Package 'igvShiny' reference manual

Title:	igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)
Description:	This package is a wrapper of Integrative Genomics Viewer (IGV). It comprises an htmlwidget version of IGV. It can be used as a module in Shiny apps.
Authors:	Paul Shannon [aut], Arkadiusz Gladki [aut, cre] , Karolina Scigocka [aut]
Maintainer:	Arkadiusz Gladki <[email protected]>
License:	MIT + file LICENSE
Version:	1.1.0
Built:	2024-06-30 02:42:17 UTC
Source:	https://github.com/bioc/igvShiny

display the already constructed and configured track

Description

display the already constructed and configured track

Usage

## S4 method for signature 'GWASTrack'
display(obj, session, id, deleteTracksOfSameName = TRUE)
## S4 method for signature 'GWASTrack'
display(obj, session, id, deleteTracksOfSameName = TRUE)

Arguments

`obj`	An object of class GWASTrack
`session`	a Shiny session object
`id`	character the identifier of the target igv object in the browser
`deleteTracksOfSameName`	logical to avoid duplications in track names

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

get_basic_genomes

Description

a helper function for basic genomes, obtains the genome codes (e.g. 'hg38')

Usage

get_basic_genomes()
get_basic_genomes()

Value

an list of short genome codes, e.g., "hg38", "dm6"

Examples

bs <- get_basic_genomes()

bs <- get_basic_genomes()

get_cas_genomes

Description

a helper function for common always available stock genomes, obtains the genome codes (e.g. 'hg38')

Usage

get_cas_genomes()
get_cas_genomes()

Value

an list of short genome codes, e.g., "hg38", "dm6"

Examples

cas <- get_cas_genomes()

cas <- get_cas_genomes()

get_css_genomes

Description

a helper function for mostly internal use, obtains the genome codes (e.g. 'hg38') supported by igv.js

Usage

get_css_genomes(test = FALSE)
get_css_genomes(test = FALSE)

Arguments

test

logical(1) defaults to FALSE

Value

an list of short genome codes, e.g., "hg38", "dm6", "tair10"

Examples

css <- get_css_genomes(test = TRUE)

css <- get_css_genomes(test = TRUE)

get_tracks_dir Get the directory where tracks are stored. The directory can be defined with environmental variable. If not defined the default is a directory called "tracks" in the temp directory. We need a local directory to write files - for instance, a vcf file representing a genomic region of interest. We then tell shiny about that directory, so that shiny's built-in http server can serve up files we write there, ultimately consumed by igv.js

Description

get_tracks_dir Get the directory where tracks are stored. The directory can be defined with environmental variable. If not defined the default is a directory called "tracks" in the temp directory. We need a local directory to write files - for instance, a vcf file representing a genomic region of interest. We then tell shiny about that directory, so that shiny's built-in http server can serve up files we write there, ultimately consumed by igv.js

Usage

get_tracks_dir(env_var = "TRACKS_DIR")
get_tracks_dir(env_var = "TRACKS_DIR")

Arguments

env_var

The name of the environmental variable to use.

Value

string with the path to the tracks directory.

Examples

gtd <- get_tracks_dir(env_var = "TRACKS_DIR")

gtd <- get_tracks_dir(env_var = "TRACKS_DIR")

the url of the gwas table

Description

the url of the gwas table

Usage

## S4 method for signature 'GWASTrack'
getUrl(obj)
## S4 method for signature 'GWASTrack'
getUrl(obj)

Arguments

obj

An object of class GWASTrack

Value

character

Examples

file <-
  # a local gwas file
  system.file(package = "igvShiny", "extdata", "gwas-5k.tsv.gz")
tbl.gwas <- read.table(file,
                       sep = "\t",
                       header = TRUE,
                       quote = "")
track <-
  GWASTrack(
    "gwas 5k",
    tbl.gwas,
    chrom.col = 12,
    pos.col = 13,
    pval.col = 28
  )
getUrl(track)

file <-
  # a local gwas file
  system.file(package = "igvShiny", "extdata", "gwas-5k.tsv.gz")
tbl.gwas <- read.table(file,
                       sep = "\t",
                       header = TRUE,
                       quote = "")
track <-
  GWASTrack(
    "gwas 5k",
    tbl.gwas,
    chrom.col = 12,
    pos.col = 13,
    pval.col = 28
  )
getUrl(track)

Constructor for GWASTrack

Description

GWASTrack creates an IGV manhattan track from GWAS data

Usage

GWASTrack(
  trackName,
  data,
  chrom.col,
  pos.col,
  pval.col,
  trackHeight = 50,
  autoscale = TRUE,
  minY = 0,
  maxY = 30
)
GWASTrack(
  trackName,
  data,
  chrom.col,
  pos.col,
  pval.col,
  trackHeight = 50,
  autoscale = TRUE,
  minY = 0,
  maxY = 30
)

Arguments

`trackName`	A character string, used as track label by igv, we recommend unique names per track.
`data`	a data.frame or a url pointing to one, whose structure is described by chrom.col, pos.col, pval.col
`chrom.col`	numeric, the column number of the chromosome column
`pos.col`	numeric, the column number of the position column
`pval.col`	numeric, the column number of the GWAS pvalue column
`trackHeight`	numeric in pixels
`autoscale`	logical
`minY`	numeric for explicit (non-auto) scaling
`maxY`	numeric for explicit (non-auto) scaling

Value

A GWASTrack object

Examples

file <-
  # a local gwas file
  system.file(package = "igvShiny", "extdata", "gwas-5k.tsv.gz")
tbl.gwas <- read.table(file,
                       sep = "\t",
                       header = TRUE,
                       quote = "")
dim(tbl.gwas)
track <-
  GWASTrack(
    "gwas 5k",
    tbl.gwas,
    chrom.col = 12,
    pos.col = 13,
    pval.col = 28
  )
getUrl(track)

url <- "https://s3.amazonaws.com/igv.org.demo/gwas_sample.tsv.gz"
track <- GWASTrack(
  "remote url gwas",
  url,
  chrom.col = 3,
  pos.col = 4,
  pval.col = 10,
  autoscale = FALSE,
  minY = 0,
  maxY = 300,
  trackHeight = 100
)
getUrl(track)


file <-
  # a local gwas file
  system.file(package = "igvShiny", "extdata", "gwas-5k.tsv.gz")
tbl.gwas <- read.table(file,
                       sep = "\t",
                       header = TRUE,
                       quote = "")
dim(tbl.gwas)
track <-
  GWASTrack(
    "gwas 5k",
    tbl.gwas,
    chrom.col = 12,
    pos.col = 13,
    pval.col = 28
  )
getUrl(track)

url <- "https://s3.amazonaws.com/igv.org.demo/gwas_sample.tsv.gz"
track <- GWASTrack(
  "remote url gwas",
  url,
  chrom.col = 3,
  pos.col = 4,
  pval.col = 10,
  autoscale = FALSE,
  minY = 0,
  maxY = 300,
  trackHeight = 100
)
getUrl(track)

Create an igvShiny instance

Description

This function is called in the server function of your shiny app

Usage

igvShiny(
  genomeOptions,
  width = NULL,
  height = NULL,
  elementId = NULL,
  displayMode = "squished",
  tracks = list()
)
igvShiny(
  genomeOptions,
  width = NULL,
  height = NULL,
  elementId = NULL,
  displayMode = "squished",
  tracks = list()
)

Arguments

`genomeOptions`	a list with these fields: genomeName, initialLocus, annotation, dataMode, fasta, fastaIndex, stockGenome, validated
`width`	a character string, standard css notations, either e.g., "1000px" or "95%"
`height`	a character string, needs to be an explicit pixel measure, e.g., "800px"
`elementId`	a character string, the html element id within which igv is created
`displayMode`	a character string, default "SQUISHED".
`tracks`	a list of track specifications to be created and displayed at startup

Value

the created widget

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

create the UI for the widget

Description

This function is called in the ui function of your shiny app

Usage

igvShinyOutput(outputId, width = "100%", height = NULL)
igvShinyOutput(outputId, width = "100%", height = NULL)

Arguments

`outputId`	a character string, specifies the html element id
`width`	a character string, standard css notations, either e.g., "1000px" or "95%", "100%" by default
`height`	a character string, needs to be an explicit pixel measure, e.g., "800px", "400px" by default

Value

the created widget's html

Examples

io <- igvShinyOutput("igvOut")

io <- igvShinyOutput("igvOut")

load GenomicAlignments data as an igv.js alignment track

Description

load GenomicAlignments data as an igv.js alignment track

Usage

loadBamTrackFromLocalData(
  session,
  id,
  trackName,
  data,
  deleteTracksOfSameName = TRUE,
  displayMode = "EXPANDED"
)
loadBamTrackFromLocalData(
  session,
  id,
  trackName,
  data,
  deleteTracksOfSameName = TRUE,
  displayMode = "EXPANDED"
)

Arguments

`session`	an environment or list, provided and managed by shiny
`id`	character string, the html element id of this widget instance
`trackName`	character string
`data`	GenomicAlignments object
`deleteTracksOfSameName`	logical, default TRUE
`displayMode`	character string, possible values are "EXPANDED"(default), "SQUISHED" or "COLLAPSED"

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

load a bam track which, with index, is served up by http

Description

load a remote bam track

Usage

loadBamTrackFromURL(
  session,
  id,
  trackName,
  bamURL,
  indexURL,
  deleteTracksOfSameName = TRUE,
  displayMode = "EXPANDED",
  showAllBases = FALSE
)
loadBamTrackFromURL(
  session,
  id,
  trackName,
  bamURL,
  indexURL,
  deleteTracksOfSameName = TRUE,
  displayMode = "EXPANDED",
  showAllBases = FALSE
)

Arguments

`session`	an environment or list, provided and managed by shiny
`id`	character string, the html element id of this widget instance
`trackName`	character string
`bamURL`	character string http url for the bam file, typically very large
`indexURL`	character string http url for the bam file index, typically small
`deleteTracksOfSameName`	logical, default TRUE
`displayMode`	character string, possible values are "EXPANDED"(default), "SQUISHED" or "COLLAPSED"
`showAllBases`	logical, show all bases in the alignment, default FALSE

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

load a scored genome annotation track provided as a data.frame

Description

load a genome annotation track provided as a data.frame

Usage

loadBedGraphTrack(
  session,
  id,
  trackName,
  tbl,
  color = "gray",
  trackHeight = 30,
  autoscale,
  autoscaleGroup = -1,
  min = NA_real_,
  max = NA_real_,
  deleteTracksOfSameName = TRUE,
  quiet = TRUE
)
loadBedGraphTrack(
  session,
  id,
  trackName,
  tbl,
  color = "gray",
  trackHeight = 30,
  autoscale,
  autoscaleGroup = -1,
  min = NA_real_,
  max = NA_real_,
  deleteTracksOfSameName = TRUE,
  quiet = TRUE
)

Arguments

`session`	an environment or list, provided and managed by shiny
`id`	character string, the html element id of this widget instance
`trackName`	character string
`tbl`	data.frame, with at least "chrom" "start" "end" "score" columns
`color`	character string, a legal CSS color, or "random", "gray" by default
`trackHeight`	an integer, 30 (pixels) by default
`autoscale`	logical
`autoscaleGroup`	numeric(1) defaults to -1
`min`	numeric, consulted when autoscale is FALSE
`max`	numeric, consulted when autoscale is FALSE
`deleteTracksOfSameName`	logical, default TRUE
`quiet`	logical, default TRUE, controls verbosity

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

load a bedgraph track from a URL

Description

load a bedgraph track provided as a data.frame

Usage

loadBedGraphTrackFromURL(
  session,
  id,
  trackName,
  url,
  color = "gray",
  trackHeight = 30,
  autoscale = TRUE,
  min = 0,
  max = 1,
  autoscaleGroup = -1,
  deleteTracksOfSameName = TRUE,
  quiet = TRUE
)
loadBedGraphTrackFromURL(
  session,
  id,
  trackName,
  url,
  color = "gray",
  trackHeight = 30,
  autoscale = TRUE,
  min = 0,
  max = 1,
  autoscaleGroup = -1,
  deleteTracksOfSameName = TRUE,
  quiet = TRUE
)

Arguments

`session`	an environment or list, provided and managed by shiny
`id`	character string, the html element id of this widget instance
`trackName`	character string
`url`	character
`color`	character string, a legal CSS color, or "random", "gray" by default
`trackHeight`	an integer, 30 (pixels) by default
`autoscale`	logical
`min`	numeric, consulted when autoscale is FALSE
`max`	numeric, consulted when autoscale is FALSE
`autoscaleGroup`	numeric(1) defaults to -1
`deleteTracksOfSameName`	logical(1) defaults to TRUE
`quiet`	logical, default TRUE, controls verbosity

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

load a bed track provided as a data.frame

Description

load a bed track provided as a data.frame

Usage

loadBedTrack(
  session,
  id,
  trackName,
  tbl,
  color = "",
  trackHeight = 50,
  deleteTracksOfSameName = TRUE,
  quiet = TRUE
)
loadBedTrack(
  session,
  id,
  trackName,
  tbl,
  color = "",
  trackHeight = 50,
  deleteTracksOfSameName = TRUE,
  quiet = TRUE
)

Arguments

`session`	an environment or list, provided and managed by shiny
`id`	character string, the html element id of this widget instance
`trackName`	character string
`tbl`	data.frame, with at least "chrom" "start" "end" columns
`color`	character string, a legal CSS color, or "random", "gray" by default
`trackHeight`	an integer, 50 (pixels) by default
`deleteTracksOfSameName`	logical, default TRUE
`quiet`	logical, default TRUE, controls verbosity

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

load a cram track which, with index, is served up by http

Description

load a remote cram track

Usage

loadCramTrackFromURL(
  session,
  id,
  trackName,
  cramURL,
  indexURL,
  deleteTracksOfSameName = TRUE
)
loadCramTrackFromURL(
  session,
  id,
  trackName,
  cramURL,
  indexURL,
  deleteTracksOfSameName = TRUE
)

Arguments

`session`	an environment or list, provided and managed by shiny
`id`	character string, the html element id of this widget instance
`trackName`	character string
`cramURL`	character string http url for the bam file, typically very large
`indexURL`	character string http url for the bam file index, typically small
`deleteTracksOfSameName`	logical, default TRUE

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

load a GFF3 track defined by local data

Description

load a local GFF3 track file

Usage

loadGFF3TrackFromLocalData(
  session,
  id,
  trackName,
  tbl.gff3,
  color = "gray",
  colorTable,
  colorByAttribute,
  displayMode,
  trackHeight = 50,
  visibilityWindow,
  deleteTracksOfSameName = TRUE
)
loadGFF3TrackFromLocalData(
  session,
  id,
  trackName,
  tbl.gff3,
  color = "gray",
  colorTable,
  colorByAttribute,
  displayMode,
  trackHeight = 50,
  visibilityWindow,
  deleteTracksOfSameName = TRUE
)

Arguments

`session`	an environment or list, provided and managed by shiny
`id`	character string, the html element id of this widget instance
`trackName`	character string
`tbl.gff3`	data.frame in standard 9-column GFF3 format
`color`	character #RGB or a recognized color name. ignored if colorTable and colorByAttribute provided
`colorTable`	list, mapping a gff3 attribute, typically biotype, to a color
`colorByAttribute`	character, name of a gff3 attribute in column 9, typically "biotype"
`displayMode`	character, "EXPANDED", "SQUISHED" or "COLLAPSED"
`trackHeight`	numeric defaults to 50
`visibilityWindow`	numeric, Maximum window size in base pairs for which indexed annotations or variants are displayed
`deleteTracksOfSameName`	logical, default TRUE

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo-GFF3.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo-GFF3.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

load a GFF3 track which, with index, is served up by http

Description

load a remote GFF3 track

Usage

loadGFF3TrackFromURL(
  session,
  id,
  trackName,
  gff3URL,
  indexURL,
  color = "gray",
  colorTable,
  colorByAttribute,
  displayMode,
  trackHeight = 50,
  visibilityWindow,
  deleteTracksOfSameName = TRUE
)
loadGFF3TrackFromURL(
  session,
  id,
  trackName,
  gff3URL,
  indexURL,
  color = "gray",
  colorTable,
  colorByAttribute,
  displayMode,
  trackHeight = 50,
  visibilityWindow,
  deleteTracksOfSameName = TRUE
)

Arguments

`session`	an environment or list, provided and managed by shiny
`id`	character string, the html element id of this widget instance
`trackName`	character string
`gff3URL`	character string http url for the bam file, typically very large
`indexURL`	character string http url for the bam file index, typically small
`color`	character #RGB or a recognized color name. ignored if colorTable and colorByAttribute provided
`colorTable`	list, mapping a gff3 attribute, typically biotype, to a color
`colorByAttribute`	character, name of a gff3 attribute in column 9, typically "biotype"
`displayMode`	character, "EXPANDED", "SQUISHED" or "COLLAPSED"
`trackHeight`	numeric defaults to 50
`visibilityWindow`	numeric, Maximum window size in base pairs for which indexed annotations or variants are displayed
`deleteTracksOfSameName`	logical, default TRUE

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo-GFF3.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo-GFF3.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

load a GWAS (genome-wide association study) track provided as a data.frame

Description

load a GWAS (genome-wide association study) track provided as a data.frame

Usage

loadGwasTrack(
  session,
  id,
  trackName,
  tbl.gwas,
  ymin = 0,
  ymax = 35,
  deleteTracksOfSameName = TRUE
)
loadGwasTrack(
  session,
  id,
  trackName,
  tbl.gwas,
  ymin = 0,
  ymax = 35,
  deleteTracksOfSameName = TRUE
)

Arguments

`session`	an environment or list, provided and managed by shiny
`id`	character string, the html element id of this widget instance
`trackName`	character string
`tbl.gwas`	data.frame, with at least "chrom" "start" "end" columns
`ymin`	numeric defaults to 0
`ymax`	numeric defaults to 35
`deleteTracksOfSameName`	logical, default TRUE

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

load a seg track provided as a data.frame

Description

load a SEG track provided as a data.frame. igv "displays segmented data as a blue-to-red heatmap where the data range is -1.5 to 1.5... The segmented data file format is the output of the Circular Binary Segmentation algorithm (Olshen et al., 2004)".

Usage

loadSegTrack(session, id, trackName, tbl, deleteTracksOfSameName = TRUE)
loadSegTrack(session, id, trackName, tbl, deleteTracksOfSameName = TRUE)

Arguments

`session`	an environment or list, provided and managed by shiny
`id`	character string, the html element id of this widget instance
`trackName`	character string
`tbl`	data.frame, with at least "chrom" "start" "end" "score" columns
`deleteTracksOfSameName`	logical, default TRUE

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

load a VCF (variant) track provided as a Bioconductor VariantAnnotation object

Description

load a VCF (variant) track provided as a Bioconductor VariantAnnotation object

Usage

loadVcfTrack(session, id, trackName, vcfData, deleteTracksOfSameName = TRUE)
loadVcfTrack(session, id, trackName, vcfData, deleteTracksOfSameName = TRUE)

Arguments

`session`	an environment or list, provided and managed by shiny
`id`	character string, the html element id of this widget instance
`trackName`	character string
`vcfData`	VariantAnnotation object
`deleteTracksOfSameName`	logical, default TRUE

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo-withVCF.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo-withVCF.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

parseAndValidateGenomeSpec

Description

a helper function for internal use by the igvShiny constructor, but possible also of use to those building an igvShiny app, to test their genome specification for validity

Usage

parseAndValidateGenomeSpec(
  genomeName,
  initialLocus = "all",
  stockGenome = TRUE,
  dataMode = NA,
  fasta = NA,
  fastaIndex = NA,
  genomeAnnotation = NA
)
parseAndValidateGenomeSpec(
  genomeName,
  initialLocus = "all",
  stockGenome = TRUE,
  dataMode = NA,
  fasta = NA,
  fastaIndex = NA,
  genomeAnnotation = NA
)

Arguments

`genomeName`	character usually one short code of a supported ("stock") genome (e.g., "hg38") or for a user-supplied custom genome, the name you wish to use
`initialLocus`	character default "all", otherwise "chrN:start-end" or a recognized gene symbol
`stockGenome`	logical default TRUE
`dataMode`	character either "stock", "localFile" or "http"
`fasta`	character when supplying a custom (non-stock) genome, either a file path or a URL
`fastaIndex`	character when supplying a custom (non-stock) genome, either a file path or a URL, essential for all but the very small custom genomes.
`genomeAnnotation`	character when supplying a custom (non-stock) genome, a file path or URL pointing to a genome annotation file in a gff3 format

Value

an options list directly usable by igvApp.js, and thus igv.js

Examples

genomeSpec <-
  parseAndValidateGenomeSpec("hg38", "APOE")  # the simplest case
base.url <-
  "https://gladki.pl/igvr/testFiles/sarsGenome"
fasta.file <-
  sprintf("%s/%s", base.url, "Sars_cov_2.ASM985889v3.dna.toplevel.fa")
fastaIndex.file <-
  sprintf("%s/%s",
          base.url,
          "Sars_cov_2.ASM985889v3.dna.toplevel.fa.fai")
annotation.file <-
  sprintf("%s/%s", base.url, "Sars_cov_2.ASM985889v3.101.gff3")
custom.genome.title <- "SARS-CoV-2"
genomeOptions <-
  parseAndValidateGenomeSpec(
    genomeName = custom.genome.title,
    initialLocus = "all",
    stockGenome = FALSE,
    dataMode = "http",
    fasta = fasta.file,
    fastaIndex = fastaIndex.file,
    genomeAnnotation = annotation.file
  )

genomeSpec <-
  parseAndValidateGenomeSpec("hg38", "APOE")  # the simplest case
base.url <-
  "https://gladki.pl/igvr/testFiles/sarsGenome"
fasta.file <-
  sprintf("%s/%s", base.url, "Sars_cov_2.ASM985889v3.dna.toplevel.fa")
fastaIndex.file <-
  sprintf("%s/%s",
          base.url,
          "Sars_cov_2.ASM985889v3.dna.toplevel.fa.fai")
annotation.file <-
  sprintf("%s/%s", base.url, "Sars_cov_2.ASM985889v3.101.gff3")
custom.genome.title <- "SARS-CoV-2"
genomeOptions <-
  parseAndValidateGenomeSpec(
    genomeName = custom.genome.title,
    initialLocus = "all",
    stockGenome = FALSE,
    dataMode = "http",
    fasta = fasta.file,
    fastaIndex = fastaIndex.file,
    genomeAnnotation = annotation.file
  )

remove tracks from the browser

Description

delete tracks on the browser

Usage

removeTracksByName(session, id, trackNames)
removeTracksByName(session, id, trackNames)

Arguments

`session`	an environment or list, provided and managed by shiny
`id`	character string, the html element id of this widget instance
`trackNames`	a vector of character strings

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

remove only those tracks explicitly added by your app

Description

remove only those tracks explicitly added by your app. stock tracks (i.e., #' Refseq Genes) remain

Usage

removeUserAddedTracks(session, id)
removeUserAddedTracks(session, id)

Arguments

`session`	an environment or list, provided and managed by shiny
`id`	character string, the html element id of this widget instance

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

draw the igv genome browser element

Description

This function is called in the server function of your shiny app

Usage

renderIgvShiny(expr, env = parent.frame(), quoted = FALSE)
renderIgvShiny(expr, env = parent.frame(), quoted = FALSE)

Arguments

`expr`	an expression that generates an HTML widget
`env`	the environment in which to evaluate expr
`quoted`	logical flag indicating if expr a quoted expression

Value

an output or render function that enables the use of the widget within Shiny applications

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

focus igv on a region

Description

zoom in or out to show the nominated region, by chromosome locus or gene symbol

return the current region displayed by your igv instance

Usage

showGenomicRegion(session, id, region)

getGenomicRegion(session, id)
showGenomicRegion(session, id, region)

getGenomicRegion(session, id)

Arguments

`session`	an environment or list, provided and managed by shiny
`id`	character string, the html element id of this widget instance
`region`	a character string, either e.g. "chr5:92,221,640-92,236,523" or "MEF2C"

Value

a character string of format "chrom:start-end"

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

Package 'igvShiny'

Help Index

display the already constructed and configured track

Description

Usage

Arguments

Value

Examples

get_basic_genomes

Description

Usage

Value

Examples

get_cas_genomes

Description

Usage

Value

Examples

get_css_genomes

Description

Usage

Arguments

Value

Examples

Description

Usage

Arguments

Value

Examples

the url of the gwas table

Description

Usage

Arguments

Value

Examples

Constructor for GWASTrack

Description

Usage

Arguments

Value

Examples

Create an igvShiny instance

Description

Usage

Arguments

Value

Examples

create the UI for the widget

Description

Usage

Arguments

Value

Examples

load GenomicAlignments data as an igv.js alignment track

Description

Usage

Arguments

Value

Examples

load a bam track which, with index, is served up by http

Description

Usage

Arguments

Value

Examples

load a scored genome annotation track provided as a data.frame

Description

Usage

Arguments

Value

Examples

load a bedgraph track from a URL

Description

Usage

Arguments

Value

Examples

load a bed track provided as a data.frame

Description

Usage