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rebase (#1718)
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* Bug fix: group autoscale set/unset now works properly (#1708)

* Multi select bug fix. (#1710)

* Prep for maintaining multi-select state in sessions (#1711)

* cnvpytor track update: improve y axis labels (#1712)

* cnvpytor track update: improve y axis labels

* update scale and bug fix for default cnv caller

* Group Autoscale Colored Axes (#1715)

* Use color to indicate tracks in a common autoscale group
* Alpha adjustment is now supported for MergeTrack, with live update of OverlayTrack transparency.

---------

Co-authored-by: Douglass Turner <douglass.turner@gmail.com>
Co-authored-by: Arijit Panda <arijpanda@gmail.com>
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@jrobinso @turner @arpanda
3 people authored Oct 20, 2023
1 parent d226689 commit ed7601e
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3 changes: 2 additions & 1 deletion css/_igv-menu-popup.scss
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Expand Up @@ -12,7 +12,8 @@ $igv-menu-popup-grey: #7F7F7F;
//min-width: 132px;
width: max-content;

z-index: 4096;
//z-index: 4096;
z-index: 512;

cursor: pointer;

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2 changes: 1 addition & 1 deletion css/dom.css
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3 changes: 2 additions & 1 deletion css/dom.css.map
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240 changes: 185 additions & 55 deletions dev/misc/multi-select.html → dev/multi-select/multi-select-examples.html
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Expand Up @@ -174,7 +174,7 @@
]
};

const overlay_tracks_config =
const group_autoscale_config =
{
"version": "2.16.0",
"showSampleNames": false,
Expand All @@ -200,6 +200,33 @@
"type": "sequence",
"order": -9007199254740991
},
{
"name": "Homo sapiens angular gyrus tissue male adult (81 years) H3K36me3 ",
"url": "https://www.encodeproject.org/files/ENCFF202ZTM/@@download/ENCFF202ZTM.bigWig",
"color": "#008cff",
"metadata": {
"Biosample": "Homo sapiens angular gyrus tissue male adult (81 years)",
"AssayType": "ChIP-seq",
"Target": "H3K36me3 ",
"BioRep": "1",
"TechRep": "1_3",
"OutputType": "signal p-value",
"Format": "bigWig",
"Lab": "Bradley Bernstein, Broad",
"Accession": "ENCFF202ZTM",
"Experiment": "ENCSR340DBD"
},
"order": 1,
"format": "bigwig",
"type": "wig",
"height": 128,
// "autoscaleGroup": 'annaBirna'
},
{
name: "ENCODE bigwig",
url: 'https://www.encodeproject.org/files/ENCFF206QIK/@@download/ENCFF206QIK.bigWig',
// autoscaleGroup: 'annaBirna'
},
{
"name": "Homo sapiens A549 SIN3A ",
"url": "https://www.encodeproject.org/files/ENCFF582HJY/@@download/ENCFF582HJY.bigWig",
Expand All @@ -219,7 +246,8 @@
"order": 1,
"format": "bigwig",
"type": "wig",
"height": 128
"height": 128,
"autoscaleGroup": 'billyBobThornton'
},
{
"name": "Homo sapiens A549 treated with 0.02% ethanol for 1 hour YY1 ",
Expand All @@ -240,28 +268,8 @@
"order": 1,
"format": "bigwig",
"type": "wig",
"height": 128
},
{
"name": "Homo sapiens angular gyrus tissue male adult (81 years) H3K36me3 ",
"url": "https://www.encodeproject.org/files/ENCFF202ZTM/@@download/ENCFF202ZTM.bigWig",
"color": "#008cff",
"metadata": {
"Biosample": "Homo sapiens angular gyrus tissue male adult (81 years)",
"AssayType": "ChIP-seq",
"Target": "H3K36me3 ",
"BioRep": "1",
"TechRep": "1_3",
"OutputType": "signal p-value",
"Format": "bigWig",
"Lab": "Bradley Bernstein, Broad",
"Accession": "ENCFF202ZTM",
"Experiment": "ENCSR340DBD"
},
"order": 1,
"format": "bigwig",
"type": "wig",
"height": 128
"height": 128,
"autoscaleGroup": 'billyBobThornton'
},
{
"name": "Refseq Genes",
Expand All @@ -278,7 +286,7 @@
]
};

const overlay_throws_error_config =
const whole_lotta_wigs_config =
{
"version": "2.16.0",
"showSampleNames": false,
Expand All @@ -291,72 +299,194 @@
"aliasURL": "https://s3.amazonaws.com/igv.org.genomes/hg19/hg19_alias.tab",
"chromosomeOrder": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY"
},
"locus": "chr5:1-180,915,260",
"locus": "chr8:128,745,581-128,755,100",
"gtexSelections": {
"chr8:128,745,581-128,755,100": {
"gene": "MYC",
"snp": null
}
},
"roi": [],
"tracks": [
{
"type": "sequence",
"order": -9007199254740991
},
{
"name": "Homo sapiens A549 CTCF ",
"url": "https://www.encodeproject.org/files/ENCFF023NXW/@@download/ENCFF023NXW.bigWig",
"name": "Homo sapiens HepG2 PRPF4 ",
"url": "https://www.encodeproject.org/files/ENCFF059CKF/@@download/ENCFF059CKF.bigWig",
"metadata": {
"Biosample": "Homo sapiens A549",
"Biosample": "Homo sapiens HepG2",
"AssayType": "ChIP-seq",
"Target": "PRPF4 ",
"BioRep": "1,2",
"TechRep": "1_1,2_1",
"OutputType": "fold change over control",
"Format": "bigWig",
"Lab": "Xiang-Dong Fu, UCSD",
"Accession": "ENCFF059CKF",
"Experiment": "ENCSR243LNQ"
},
"order": 0,
"format": "bigwig",
"type": "wig",
"height": 128,
"windowFunction": "mean",
"color": "rgb(255, 41, 135)"
},
{
"name": "Homo sapiens GM13977 CTCF ",
"url": "https://www.encodeproject.org/files/ENCFF000RQI/@@download/ENCFF000RQI.bigWig",
"metadata": {
"Biosample": "Homo sapiens GM13977",
"AssayType": "ChIP-seq",
"Target": "CTCF ",
"BioRep": "1",
"TechRep": "1_1",
"OutputType": "base overlap signal",
"Format": "bigWig",
"Lab": "Vishwanath Iyer, UTA",
"Accession": "ENCFF000RQI",
"Experiment": "ENCSR000DLB"
},
"order": 1,
"format": "bigwig",
"type": "wig",
"height": 128,
"windowFunction": "mean",
"color": "rgb(5, 248, 2)"
},
{
"name": "Homo sapiens GM12878 BCLAF1 ",
"url": "https://www.encodeproject.org/files/ENCFF036IRJ/@@download/ENCFF036IRJ.bigWig",
"metadata": {
"Biosample": "Homo sapiens GM12878",
"AssayType": "ChIP-seq",
"Target": "BCLAF1 ",
"BioRep": "2",
"TechRep": "2_1",
"OutputType": "fold change over control",
"Format": "bigWig",
"Lab": "Richard Myers, HAIB",
"Accession": "ENCFF036IRJ",
"Experiment": "ENCSR000BJZ"
},
"order": 2,
"format": "bigwig",
"type": "wig",
"height": 128,
"windowFunction": "mean",
"color": "rgb(0, 46, 255)"
},
{
"name": "Homo sapiens K562 ZNF274 ",
"url": "https://www.encodeproject.org/files/ENCFF555CQE/@@download/ENCFF555CQE.bigWig",
"metadata": {
"Biosample": "Homo sapiens K562",
"AssayType": "ChIP-seq",
"Target": "ZNF274 ",
"BioRep": "2",
"TechRep": "2_1",
"OutputType": "fold change over control",
"Format": "bigWig",
"Lab": "Peggy Farnham, USC",
"Accession": "ENCFF555CQE",
"Experiment": "ENCSR000EWE"
},
"order": 3,
"format": "bigwig",
"type": "wig",
"height": 128,
"windowFunction": "mean",
"color": "rgb(106, 207, 255)"
},
{
"name": "Homo sapiens 22Rv1 ZFX ",
"url": "https://www.encodeproject.org/files/ENCFF420XMW/@@download/ENCFF420XMW.bigWig",
"metadata": {
"Biosample": "Homo sapiens 22Rv1",
"AssayType": "ChIP-seq",
"Target": "ZFX ",
"BioRep": "2",
"TechRep": "2_1",
"OutputType": "signal p-value",
"Format": "bigWig",
"Lab": "John Stamatoyannopoulos, UW",
"Accession": "ENCFF023NXW",
"Experiment": "ENCSR000DPF"
"Lab": "Michael Snyder, Stanford",
"Accession": "ENCFF420XMW",
"Experiment": "ENCSR246MLJ"
},
"order": 0,
"order": 4,
"format": "bigwig",
"type": "wig"
"type": "wig",
"height": 128,
"windowFunction": "mean",
"color": "rgb(137, 30, 136)"
},
{
"name": "Homo sapiens A549 treated with 0.02% ethanol for 1 hour H3K9ac ",
"url": "https://www.encodeproject.org/files/ENCFF537QDO/@@download/ENCFF537QDO.bigWig",
"color": "rgb(100,0,0)",
"name": "Homo sapiens A549 CHD4 ",
"url": "https://www.encodeproject.org/files/ENCFF725AXM/@@download/ENCFF725AXM.bigWig",
"metadata": {
"Biosample": "Homo sapiens A549 treated with 0.02% ethanol for 1 hour",
"Biosample": "Homo sapiens A549",
"AssayType": "ChIP-seq",
"Target": "H3K9ac ",
"Target": "CHD4 ",
"BioRep": "1",
"TechRep": "1_1",
"OutputType": "fold change over control",
"Format": "bigWig",
"Lab": "Bradley Bernstein, Broad",
"Accession": "ENCFF537QDO",
"Experiment": "ENCSR000ASV"
"Accession": "ENCFF725AXM",
"Experiment": "ENCSR550SCU"
},
"order": 3,
"order": 5,
"format": "bigwig",
"type": "wig",
"height": 128
"height": 128,
"windowFunction": "mean",
"color": "rgb(255, 114, 110)"
},
{
"name": "Homo sapiens A549 treated with 0.02% ethanol for 1 hour SIN3A ",
"url": "https://www.encodeproject.org/files/ENCFF620FRR/@@download/ENCFF620FRR.bigWig",
"name": "Homo sapiens aorta tissue male adult (34 years) H3K27ac ",
"url": "https://www.encodeproject.org/files/ENCFF162CIW/@@download/ENCFF162CIW.bigWig",
"color": "rgb(200,0,0)",
"metadata": {
"Biosample": "Homo sapiens A549 treated with 0.02% ethanol for 1 hour",
"Biosample": "Homo sapiens aorta tissue male adult (34 years)",
"AssayType": "ChIP-seq",
"Target": "SIN3A ",
"BioRep": "1,2",
"TechRep": "1_1,2_1",
"Target": "H3K27ac ",
"BioRep": "2",
"TechRep": "2_1",
"OutputType": "signal p-value",
"Format": "bigWig",
"Lab": "Richard Myers, HAIB",
"Accession": "ENCFF620FRR",
"Experiment": "ENCSR000BRM"
"Lab": "Bing Ren, UCSD",
"Accession": "ENCFF162CIW",
"Experiment": "ENCSR519CFV"
},
"order": 3,
"order": 6,
"format": "bigwig",
"type": "wig",
"height": 128,
"windowFunction": "mean"
},
{
"name": "Homo sapiens with nonobstructive coronary artery disease; liver tissue male adult (32 years) H3K9me3 ",
"url": "https://www.encodeproject.org/files/ENCFF566FON/@@download/ENCFF566FON.bigWig",
"color": "rgb(100,0,0)",
"metadata": {
"Biosample": "Homo sapiens with nonobstructive coronary artery disease; liver tissue male adult (32 years)",
"AssayType": "ChIP-seq",
"Target": "H3K9me3 ",
"BioRep": "1",
"TechRep": "1_1",
"OutputType": "fold change over control",
"Format": "bigWig",
"Lab": "Bing Ren, UCSD",
"Accession": "ENCFF566FON",
"Experiment": "ENCSR563YGF"
},
"order": 8,
"format": "bigwig",
"type": "wig",
"height": 128
"height": 128,
"windowFunction": "mean"
},
{
"name": "Refseq Genes",
Expand All @@ -373,7 +503,7 @@
]
};

igv.createBrowser(document.getElementById("myDiv"), overlay_throws_error_config).then(function (browser) {})
igv.createBrowser(document.getElementById("myDiv"), group_autoscale_config).then(function (browser) {})


</script>
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9 changes: 6 additions & 3 deletions dev/multi-select/multi-select.html
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Expand Up @@ -177,15 +177,15 @@ <h1>Multiple Track Selection</h1>

};

const MergedTracksConfig =
const overyTrackConfig =
{
genome: "hg19",
locus: "chr1:155,138,124-155,153,715",
tracks:
[
{
name: "Merged - configuration",
height: 50,
height: 256,
type: "merged",
tracks: [
{
Expand Down Expand Up @@ -231,18 +231,21 @@ <h1>Multiple Track Selection</h1>
format: "bigwig",
url: 'https://www.encodeproject.org/files/ENCFF206QIK/@@download/ENCFF206QIK.bigWig',
color: "red",
height: 128,
},
{
type: "wig",
format: "bigwig",
url: "https://www.encodeproject.org/files/ENCFF000ASJ/@@download/ENCFF000ASJ.bigWig",
color: "green",
height: 128,
},
{
type: "wig",
format: "bigwig",
url: "https://www.encodeproject.org/files/ENCFF351WPV/@@download/ENCFF351WPV.bigWig",
color: "blue",
height: 128,
}
]
};
Expand Down Expand Up @@ -288,7 +291,7 @@ <h1>Multiple Track Selection</h1>
]
}

igv.createBrowser(document.getElementById("igvDiv"), kitchenSinkConfig)
igv.createBrowser(document.getElementById("igvDiv"), overyTrackConfig)
.then(function (browser) {
console.log("Created IGV browser");
})
Expand Down
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