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Annotation Track
Jim Robinson edited this page Oct 20, 2021
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type = 'annotation'
- bed
- gff3
- gtf
- genePred
- genePredExt
- peaks
- narrowPeak
- broadPeak
- bigBed
- bedpe
Configuration options specific to annotation tracks. All properties below are optional.
Property | Description | Default |
---|---|---|
displayMode | Annotation display mode, one of "COLLAPSED", "EXPANDED", "SQUISHED" | "COLLAPSED" |
expandedRowHeight | Height of each row of features in "EXPANDED" mode | 30 |
squishedRowHeight | Height of each row of features in "SQUISHED" mode | 15 |
nameField | For GFF/GTF file formats. Name of column 9 property to be used for feature label. | |
maxRows | Maximum number of rows of features to display | 500 |
searchable | If true, feature names for this track can be searched for. Use this option with caution, it is memory intensive. This option will not work with indexed tracks. | false |
searchableFields | For use with the searchable option in conjunction with GFF files. An array of field (column 9) names to be included in feature searches. When searching for feature attributes spaces need to be escaped with a "+" sign or percent encoded ("%20). |
|
filterTypes | Array of gff feature types to filter from display. | ['chromosome, 'gene'] |
color | CSS color value for track features, e.g. "#ff0000" or "rgb(100,0,100)". | rgb(0,0,150) |
altColor | If supplied, used for features on negative strand | |
colorBy | Used with GFF/GTF files. Name of column 9 attribute to color features by. | |
colorTable | Used in conjunction with colorBy property. Maps attribute values to CSS colors. See example below. |
The coloryBy
property takes an object specifying the name of the field to color by, used in conjunction with the colorTable
property. Fields are defined in GFF column 9.
{
name: "Color by attribute biotype",
type: "annotation",
format: "gff3",
displayMode: "expanded",
height: 300,
url: "https://s3.amazonaws.com/igv.org.genomes/hg38/Homo_sapiens.GRCh38.94.chr.gff3.gz",
indexURL: "https://s3.amazonaws.com/igv.org.genomes/hg38/Homo_sapiens.GRCh38.94.chr.gff3.gz.tbi",
visibilityWindow: 1000000,
colorBy: "biotype",
colorTable: {
"antisense": "blueviolet",
"protein_coding": "blue",
"retained_intron": "rgb(0, 150, 150)",
"processed_transcript": "purple",
"processed_pseudogene": "#7fff00",
"unprocessed_pseudogene": "#d2691e",
"*": "black"
}
},
Beginning with igv.js version 2.10.1 the color and altColor properties can be specified with a function that takes a feature object as an argument and returns a CSS color string (e.g. "blue", "rgb(0,150,150)", "#d2691e").
Example
{
name: "Color by function",
format: "gff3",
displayMode: "expanded",
height: 300,
url: "https://s3.amazonaws.com/igv.org.genomes/hg38/Homo_sapiens.GRCh38.94.chr.gff3.gz",
indexURL: "https://s3.amazonaws.com/igv.org.genomes/hg38/Homo_sapiens.GRCh38.94.chr.gff3.gz.tbi",
visibilityWindow: 1000000,
color: (feature) => {
switch (feature.getAttributeValue("biotype")) {
case "antisense":
return "blueviolet"
case "protein_coding":
return "blue"
case "retained_intron":
return "rgb(0, 150, 150)"
case "processed_transcript":
return "purple"
case "processed_pseudogene":
return "#7fff00"
case "unprocessed_pseudogene":
return "#d2691e"
default:
return "black"
}
}
}
The feature object passed to the color function is described below
{
chr: chr,
start: integer,
end: integer,
name: string
score: float,
strand: string,
cdStart: integer,
cdEnd: integer,
color: string,
exons: array
getAttributeValue(attributeName): function -- returns value of a GFF/GTF column 9 attribute
}
\\ Exon array
[
{
start: integer,
end: integer,
cdStart: integer,
cdEnd: integer,
utr: boolean
}
]