| Title: | igvR: integrative genomics viewer |
|---|---|
| Description: | Access to igv.js, the Integrative Genomics Viewer running in a web browser. |
| Authors: | Paul Shannon |
| Maintainer: | Arkadiusz Gladki <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.25.0 |
| Built: | 2024-06-30 06:44:30 UTC |
| Source: | https://github.com/bioc/igvR |
BedpeInteractionsTrack creates an IGV track for two-location annotations
BedpeInteractionsTrack( trackName, table, color = "darkBlue", trackHeight = 50, displayMode = "EXPANDED", visibilityWindow = 1e+05 )BedpeInteractionsTrack( trackName, table, color = "darkBlue", trackHeight = 50, displayMode = "EXPANDED", visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
table |
data.frame of 6 or more columns |
color |
A css color name (e.g., "red" or "#FF0000" |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
displayMode |
"COLLAPSED", "SQUISHED" or "EXPANDED". Spelling and case must be precise. |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
A BedpeInteractionsTrack object
#---------------------------- # first, from a local file #---------------------------- file <- system.file(package="igvR", "extdata", "sixColumn-demo1.bedpe") tbl.bedpe <- read.table(file, sep="\t", as.is=TRUE, header=TRUE) dim(tbl.bedpe) # 32 6 track <- BedpeInteractionsTrack("bedpe-6", tbl.bedpe) #------------------------------------------ # show the relevant portion of the genome #------------------------------------------ shoulder <- 10000 if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "Paired End Demo") roi <- with(tbl.bedpe, sprintf("%s:%d-%d", chrom1[1], min(start1)-shoulder, max(end2) + shoulder)) showGenomicRegion(igv, roi) displayTrack(igv, track) }#---------------------------- # first, from a local file #---------------------------- file <- system.file(package="igvR", "extdata", "sixColumn-demo1.bedpe") tbl.bedpe <- read.table(file, sep="\t", as.is=TRUE, header=TRUE) dim(tbl.bedpe) # 32 6 track <- BedpeInteractionsTrack("bedpe-6", tbl.bedpe) #------------------------------------------ # show the relevant portion of the genome #------------------------------------------ shoulder <- 10000 if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "Paired End Demo") roi <- with(tbl.bedpe, sprintf("%s:%d-%d", chrom1[1], min(start1)-shoulder, max(end2) + shoulder)) showGenomicRegion(igv, roi) displayTrack(igv, track) }
a helper function for mostly internal use, obtains the genome codes (e.g. 'hg38') supported by igv.js
currently.supported.stock.genomes(test = FALSE)currently.supported.stock.genomes(test = FALSE)
test |
logical |
an list of short genome codes, e.g., "hg38", "dm6", "tair10"
DataFrameAnnotationTrack creates an IGV track for bed objects imported using rtracklayer
DataFrameAnnotationTrack( trackName, annotation, color = "", displayMode = "SQUISHED", trackHeight = 50, expandedRowHeight = 30, squishedRowHeight = 15, maxRows = 500, searchable = FALSE, visibilityWindow = 1e+05 )DataFrameAnnotationTrack( trackName, annotation, color = "", displayMode = "SQUISHED", trackHeight = 50, expandedRowHeight = 30, squishedRowHeight = 15, maxRows = 500, searchable = FALSE, visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
annotation |
A base R |
color |
A CSS color name (e.g., "red" or "#FF0000"), leave as default empty string if supplying bed9 format with itemRgb. |
displayMode |
"COLLAPSED", "SQUISHED" or "EXPANDED". Spelling and case must be precise. |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
expandedRowHeight |
Height of each row of features in "EXPANDED" mode. |
squishedRowHeight |
Height of each row of features in "SQUISHED" mode, for compact viewing. |
maxRows |
of features to display |
searchable |
If TRUE, labels on annotation elements may be used in search |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
Detailed description goes here
A DataFrameAnnotationTrack object
base.loc <- 88883100 tbl <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=c("a", "b", "c"), score=runif(3), strand=rep("*", 3), stringsAsFactors=FALSE) track <- DataFrameAnnotationTrack("data.frame demo", tbl) if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "DataFrameAnnotationTrack demo") displayTrack(igv, track) roi <- sprintf("%s:%d-%d", tbl$chrom[1], min(tbl$start)-100, max(tbl$start) + 100) showGenomicRegion(igv, roi) Sys.sleep(1) zoomOut(igv) }base.loc <- 88883100 tbl <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=c("a", "b", "c"), score=runif(3), strand=rep("*", 3), stringsAsFactors=FALSE) track <- DataFrameAnnotationTrack("data.frame demo", tbl) if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "DataFrameAnnotationTrack demo") displayTrack(igv, track) roi <- sprintf("%s:%d-%d", tbl$chrom[1], min(tbl$start)-100, max(tbl$start) + 100) showGenomicRegion(igv, roi) Sys.sleep(1) zoomOut(igv) }
DataFrameQuantitativeTrack creates and IGV track for bed objects imported using rtracklayer
DataFrameQuantitativeTrack( trackName, quantitativeData, color = "blue", trackHeight = 50, autoscale, min = NA_real_, max = NA_real_, visibilityWindow = 1e+05 )DataFrameQuantitativeTrack( trackName, quantitativeData, color = "blue", trackHeight = 50, autoscale, min = NA_real_, max = NA_real_, visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
quantitativeData |
A base R |
color |
A CSS color name (e.g., "red" or "#FF0000") |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
autoscale |
Autoscale track to maximum value in view |
min |
Sets the minimum value for the data (y-axis) scale. Usually zero. |
max |
Sets the maximum value for the data (y-axis) scale. This value is ignored if autoscale is TRUE |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
Detailed description goes here
A DataFrameQuantitativeTrack object
DataFrameAnnotationTrack
GRangesQuantitativeTrack
GRangesAnnotationTrack
DataFrameAnnotationTrack
DataFrameQuantitativeTrack
GRangesAnnotationTrack
GRangesQuantitativeTrack
GenomicAlignmentTrack
UCSCBedAnnotationTrack
UCSCBedGraphQuantitativeTrack
VariantTrack
igvAnnotationTrack
base.loc <- 88883100 tbl.blocks <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), score=runif(3), stringsAsFactors=FALSE) track.blocks <- DataFrameQuantitativeTrack("blocks", tbl.blocks, autoscale=TRUE) locs <- seq(from=base.loc, length.out=1000) tbl.wig <- data.frame(chrom=rep("chr5", 1000), start=locs-1, end=locs, score=runif(n=1000, min=-1, max=1)) track.wig <- DataFrameQuantitativeTrack("wig", tbl.wig, autoscale=FALSE, min=min(tbl.wig$score), max=max(tbl.wig$score), color="random") if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "DataFrameQuantitativeTrack demo") displayTrack(igv, track.blocks) roi <- sprintf("%s:%d-%d", tbl.blocks$chrom[1], min(tbl.blocks$start)-1000, max(tbl.blocks$end) + 1000) showGenomicRegion(igv, roi) displayTrack(igv, track.wig) }base.loc <- 88883100 tbl.blocks <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), score=runif(3), stringsAsFactors=FALSE) track.blocks <- DataFrameQuantitativeTrack("blocks", tbl.blocks, autoscale=TRUE) locs <- seq(from=base.loc, length.out=1000) tbl.wig <- data.frame(chrom=rep("chr5", 1000), start=locs-1, end=locs, score=runif(n=1000, min=-1, max=1)) track.wig <- DataFrameQuantitativeTrack("wig", tbl.wig, autoscale=FALSE, min=min(tbl.wig$score), max=max(tbl.wig$score), color="random") if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "DataFrameQuantitativeTrack demo") displayTrack(igv, track.blocks) roi <- sprintf("%s:%d-%d", tbl.blocks$chrom[1], min(tbl.blocks$start)-1000, max(tbl.blocks$end) + 1000) showGenomicRegion(igv, roi) displayTrack(igv, track.wig) }
display the specified track in igv
## S4 method for signature 'igvR' displayTrack(obj, track, deleteTracksOfSameName = TRUE)## S4 method for signature 'igvR' displayTrack(obj, track, deleteTracksOfSameName = TRUE)
obj |
An object of class igvR |
track |
An object of some terminal (leaf) subclass of Track |
deleteTracksOfSameName |
logical, default TRUE |
""
if(interactive()){ igv <- igvR() setGenome(igv, "hg38") showGenomicRegion(igv, "MEF2C") base.loc <- 88883100 tbl <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=c("a", "b", "c"), score=runif(3), strand=rep("*", 3), stringsAsFactors=FALSE) track <- DataFrameAnnotationTrack("dataframeTest", tbl, color="red", displayMode="EXPANDED") showGenomicRegion(igv, "chr5:88,881,962-88,885,045") displayTrack(igv, track) }if(interactive()){ igv <- igvR() setGenome(igv, "hg38") showGenomicRegion(igv, "MEF2C") base.loc <- 88883100 tbl <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=c("a", "b", "c"), score=runif(3), strand=rep("*", 3), stringsAsFactors=FALSE) track <- DataFrameAnnotationTrack("dataframeTest", tbl, color="red", displayMode="EXPANDED") showGenomicRegion(igv, "chr5:88,881,962-88,885,045") displayTrack(igv, track) }
Some tracks represent transcription factor binding sites, traditionally represented as a motif logo. use this method to enable that capability - which depends upon a properly constructed tbl.regions data.frame in a DataFrameAnnotationTrack: in addition to the usual (and mandatory) chrom, start, and end columns. To enable track-click popups over binding site, tbl.regions data.frame must also have a "name" column, which this format, by example: "MotifDb::Hsapiens-HOCOMOCOv10-MEF2C_HUMAN.H10MO.C" The first part of the name, "MotifDb::", tells igv you want to view the specified MotifDb pwm (motif logo, a matrix) when the binding site track element is clicked.
Limitations: This method only works after a call to setGenome(igv, "your genome of interest"). It only works with DataFrameAnnotationTrack objects (for now)
## S4 method for signature 'igvR' enableMotifLogoPopups(obj, status)## S4 method for signature 'igvR' enableMotifLogoPopups(obj, status)
obj |
An object of class igvR |
status |
TRUE or FALSE |
if(interactive()){ igv <- igvR() setGenome(igv, "hg38") new.region <- "chr5:88,882,214-88,884,364" showGenomicRegion(igv, new.region) base.loc <- 88883100 element.names <- c("MotifDb::Hsapiens-HOCOMOCOv10-MEF2C_HUMAN.H10MO.C", "fubar", "MotifDb::Hsapiens-jaspar2018-MEF2C-MA0497.1") tbl.regions <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=element.names, score=round(runif(3), 2), strand=rep("*", 3), stringsAsFactors=FALSE) track <- DataFrameAnnotationTrack("dataframeTest", tbl.regions, color="darkGreen", displayMode="EXPANDED") displayTrack(igv, track) }if(interactive()){ igv <- igvR() setGenome(igv, "hg38") new.region <- "chr5:88,882,214-88,884,364" showGenomicRegion(igv, new.region) base.loc <- 88883100 element.names <- c("MotifDb::Hsapiens-HOCOMOCOv10-MEF2C_HUMAN.H10MO.C", "fubar", "MotifDb::Hsapiens-jaspar2018-MEF2C-MA0497.1") tbl.regions <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=element.names, score=round(runif(3), 2), strand=rep("*", 3), stringsAsFactors=FALSE) track <- DataFrameAnnotationTrack("dataframeTest", tbl.regions, color="darkGreen", displayMode="EXPANDED") displayTrack(igv, track) }
GenomicAlignmentTrack creates and IGV track for bed-like objects expressed as GRanges
GenomicAlignmentTrack( trackName, alignment, trackHeight = 50, visibilityWindow = 30000, color = "gray" )GenomicAlignmentTrack( trackName, alignment, trackHeight = 50, visibilityWindow = 30000, color = "gray" )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
alignment |
A GAlignments object |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
color |
A character string, either a reconized color ("red") or a hex string ("#FF8532") |
Detailed description goes here
A GenomicAlignmentTrack object
bamFile <- system.file(package="igvR", "extdata", "tumor.bam") which <- GRanges(seqnames = "21", ranges = IRanges(10400126, 10400326)) param <- ScanBamParam(which=which, what = scanBamWhat()) x <- readGAlignments(bamFile, use.names=TRUE, param=param) track <- GenomicAlignmentTrack("tumor", x)bamFile <- system.file(package="igvR", "extdata", "tumor.bam") which <- GRanges(seqnames = "21", ranges = IRanges(10400126, 10400326)) param <- ScanBamParam(which=which, what = scanBamWhat()) x <- readGAlignments(bamFile, use.names=TRUE, param=param) track <- GenomicAlignmentTrack("tumor", x)
Some caution is needed with this function when called right after a lengthy browser operation - of which the main example is display a GenomicAlignmentTrack. igv.js does not at present allow us to delay the return from javascript pending completion of the track rendering. This does not pose much of a problem when you manipulate igv in the browser from R in normal interactive mode: simply wait for your last command to complete. But if you are running in programmatic mode, as we do when testing igvR, then caution is advised. See the test_displayAlignment function in unitTests/test_igvR.R.
## S4 method for signature 'igvR' getGenomicRegion(obj)## S4 method for signature 'igvR' getGenomicRegion(obj)
obj |
An object of class igvR |
A list with four fields: chrom (character), start(numeric), end(numeric), string(character)
if(interactive()){ igv <- igvR() setGenome(igv, "hg38") showGenomicRegion(igv, "MEF2C") getGenomicRegion(igv) # list(chrom="chr5", start=88717241, end=88884466, string="chr5:88,717,241-88,884,466") }if(interactive()){ igv <- igvR() setGenome(igv, "hg38") showGenomicRegion(igv, "MEF2C") getGenomicRegion(igv) # list(chrom="chr5", start=88717241, end=88884466, string="chr5:88,717,241-88,884,466") }
Get the shorthand codes (eg, "hg38") for the genomes currently supported by our use of igv.js
## S4 method for signature 'igvR' getSupportedGenomes(obj)## S4 method for signature 'igvR' getSupportedGenomes(obj)
obj |
An object of class igvR |
A character vector, the short form names of the currently supported genomes
if(interactive()){ igv <- igvR() getSupportedGenomes(igv) }if(interactive()){ igv <- igvR() getSupportedGenomes(igv) }
Get the names of all the tracks currently displayed in igv
## S4 method for signature 'igvR' getTrackNames(obj)## S4 method for signature 'igvR' getTrackNames(obj)
obj |
An object of class igvR |
A character vector
if(interactive()){ igv <- igvR() setGenome(igv, "hg19") getTrackNames(igv) # "Gencode v18" }if(interactive()){ igv <- igvR() setGenome(igv, "hg19") getTrackNames(igv) # "Gencode v18" }
GFF3Track creates an IGV track for 9-column gene annotation tables
GFF3Track( trackName, tbl.track = data.frame(), url = NA_character_, indexURL = NA_character_, trackColor = "black", colorByAttribute = NA_character_, colorTable = list(), displayMode, trackHeight, visibilityWindow )GFF3Track( trackName, tbl.track = data.frame(), url = NA_character_, indexURL = NA_character_, trackColor = "black", colorByAttribute = NA_character_, colorTable = list(), displayMode, trackHeight, visibilityWindow )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
tbl.track |
data.frame with 9 columns as defined at http://uswest.ensembl.org/info/website/upload/gff3.html |
url |
character the web location of a 9-column table, gzipped or not |
indexURL |
character the matching tabix index file |
trackColor |
character a recognized color name or RGB triple |
colorByAttribute |
a name from a column 9 attribute |
colorTable |
list which maps the colorByAttribute values to different colors |
displayMode |
"COLLAPSED", "SQUISHED" or "EXPANDED". Spelling and case must be precise. |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
Detailed description goes here
A GFF3Track object
tbl.gff3 <- read.table(system.file(package="igvR", "extdata", "GRCh38.94.NDUFS2.gff3"), sep="\t", as.is=TRUE) colnames(tbl.gff3) <- c("seqid", "source", "type", "start", "end", "score", "strand", "phase", "attributes") colors <- list("antisense" = "blueviolet", "protein_coding" = "blue", "retained_intron" = "rgb(0, 150, 150)", "processed_transcript" = "purple", "processed_pseudogene" = "#7fff00", "unprocessed_pseudogene" = "#d2691e", "default" = "black") track <- GFF3Track("dataframe gff3", tbl.gff3, colorByAttribute="biotype", colorTable=colors, url=NA_character_, indexURL=NA_character_, displayMode="EXPANDED", trackHeight=200, visibilityWindow=100000) # gff3 table structure is not bed-like. find chrom, start, end as seen below roi <- with(tbl.gff3, sprintf("%s:%d-%d", seqid[1], as.integer(min(start)) - 1000, as.integer(max(end)) + 1000)) if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "GWAS demo") showGenomicRegion(igv, roi) displayTrack(igv, track) }tbl.gff3 <- read.table(system.file(package="igvR", "extdata", "GRCh38.94.NDUFS2.gff3"), sep="\t", as.is=TRUE) colnames(tbl.gff3) <- c("seqid", "source", "type", "start", "end", "score", "strand", "phase", "attributes") colors <- list("antisense" = "blueviolet", "protein_coding" = "blue", "retained_intron" = "rgb(0, 150, 150)", "processed_transcript" = "purple", "processed_pseudogene" = "#7fff00", "unprocessed_pseudogene" = "#d2691e", "default" = "black") track <- GFF3Track("dataframe gff3", tbl.gff3, colorByAttribute="biotype", colorTable=colors, url=NA_character_, indexURL=NA_character_, displayMode="EXPANDED", trackHeight=200, visibilityWindow=100000) # gff3 table structure is not bed-like. find chrom, start, end as seen below roi <- with(tbl.gff3, sprintf("%s:%d-%d", seqid[1], as.integer(min(start)) - 1000, as.integer(max(end)) + 1000)) if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "GWAS demo") showGenomicRegion(igv, roi) displayTrack(igv, track) }
GRangesAnnotationTrack creates and IGV track for bed-like objects expressed as GRanges
GRangesAnnotationTrack( trackName, annotationData, color = "darkGrey", displayMode = "SQUISHED", trackHeight = 50, expandedRowHeight = 30, squishedRowHeight = 15, maxRows = 500, searchable = FALSE, visibilityWindow = 1e+05 )GRangesAnnotationTrack( trackName, annotationData, color = "darkGrey", displayMode = "SQUISHED", trackHeight = 50, expandedRowHeight = 30, squishedRowHeight = 15, maxRows = 500, searchable = FALSE, visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
annotationData |
A GRanges object with optional name metadata column |
color |
A CSS color name (e.g., "red" or "#FF0000") |
displayMode |
"COLLAPSED", "SQUISHED" or "EXPANDED". Spelling and case must be precise. |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
expandedRowHeight |
Height of each row of features in "EXPANDED" mode. |
squishedRowHeight |
Height of each row of features in "SQUISHED" mode, for compact viewing. |
maxRows |
of features to display |
searchable |
If TRUE, labels on annotation elements may be used in search |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
Detailed description goes here
A GRangesAnnotationTrack object
base.loc <- 88883100 tbl <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=c("a", "b", "c"), strand=rep("*", 3), stringsAsFactors=FALSE) gr <- GRanges(tbl) track <- GRangesAnnotationTrack("GRangesQTest", gr)base.loc <- 88883100 tbl <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=c("a", "b", "c"), strand=rep("*", 3), stringsAsFactors=FALSE) gr <- GRanges(tbl) track <- GRangesAnnotationTrack("GRangesQTest", gr)
GRangesQuantitativeTrack creates and IGV track for bed objects imported using rtracklayer
GRangesQuantitativeTrack( trackName, quantitativeData, color = "blue", trackHeight = 50, autoscale = TRUE, min = NA_real_, max = NA_real_, visibilityWindow = 1e+05 )GRangesQuantitativeTrack( trackName, quantitativeData, color = "blue", trackHeight = 50, autoscale = TRUE, min = NA_real_, max = NA_real_, visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
quantitativeData |
A GRanges object with (at least) a "score" metadata column |
color |
A CSS color name (e.g., "red" or "#FF0000") |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
autoscale |
Autoscale track to maximum value in view |
min |
Sets the minimum value for the data (y-axis) scale. Usually zero. |
max |
Sets the maximum value for the data (y-axis) scale. This value is ignored if autoscale is TRUE |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
Detailed description goes here
A GRangesQuantitativeTrack object
base.loc <- 88883100 tbl <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=c("a", "b", "c"), score=runif(3), strand=rep("*", 3), stringsAsFactors=FALSE) gr <- GRanges(tbl) track <- GRangesQuantitativeTrack("GRangesQTest", gr)base.loc <- 88883100 tbl <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=c("a", "b", "c"), score=runif(3), strand=rep("*", 3), stringsAsFactors=FALSE) gr <- GRanges(tbl) track <- GRangesQuantitativeTrack("GRangesQTest", gr)
GWASTrack creates an IGV manhattan track GWAS data
GWASTrack( trackName, table, chrom.col, pos.col, pval.col, colorTable = list(), autoscale = TRUE, min = 0, max = 10, trackHeight = 50, visibilityWindow = 1e+05 )GWASTrack( trackName, table, chrom.col, pos.col, pval.col, colorTable = list(), autoscale = TRUE, min = 0, max = 10, trackHeight = 50, visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
table |
data.frame of 6 or more columns |
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 colum |
colorTable |
a named list of CSS colors, by chromosome name - exact matches to the names in the GWAS table. |
autoscale |
logical, controls how min and max of the y-axis are determined |
min |
numeric when autoscale is FALSE, use this minimum y |
max |
numeric when autoscale is FALSE, use this maximum y |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
A GWASTrack object
file <- system.file(package="igvR", "extdata", "gwas-5k.tsv") 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) if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "GWAS demo") displayTrack(igv, track) Sys.sleep(1) # pause before zooming in showGenomicRegion(igv, "chr6:32,240,829-32,929,353") }file <- system.file(package="igvR", "extdata", "gwas-5k.tsv") 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) if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "GWAS demo") displayTrack(igv, track) Sys.sleep(1) # pause before zooming in showGenomicRegion(igv, "chr6:32,240,829-32,929,353") }
GWASUrlTrack creates an IGV manhattan track GWAS data
GWASUrlTrack( trackName, url, chrom.col, pos.col, pval.col, colorTable = list(), autoscale = TRUE, min = 0, max = 10, trackHeight = 50, visibilityWindow = 1e+05 )GWASUrlTrack( trackName, url, chrom.col, pos.col, pval.col, colorTable = list(), autoscale = TRUE, min = 0, max = 10, trackHeight = 50, visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
url |
character |
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 colum |
colorTable |
a named list of CSS colors, by chromosome name - exact matches to the names in the GWAS table. |
autoscale |
logical, controls how min and max of the y-axis are determined |
min |
numeric when autoscale is FALSE, use this minimum y |
max |
numeric when autoscale is FALSE, use this maximum y |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
A GWASUrlTrack object
track <- GWASUrlTrack("GWAS from url", "https://s3.amazonaws.com/igv.org.demo/gwas_sample.tsv.gz", chrom.col=12, pos.col=13, pval.col=28) # note: this track is autoscaled. apparently some infinite values in the file, # leading to a flat, low track. reproduce this in static html, report issue to igv.js # temporary workaround: use the interactive track gear to set display range. if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "GWAS URL demo") displayTrack(igv, track) }track <- GWASUrlTrack("GWAS from url", "https://s3.amazonaws.com/igv.org.demo/gwas_sample.tsv.gz", chrom.col=12, pos.col=13, pval.col=28) # note: this track is autoscaled. apparently some infinite values in the file, # leading to a flat, low track. reproduce this in static html, report issue to igv.js # temporary workaround: use the interactive track gear to set display range. if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "GWAS URL demo") displayTrack(igv, track) }
Constructor for igvAnnotationTrack
igvAnnotationTrack( trackName, annotation, fileFormat = c("bed"), color = "gray", displayMode = c("SQUISHED", "COLLAPSED", "EXPANDED"), sourceType = "file", trackHeight = 30, expandedRowHeight = 30, squishedRowHeight = 15, maxRows = 500, searchable = FALSE, visibilityWindow = 1e+05 )igvAnnotationTrack( trackName, annotation, fileFormat = c("bed"), color = "gray", displayMode = c("SQUISHED", "COLLAPSED", "EXPANDED"), sourceType = "file", trackHeight = 30, expandedRowHeight = 30, squishedRowHeight = 15, maxRows = 500, searchable = FALSE, visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
annotation |
An opague type, currently either a data.frame, GRanges, or UCSCBed object from rtracklayer. |
fileFormat |
Only "bed" is currently supported. |
color |
A CSS color name (e.g., "red" or "#FF0000") |
displayMode |
"COLLAPSED", "EXPANDED", or "SQUISHED" |
sourceType |
Only "file" sources are currently supported. |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
expandedRowHeight |
Height of each row of features in "EXPANDED" mode. |
squishedRowHeight |
Height of each row of features in "SQUISHED" mode, for compact viewing. |
maxRows |
of features to display |
searchable |
If TRUE, labels on annotation elements may be used in search |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
An igvAnnotationTrack object
The igvR class provides an R interface to igv.js, a rich, interactive, full-featured, javascript browser-based genome browser. One constructs an igvR instance on a specified port (default 9000), the browser code is loaded, and a websocket connection openend. After specifying the reference genome, any number of genome tracks may be created, displayed, and navigated.
igvR( portRange = 15000:15100, host = "localhost", title = "igvR", browserFile = igvBrowserFile, quiet = TRUE )igvR( portRange = 15000:15100, host = "localhost", title = "igvR", browserFile = igvBrowserFile, quiet = TRUE )
portRange |
The constructor looks for a free websocket port in this range. 15000:15100 by default |
host |
character, often "localhost" but (as with RStudio Server deployment) can be a remote host |
title |
Used for the web browser window, "igvR" by default |
browserFile |
The full path to the bundled html, js and libraries, and css which constitute the browser app |
quiet |
A logical variable controlling verbosity during execution |
An object of the igvR class
if(interactive()){ igv <- igvR(title="igv demo") setGenome(igv, "hg38") showGenomicRegion(igv, "MEF2C") #--------------------------------------------------------------- # an easy transparent way to create a bed track #--------------------------------------------------------------- base.loc <- 88883100 tbl <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=c("a", "b", "c"), score=runif(3), strand=rep("*", 3), stringsAsFactors=FALSE) track <- DataFrameAnnotationTrack("dataframeTest", tbl, color="red", displayMode="EXPANDED") displayTrack(igv, track) showGenomicRegion(igv, sprintf("chr5:%d-%d", base.loc-100, base.loc+350)) } # if interactiveif(interactive()){ igv <- igvR(title="igv demo") setGenome(igv, "hg38") showGenomicRegion(igv, "MEF2C") #--------------------------------------------------------------- # an easy transparent way to create a bed track #--------------------------------------------------------------- base.loc <- 88883100 tbl <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=c("a", "b", "c"), score=runif(3), strand=rep("*", 3), stringsAsFactors=FALSE) track <- DataFrameAnnotationTrack("dataframeTest", tbl, color="red", displayMode="EXPANDED") displayTrack(igv, track) showGenomicRegion(igv, sprintf("chr5:%d-%d", base.loc-100, base.loc+350)) } # if interactive
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
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 )
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 |
an options list directly usable by igvApp.js, and thus igv.js
[currently.supported.stock.genomes()] for stock genomes we support.
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)
Test the connection between your R session and the webapp
## S4 method for signature 'igvR' ping(obj, msecDelay = 0)## S4 method for signature 'igvR' ping(obj, msecDelay = 0)
obj |
An object of class igvR |
msecDelay |
don't return until these many milliseconds have passed, default 0 |
"pong"
if(interactive()){ igv <- igvR() ping(igv) }if(interactive()){ igv <- igvR() ping(igv) }
QuantitativeTrack creates an IGV track for genomic tracks in which a numerical value is
associated with each reported location.
QuantitativeTrack( trackName, quantitativeData, fileFormat = c("wig", "bigWig", "bedGraph", "gwas"), color = "gray", sourceType = c("file", "url"), trackHeight = 50, autoscale = TRUE, min = NA_real_, max = NA_real_, visibilityWindow = 1e+05 )QuantitativeTrack( trackName, quantitativeData, fileFormat = c("wig", "bigWig", "bedGraph", "gwas"), color = "gray", sourceType = c("file", "url"), trackHeight = 50, autoscale = TRUE, min = NA_real_, max = NA_real_, visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
quantitativeData |
A polyvalent object, either a data.frame, GRanges, or UCSCBedGraphQuantitative object |
fileFormat |
only "bedGraph" supported at present; wig and bigWig support soon. |
color |
A CSS color name (e.g., "red" or "#FF0000") |
sourceType |
only "file" supported at present ("gcs" for Google Cloud Storage, and "ga4gh" for the Global Alliance API may come) |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
autoscale |
Autoscale track to maximum value in view |
min |
Sets the minimum value for the data (y-axis) scale. Usually zero. |
max |
Sets the maximum value for the data (y-axis) scale. This value is ignored if autoscale is TRUE |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
Detailed description will go here
A QuantitativeTrack object
RemoteAlignmentTrack creates an IGV track for remote bam files
RemoteAlignmentTrack( trackName, bamUrl, bamIndex = NULL, trackHeight = 50, visibilityWindow = 30000, color = "gray" )RemoteAlignmentTrack( trackName, bamUrl, bamIndex = NULL, trackHeight = 50, visibilityWindow = 30000, color = "gray" )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
bamUrl |
The URL of a bam file |
bamIndex |
The URL of a bam index file. Defaults to <bamUrl>.bai |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
color |
A character string, either a reconized color ("red") or a hex string ("#FF8532") |
Detailed description goes here
A RemoteAlignmentTrack object
Remove named tracks
## S4 method for signature 'igvR' removeTracksByName(obj, trackNames)## S4 method for signature 'igvR' removeTracksByName(obj, trackNames)
obj |
An object of class igvR |
trackNames |
a character vector |
A character vector
getTrackNames
if(interactive()){ igv <- igvR() setGenome(igv, "hg19") showGenomicRegion(igv, "MEF2C") # create three arbitrary tracks base.loc <- 88883100 tbl <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=c("a", "b", "c"), score=runif(3), strand=rep("*", 3), stringsAsFactors=FALSE) track.1 <- DataFrameAnnotationTrack("track.1", tbl, color="red", displayMode="SQUISHED") track.2 <- DataFrameAnnotationTrack("track.2", tbl, color="blue", displayMode="SQUISHED") track.3 <- DataFrameAnnotationTrack("track.3", tbl, color="green", displayMode="SQUISHED") displayTrack(igv, track.1) displayTrack(igv, track.2) displayTrack(igv, track.3) removeTracksByName(igv, "track.2") #---------------------------------------- # bulk removal of the remaining tracks, # but leave the h19 reference track #---------------------------------------- removeTracksByName(igv, getTrackNames(igv)[-1]) }if(interactive()){ igv <- igvR() setGenome(igv, "hg19") showGenomicRegion(igv, "MEF2C") # create three arbitrary tracks base.loc <- 88883100 tbl <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=c("a", "b", "c"), score=runif(3), strand=rep("*", 3), stringsAsFactors=FALSE) track.1 <- DataFrameAnnotationTrack("track.1", tbl, color="red", displayMode="SQUISHED") track.2 <- DataFrameAnnotationTrack("track.2", tbl, color="blue", displayMode="SQUISHED") track.3 <- DataFrameAnnotationTrack("track.3", tbl, color="green", displayMode="SQUISHED") displayTrack(igv, track.1) displayTrack(igv, track.2) displayTrack(igv, track.3) removeTracksByName(igv, "track.2") #---------------------------------------- # bulk removal of the remaining tracks, # but leave the h19 reference track #---------------------------------------- removeTracksByName(igv, getTrackNames(igv)[-1]) }
Get entire igv browser image in svg
## S4 method for signature 'igvR' saveToSVG(obj, filename)## S4 method for signature 'igvR' saveToSVG(obj, filename)
obj |
An object of class igvR |
filename |
character string, the name of the file to which the svg text will be written |
A character vector
Specify the reference genome you wish to use, via full specification of all urls
## S4 method for signature 'igvR' setCustomGenome( obj, id, genomeName, fastaURL, fastaIndexURL, chromosomeAliasURL = NA, cytobandURL = NA, geneAnnotationName = NA, geneAnnotationURL = NA, geneAnnotationTrackHeight = 200, geneAnnotationTrackColor = "darkblue", initialLocus = "all", visibilityWindow = 1e+06 )## S4 method for signature 'igvR' setCustomGenome( obj, id, genomeName, fastaURL, fastaIndexURL, chromosomeAliasURL = NA, cytobandURL = NA, geneAnnotationName = NA, geneAnnotationURL = NA, geneAnnotationTrackHeight = 200, geneAnnotationTrackColor = "darkblue", initialLocus = "all", visibilityWindow = 1e+06 )
obj |
An object of class igvR |
id |
character string, a short name, displayed in the browser, e.g., "hg38", "tair10". |
genomeName |
character string, possibly longer, more descirptive then the id, e.g., "Human (GRCh38/hg38)" |
fastaURL |
character string, e.g."https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa" |
fastaIndexURL |
character string, e.g. "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai" |
chromosomeAliasURL |
character string, default NA, a tab-delimited file supporting multiple equivalent chromosome names. see details |
cytobandURL |
character string, default NA, a cytoband ideogram file in UCSC format, e.g. "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt" |
geneAnnotationName |
character string, e.g. "Refseq Genes", default NA |
geneAnnotationURL |
character string, e.g. "https://s3.amazonaws.com/igv.org.genomes/hg38/refGene.txt.gz", default NA |
geneAnnotationTrackHeight |
numeric, pixels, e.g. 500. default 200 |
geneAnnotationTrackColor |
character string, any legal CSS color, default "darkblue" |
initialLocus |
character string, e.g. "chr5:88,621,308-89,001,037" or "MEF2C" |
visibilityWindow |
numeric, number of bases over which to display features, default 1000000 |
An empty string, an error message if any of the urls could not be reached
if(interactive()){ igv <- igvR() setCustomGenome(igv, id="hg38", genomeName="Human (GRCh38/hg38)", fastaURL="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa", fastaIndexURL="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai", chromosomeAliasURL=NA, cytobandURL="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt", geneAnnotationName="Refseq Genes", geneAnnotationURL="https://s3.amazonaws.com/igv.org.genomes/hg38/refGene.txt.gz", geneAnnotationTrackHeight=300, geneAnnotationTrackColor="darkgreen", initialLocus="chr5:88,621,308-89,001,037", visibilityWindow=5000000) }if(interactive()){ igv <- igvR() setCustomGenome(igv, id="hg38", genomeName="Human (GRCh38/hg38)", fastaURL="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa", fastaIndexURL="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai", chromosomeAliasURL=NA, cytobandURL="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt", geneAnnotationName="Refseq Genes", geneAnnotationURL="https://s3.amazonaws.com/igv.org.genomes/hg38/refGene.txt.gz", geneAnnotationTrackHeight=300, geneAnnotationTrackColor="darkgreen", initialLocus="chr5:88,621,308-89,001,037", visibilityWindow=5000000) }
Specify the reference genome, currently limited to hg38, hg19, mm10, tair10.
## S4 method for signature 'igvR' setGenome(obj, genomeName)## S4 method for signature 'igvR' setGenome(obj, genomeName)
obj |
An object of class igvR |
genomeName |
A character string, one of "hg38", "hg19", "mm10", "tair10" |
An empty string, an error message if the requested genome is not yet supported
if(interactive()){ igv <- igvR() setGenome(igv, "mm10") }if(interactive()){ igv <- igvR() setGenome(igv, "mm10") }
Specify (supply) the javascript function run on track click event
## S4 method for signature 'igvR' setTrackClickFunction(obj, javascriptFunction)## S4 method for signature 'igvR' setTrackClickFunction(obj, javascriptFunction)
obj |
An object of class igvR |
javascriptFunction |
expressed as a 2-element named list: body + args |
""
Remove named tracks
## S4 method for signature 'igvR' setTrackHeight(obj, trackName, newHeight)## S4 method for signature 'igvR' setTrackHeight(obj, trackName, newHeight)
obj |
An object of class igvR |
trackName |
a character string |
newHeight |
integer, in ixels |
nothing
getTrackNames
Set the visible region, by explicit chromLoc string, or by named features in any curently loaded annotation tracks
## S4 method for signature 'igvR' showGenomicRegion(obj, region)## S4 method for signature 'igvR' showGenomicRegion(obj, region)
obj |
An object of class igvR |
region |
A genomic location (rendered "chr5:9,234,343-9,236,000" or as a list: list(chrom="chr9", start=9234343, end=9236000)) or a labeled annotation in a searchable track, often a gene symbol, eg "MEF2C" |
""
if(interactive()){ igv <- igvR() setGenome(igv, "hg38") showGenomicRegion(igv, "MEF2C") x <- getGenomicRegion(igv) #-------------------- # zoom out 2kb #-------------------- showGenomicRegion(igv, with(x, sprintf("%s:%d-%d", chrom, start-1000, end+1000))) }if(interactive()){ igv <- igvR() setGenome(igv, "hg38") showGenomicRegion(igv, "MEF2C") x <- getGenomicRegion(igv) #-------------------- # zoom out 2kb #-------------------- showGenomicRegion(igv, with(x, sprintf("%s:%d-%d", chrom, start-1000, end+1000))) }
Hide or show igv track labels
## S4 method for signature 'igvR' showTrackLabels(obj, newState)## S4 method for signature 'igvR' showTrackLabels(obj, newState)
obj |
An object of class igvR |
newState |
logigal, either TRUE or FALSE |
""
Constructor for Track
Track( trackType = c("annotation", "quantitative", "alignment", "variant", "gwas"), sourceType = c("file", "gcs", "ga4gh"), fileFormat = c("bed", "gff", "gff3", "gtf", "wig", "bigWig", "bedGraph", "bam", "vcf", "seg"), trackName, onScreenOrder, color, height, autoTrackHeight, minTrackHeight, maxTrackHeight, visibilityWindow )Track( trackType = c("annotation", "quantitative", "alignment", "variant", "gwas"), sourceType = c("file", "gcs", "ga4gh"), fileFormat = c("bed", "gff", "gff3", "gtf", "wig", "bigWig", "bedGraph", "bam", "vcf", "seg"), trackName, onScreenOrder, color, height, autoTrackHeight, minTrackHeight, maxTrackHeight, visibilityWindow )
trackType |
One of "annotation", "quantitative", "variant". |
sourceType |
Only "file" is currently supported. |
fileFormat |
One of "bed", "bedGraph", "vcf" |
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
onScreenOrder |
Numeric, for explicit placement of track within the current set. |
color |
A CSS color name (e.g., "red" or "#FF0000") |
height |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
autoTrackHeight |
If true, then track height is adjusted dynamically, within the bounds set by minHeight and maxHeight, to accomdodate features in view |
minTrackHeight |
In pixels, minimum allowed |
maxTrackHeight |
In pixels, maximum allowed |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
An object of class Track
https://github.com/igvteam/igv.js/wiki/Tracks
https://www.w3schools.com/cssref/css_colors.asp
Get basic info about a track: its type, file format, source and S4 class name
## S4 method for signature 'Track' trackInfo(obj)## S4 method for signature 'Track' trackInfo(obj)
obj |
An object of base class Track |
A list with four fields: trackType, fileFormat, source, class name
Retrieve the size of the BedpeInteractionsTrack
## S4 method for signature 'BedpeInteractionsTrack' trackSize(obj)## S4 method for signature 'BedpeInteractionsTrack' trackSize(obj)
obj |
An object of class BedpeInteractionsTrack |
The number of elements
Retrieve the size of the DataFrameAnnotationTrack
## S4 method for signature 'DataFrameAnnotationTrack' trackSize(obj)## S4 method for signature 'DataFrameAnnotationTrack' trackSize(obj)
obj |
An object of class UCSCBedAnnotationTrack |
The number of elements
base.loc <- 88883100 tbl <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=c("a", "b", "c"), score=runif(3), strand=rep("*", 3), stringsAsFactors=FALSE) track <- DataFrameAnnotationTrack("dataframeTest", tbl) trackSize(track)base.loc <- 88883100 tbl <- data.frame(chrom=rep("chr5", 3), start=c(base.loc, base.loc+100, base.loc + 250), end=c(base.loc + 50, base.loc+120, base.loc+290), name=c("a", "b", "c"), score=runif(3), strand=rep("*", 3), stringsAsFactors=FALSE) track <- DataFrameAnnotationTrack("dataframeTest", tbl) trackSize(track)
Retrieve the size of the DataFrameQuantitativeTrack
## S4 method for signature 'DataFrameQuantitativeTrack' trackSize(obj)## S4 method for signature 'DataFrameQuantitativeTrack' trackSize(obj)
obj |
An object of class DataFrameQuantitativeTrack |
The number of elements
Retrieve the size of the GenomicAlignmentTrack
## S4 method for signature 'GenomicAlignmentTrack' trackSize(obj)## S4 method for signature 'GenomicAlignmentTrack' trackSize(obj)
obj |
An object of class GenomicAlignmentTrack |
The number of elements
Retrieve the size of the GFF3Track
## S4 method for signature 'GFF3Track' trackSize(obj)## S4 method for signature 'GFF3Track' trackSize(obj)
obj |
An object of class UCSCBedAnnotationTrack |
The number of elements
Retrieve the size of the GRangesAnnotationTrack
## S4 method for signature 'GRangesAnnotationTrack' trackSize(obj)## S4 method for signature 'GRangesAnnotationTrack' trackSize(obj)
obj |
An object of class GRangesAnnotationTrack |
The number of elements
Retrieve the size of the GRangesQuantitativeTrack
## S4 method for signature 'GRangesQuantitativeTrack' trackSize(obj)## S4 method for signature 'GRangesQuantitativeTrack' trackSize(obj)
obj |
An object of class GRangesQuantitativeTrack |
The number of elements
Retrieve the size of the GWASTrack
## S4 method for signature 'GWASTrack' trackSize(obj)## S4 method for signature 'GWASTrack' trackSize(obj)
obj |
An object of class GWASTrack |
The number of elements
Retrieve the size of the GWASUrlTrack
## S4 method for signature 'GWASUrlTrack' trackSize(obj)## S4 method for signature 'GWASUrlTrack' trackSize(obj)
obj |
An object of class GWASUrlTrack |
The number of elements
Retrieve the size of the QuantitativeTrack
## S4 method for signature 'QuantitativeTrack' trackSize(obj)## S4 method for signature 'QuantitativeTrack' trackSize(obj)
obj |
An object of class UCSCBedAnnotationTrack |
The number of elements
Retrieve the size of theUCSCBedAnnotationTrack
## S4 method for signature 'UCSCBedAnnotationTrack' trackSize(obj)## S4 method for signature 'UCSCBedAnnotationTrack' trackSize(obj)
obj |
An object of class UCSCBedAnnotationTrack |
The number of elements
bed.filepath <- system.file(package = "rtracklayer", "tests", "test.bed") gr.bed <- rtracklayer::import(bed.filepath) track.1 <- UCSCBedAnnotationTrack("UCSC bed", gr.bed, color="blue", displayMode="SQUISHED") trackSize(track.1)bed.filepath <- system.file(package = "rtracklayer", "tests", "test.bed") gr.bed <- rtracklayer::import(bed.filepath) track.1 <- UCSCBedAnnotationTrack("UCSC bed", gr.bed, color="blue", displayMode="SQUISHED") trackSize(track.1)
Retrieve the size of the UCSCBedGraphQuantitativeTrack
## S4 method for signature 'UCSCBedGraphQuantitativeTrack' trackSize(obj)## S4 method for signature 'UCSCBedGraphQuantitativeTrack' trackSize(obj)
obj |
An object of class UCSCBedGraphQuantitativeTrack |
The number of elements
Retrieve the size of the VariantTrack
## S4 method for signature 'VariantTrack' trackSize(obj)## S4 method for signature 'VariantTrack' trackSize(obj)
obj |
An object of class VariantTrack |
The number of elements
UCSCBedAnnotationTrack creates and IGV track for bed objects imported using rtracklayer
UCSCBedAnnotationTrack( trackName, annotation, color = "darkGrey", displayMode = "SQUISHED", trackHeight = 50, expandedRowHeight = 30, squishedRowHeight = 15, maxRows = 500, searchable = FALSE, visibilityWindow = 1e+05 )UCSCBedAnnotationTrack( trackName, annotation, color = "darkGrey", displayMode = "SQUISHED", trackHeight = 50, expandedRowHeight = 30, squishedRowHeight = 15, maxRows = 500, searchable = FALSE, visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
annotation |
A UCSCData object imported by |
color |
A CSS color name (e.g., "red" or "#FF0000") |
displayMode |
"COLLAPSED", "SQUISHED" or "EXPANDED". Spelling and case must be precise. |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
expandedRowHeight |
Height of each row of features in "EXPANDED" mode. |
squishedRowHeight |
Height of each row of features in "SQUISHED" mode, for compact viewing. |
maxRows |
of features to display |
searchable |
If TRUE, labels on annotation elements may be used in search |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
Detailed description goes here
A UCSCBedAnnotationTrack object
bed.filepath <- system.file(package = "rtracklayer", "tests", "test.bed") gr.bed <- rtracklayer::import(bed.filepath) track <- UCSCBedAnnotationTrack("UCSC bed", gr.bed, color="blue", displayMode="SQUISHED") if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "UCSC bed10 demo") showGenomicRegion(igv, "chr7:127,469,879-127,476,276") displayTrack(igv, track) }bed.filepath <- system.file(package = "rtracklayer", "tests", "test.bed") gr.bed <- rtracklayer::import(bed.filepath) track <- UCSCBedAnnotationTrack("UCSC bed", gr.bed, color="blue", displayMode="SQUISHED") if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "UCSC bed10 demo") showGenomicRegion(igv, "chr7:127,469,879-127,476,276") displayTrack(igv, track) }
UCSCBedGraphQuantitativeTrack creates an IGV track for bedGraph objects
imported with rtracklayer
UCSCBedGraphQuantitativeTrack( trackName, quantitativeData, color = "blue", trackHeight = 50, autoscale = TRUE, min = NA_real_, max = NA_real_, visibilityWindow = 1e+05 )UCSCBedGraphQuantitativeTrack( trackName, quantitativeData, color = "blue", trackHeight = 50, autoscale = TRUE, min = NA_real_, max = NA_real_, visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
quantitativeData |
A GRanges object with (at least) a "score" metadata column |
color |
A CSS color name (e.g., "red" or "#FF0000") |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
autoscale |
Autoscale track to maximum value in view |
min |
Sets the minimum value for the data (y-axis) scale. Usually zero. |
max |
Sets the maximum value for the data (y-axis) scale. This value is ignored if autoscale is TRUE |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
Detailed description goes here
A UCSCBedGraphQuantitativeTrack object
bedGraph.filepath <- system.file(package = "rtracklayer", "tests", "test.bedGraph") gr.bedGraph <- rtracklayer::import(bedGraph.filepath) track <- UCSCBedGraphQuantitativeTrack("UCSCBedGraphTest", gr.bedGraph) if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "UCSC BedGraph demo") displayTrack(igv, track) Sys.sleep(1) # pause before zoomin showGenomicRegion(igv, "chr18:59,103,373-59,105,673") }bedGraph.filepath <- system.file(package = "rtracklayer", "tests", "test.bedGraph") gr.bedGraph <- rtracklayer::import(bedGraph.filepath) track <- UCSCBedGraphQuantitativeTrack("UCSCBedGraphTest", gr.bedGraph) if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "UCSC BedGraph demo") displayTrack(igv, track) Sys.sleep(1) # pause before zoomin showGenomicRegion(igv, "chr18:59,103,373-59,105,673") }
a helper function for mostly internal use, tests for availability of a url, modeled after file.exists
a helper function for mostly internal use, tests for availability of a url, modeled after file.exists
url.exists(url) url.exists(url)url.exists(url) url.exists(url)
url |
character the http address to test |
logical TRUE or FALSE
logical TRUE or FALSE
if(interactive()){ igv <- igvR() ping(igv) }if(interactive()){ igv <- igvR() ping(igv) }
VariantTrack creates an IGV track for VCF (variant call format) objects, either local or at a remote url
VariantTrack( trackName, vcf, trackHeight = 50, anchorColor = "pink", homvarColor = "rgb(17,248,254)", hetvarColor = "rgb(34,12,253)", homrefColor = "rgb(200,200,200)", displayMode = "EXPANDED", visibilityWindow = 1e+05 )VariantTrack( trackName, vcf, trackHeight = 50, anchorColor = "pink", homvarColor = "rgb(17,248,254)", hetvarColor = "rgb(34,12,253)", homrefColor = "rgb(200,200,200)", displayMode = "EXPANDED", visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
vcf |
A VCF object from the VariantAnnotation package, or a list(url=x, index=y) pointing to a vcf file |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
anchorColor |
CSS color name (e.g., "red" or "#FF0000") for the "anchoring" graphical segment in the track |
homvarColor |
CSS color name for homozygous variant samples, rgb(17,248,254) by default (~turquoise) |
hetvarColor |
CSS color name for heterzygous variant samples, rgb(34,12,253) by default (~royalBlue) |
homrefColor |
CSS color names for homozygous reference samples, rgb(200,200,200) by default (~lightGray) |
displayMode |
"COLLAPSED", "EXPANDED", or "SQUISHED" |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
Detailed description goes here
A VariantTrack object
#---------------------------- # first, from a local file #---------------------------- f <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation") roi <- GRanges(seqnames="22", ranges=IRanges(start=c(50301422, 50989541), end=c(50312106, 51001328), names=c("gene_79087", "gene_644186"))) vcf.sub <- VariantAnnotation::readVcf(f, "hg19", param=roi) track.local <- VariantTrack("chr22-tiny", vcf.sub) #---------------------------- # now try a url track #---------------------------- data.url <- sprintf("%s/%s", "https://s3.amazonaws.com/1000genomes/release/20130502", "ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz") index.url <- sprintf("%s.tbi", data.url) url <- list(data=data.url, index=index.url) track.url <- VariantTrack("1kg", url)#---------------------------- # first, from a local file #---------------------------- f <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation") roi <- GRanges(seqnames="22", ranges=IRanges(start=c(50301422, 50989541), end=c(50312106, 51001328), names=c("gene_79087", "gene_644186"))) vcf.sub <- VariantAnnotation::readVcf(f, "hg19", param=roi) track.local <- VariantTrack("chr22-tiny", vcf.sub) #---------------------------- # now try a url track #---------------------------- data.url <- sprintf("%s/%s", "https://s3.amazonaws.com/1000genomes/release/20130502", "ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz") index.url <- sprintf("%s.tbi", data.url) url <- list(data=data.url, index=index.url) track.url <- VariantTrack("1kg", url)
zoom the genome view in by a factor of 2
## S4 method for signature 'igvR' zoomIn(obj)## S4 method for signature 'igvR' zoomIn(obj)
obj |
An object of class igvR |
""
zoom the genome view out by a factor of 2
## S4 method for signature 'igvR' zoomOut(obj)## S4 method for signature 'igvR' zoomOut(obj)
obj |
An object of class igvR |
""