htmlwidget of the JBrowse 2 linear genome view.
Shiny bindings for JBrowseR
Description
Output and render functions for using JBrowseR within Shiny applications and interactive Rmd documents.
Usage
JBrowseROutput(outputId, width = "100%", height = "400px")
renderJBrowseR(expr, env = parent.frame(), quoted = FALSE)
JBrowseR_html(id, style, class, ...)
Arguments
outputId |
output variable to read from |
width |
Must be a valid CSS unit or a number, which will be coerced to a string and have |
height |
Must be a valid CSS unit or a number, which will be coerced to a string and have |
expr |
An expression that generates a JBrowseR |
env |
The environment in which to evaluate |
quoted |
Is |
id |
htmltools id |
style |
htmltools style |
class |
htmltools class |
... |
Additional arguments passed on |
Value
the Shiny UI bindings for a JBrowseR htmlwidget
the Shiny server bindings for a JBrowseR htmlwidget
the root HTML element to render the React component in
Create an assembly for a custom JBrowse view
Description
Creates the necessary configuration string for an indexed fasta or bgzip fasta so that it can be used as the assembly in a JBrowse custom linear genome view.
Usage
assembly(assembly_data, bgzip = FALSE, aliases = NULL, refname_aliases = NULL)
Arguments
assembly_data |
the URL to your fasta file |
bgzip |
whether or not your fasta is bgzip compressed |
aliases |
a vector of strings of the aliases for the assembly |
refname_aliases |
the URL to a file containing reference name aliases. For more info see https://jbrowse.org/jb2/docs/config_guide#configuring-reference-name-aliasing |
Details
The string returned by assembly is stringified JSON.
JBrowseR is an interface to JBrowse 2, which receives its
configuration in JSON format. The stringified JSON returned
by assembly is parsed into a JavaScript object in the
browser, and is used to configure the genome browser.
It is important to note that while only the fasta file is
passed as an argument, assembly assumes that a fasta
index of the same name is located with the fasta file (as
well as a gzi file in the case of a bgzip fasta).
For example:
assembly("data/hg38.fa")
Assumes that data/hg38.fa.fai also exists.
assembly("data/hg38.fa", bgzip = TRUE)
Assumes that data/hg38.fa.fai and data/hg38.fa.gzi both exist.
This is a JBrowse 2 convention, and the default naming output of samtools and bgzip.
For more information on creating these files, visit https://jbrowse.org/jb2/docs/quickstart_web#adding-a-genome-assembly
Value
a character vector of JBrowseR assembly configuration
Examples
assembly("https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", bgzip = TRUE)
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 |
displayed_tracks |
a vector of tracks generated by a |
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)
)
Read in a JBrowse 2 JSON configuration file
Description
Reads in a JSON file with values for configuring your browser. Looks for assembly, tracks, defaultSession, and theme. Only assembly is explicitly required for a working browser.
Usage
json_config(file)
Arguments
file |
the file path or URL to a JBrowse 2 configuration |
Details
Note: this is the most advanced API. It offers full control to do anything possible in JavaScript with an embedded JBrowse 2 React component, but comes with a steeper learning curve. For more details on JBrowse 2 configuration, visit: https://jbrowse.org/jb2/docs/config_guide
An example JSON config is provided with this package
Value
a character vector of JSON configuration from a JBrowse 2 configuration file
Examples
## Not run: json_config("./config.json")
Serve a local data directory for use with a browser
Description
This is a utility function that can be used to server a local directory with data so that it can be used in the genome browser.
Usage
serve_data(path, port = 5000)
Arguments
path |
The path to the directory with data to serve |
port |
The port to serve the directory on |
Details
Note: This is intended for local development and use. For a production deployment, refer to the vignette on creating URLs for more robust options.
Value
a list containing information about the newly created HTTP server including the host, port, interval, and URL. The list also contains the stop_server() function which can be used to stop the server
Examples
## Not run:
server <- serve_data("~/path/to/my-data")
# use server$stop_server() to stop
## End(Not run)
Create configuration for a JBrowse 2 text index
Description
Creates the necessary configuration string for an adapter to a text index for gene name search in the browser.
Usage
text_index(ix_uri, ixx_uri, meta_uri, assembly)
Arguments
ix_uri |
the URI for the ix file |
ixx_uri |
the URI for the ixx file |
meta_uri |
the URI for the JSON metadata file |
assembly |
the assembly associated with the text index |
Details
Note: this function currently only supports aggregate indices.
For more information on JBrowse 2 text indices, visit: https://jbrowse.org/jb2/docs/config_guide/#text-searching
Value
a character vector with the JSON text index adapter.
Examples
text_index(
"https://jbrowse.org/genomes/hg19/trix/hg19.ix",
"https://jbrowse.org/genomes/hg19/trix/hg19.ixx",
"https://jbrowse.org/genomes/hg19/trix/meta.json",
"hg19"
)
Create a theme for a custom JBrowse 2 view
Description
Creates the necessary configuration string for a custom theme palette for your browser. Accepts up to four hexadecimal colors. For more information on how JBrowse 2 custom themes work, visit https://jbrowse.org/jb2/docs/config_guide#configuring-the-theme
Usage
theme(primary, secondary = NULL, tertiary = NULL, quaternary = NULL)
Arguments
primary |
the primary color of your custom palette |
secondary |
the secondary color of your custom palette |
tertiary |
the tertiary color of your custom palette |
quaternary |
the quaternary color of your custom palette |
Value
a character vector of stringified theme JSON configuration to configure a custom color palette for the browser
Examples
theme("#311b92")
theme("#311b92", "#0097a7")
theme("#311b92", "#0097a7", "#f57c00")
theme("#311b92", "#0097a7", "#f57c00", "#d50000")
Create an AlignmentsTrack for a custom JBrowse 2 view
Description
Creates the necessary configuration string for an indexed BAM or CRAM alignment so that it can be used in a JBrowse custom linear genome view.
Usage
track_alignments(track_data, assembly)
Arguments
track_data |
the URL to the BAM/CRAM alignments |
assembly |
the config string generated by |
Details
It is important to note that while only the BAM/CRAM file is
passed as an argument, tracks_alignment assumes that a BAM/CRAM
index of the same name is located with the file
For example:
track_alignments("data/alignments.bam")
Assumes that data/alignments.bam.bai also exists.
This is a JBrowse 2 convention, and the default naming output of samtools
For more information on creating an index with samtools, visit https://www.htslib.org/
Value
a character vector of stringified AlignmentsTrack JSON configuration
Examples
assembly <- assembly("https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", bgzip = TRUE)
track_alignments("alignments.bam", assembly)
track_alignments("alignments.cram", assembly)
Create a track from an R data frame for a custom JBrowse 2 view
Description
Creates the necessary configuration string for an R data frame so that it can be viewed as a track in a JBrowse custom linear genome view.
Usage
track_data_frame(track_data, track_name, assembly)
Arguments
track_data |
the data frame with track data. Must have cols:
|
track_name |
the name to use for the track |
assembly |
the config string generated by |
Value
a character vector of stringified track JSON configuration
Examples
assembly <- assembly("https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", bgzip = TRUE)
df <- data.frame(
chrom = c(1, 2),
start = c(123, 456),
end = c(789, 101112),
name = c('feature1', 'feature2')
)
track_data_frame(df, "my_features", assembly)
Create a FeatureTrack for a custom JBrowse 2 view
Description
Creates the necessary configuration string for an indexed GFF3 file so that it can be used in a JBrowse custom linear genome view.
Usage
track_feature(track_data, assembly)
Arguments
track_data |
the URL to the GFF3 file |
assembly |
the config string generated by |
Details
It is important to note that while only the GFF3 file is
passed as an argument, tracks_variant assumes that a GFF3
index of the same name is located with the file
For example:
track_feature("data/features.gff")
Assumes that data/features.gff.tbi also exists.
This is a JBrowse 2 convention, and the default naming output of tabix
For more information on creating an index with tabix, visit https://www.htslib.org/
Value
a character vector of stringified FeatureTrack JSON configuration
Examples
assembly <- assembly("https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", bgzip = TRUE)
track_feature("features.gff", assembly)
Create a VariantTrack for a custom JBrowse 2 view
Description
Creates the necessary configuration string for an indexed VCF file so that it can be used in a JBrowse custom linear genome view.
Usage
track_variant(track_data, assembly)
Arguments
track_data |
the URL to the VCF file |
assembly |
the config string generated by |
Details
It is important to note that while only the VCF file is
passed as an argument, tracks_variant assumes that a VCF
index of the same name is located with the file
For example:
track_alignments("data/variants.vcf")
Assumes that data/variants.vcf.tbi also exists.
This is a JBrowse 2 convention, and the default naming output of tabix
For more information on creating an index with tabix, visit https://www.htslib.org/
Value
a character vector of stringified VariantTrack JSON configuration
Examples
assembly <- assembly("https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", bgzip = TRUE)
track_variant("variants.vcf", assembly)
Create a WiggleTrack for a custom JBrowse 2 view
Description
Creates the necessary configuration string for a bigWig file so that it can be used in a JBrowse custom linear genome view.
Usage
track_wiggle(track_data, assembly)
Arguments
track_data |
the URL to the bigWig file |
assembly |
the config string generated by |
Value
a character vector of stringified WiggleTrack JSON configuration
Examples
track_wiggle(
"https://jbrowse.org/genomes/hg19/COLO829/colo_normal.bw",
assembly("https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", bgzip = TRUE)
)
Create a set of tracks for a custom JBrowse 2 view
Description
Accepts any number of tracks, returns the configuration string necessary to load these tracks into your JBrowse view.
Usage
tracks(...)
Arguments
... |
The tracks to be added to the JBrowse 2 view |
Value
a character vector of stringified JSON configuration for all tracks to add to the browser
Examples
# create an assembly configuration and alignments track
assembly <- assembly("https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", bgzip = TRUE)
alignments <- track_alignments("alignments.bam", assembly)
# create a tracks configuration with the alignments track
tracks(alignments)