From cda350b14ce657471785c877225f7081b481fd80 Mon Sep 17 00:00:00 2001 From: Peter Kerpedjiev Date: Fri, 29 Nov 2024 21:58:41 -0800 Subject: [PATCH] Revert to original test config in index.html --- src/index.html | 187 ++++++++++++++++++++++++++++++++++++++----------- 1 file changed, 147 insertions(+), 40 deletions(-) diff --git a/src/index.html b/src/index.html index a46c9b9..3884b69 100644 --- a/src/index.html +++ b/src/index.html @@ -66,24 +66,82 @@ "exportViewUrl": "/api/v1/viewconfs", "views": [ { - "initialXDomain": [ - 1853645535.4582071, - 1853645704.8611746 - ], + //"initialXDomain": [1069795,1070508], + + // Variant + Soft Clipping (left) + "initialXDomain": [1558492965,1558493030], + + // Insertions + Soft Clipping both sides + //"initialXDomain": [105706,105906], + + // Hard Clipping (left and both sides) + //"initialXDomain": [145009,145409], + + // Deletions + //"initialXDomain": [128870,129070], + "initialYDomain": [ - -406323904.4626087, - -406323832.0176704 + 180520.26598912096, + 180863.4346387336 ], "tracks": { "top": [ + // { + // "type": "pileup", + // "uid": "WBTUIwm0SB2gcas7wzwztA", + // "tilesetUid": "NLxWZTCoSzei1lkH4yVJmg", + // "server": "https://resgen.io/api/v1", + // "options": { + // "axisPositionHorizontal": "right", + // "axisLabelFormatting": "normal", + // "outlineReadOnHover": false, + // "showMousePosition": false, + // "name": "HG002 Illumina (60x)", + // "labelPosition": "bottomLeft", + // "groupBy": null, + // "colorScale": [ + // "#08519c", + // "#6baed6", + // "#993404", + // "#fe9929", + // "#808080", + // "#DCDCDC" + // ] + // }, + // "width": 651, + // "height": 362 + // }, { - "type": "pileup", - "uid": "NgvIT-sdTf2M6eeh3WlJlw", - "tilesetUid": "OAQ516H3SfWvyutsR07oYg", - "server": "http://localhost:8000/api/v1", + "uid": "AdlJsUYFRzuJRZyYeKDX2A", + "type": "chromosome-labels", + "width": 811, + "height": 30, + "server": "//higlass.io/api/v1", "options": { - "axisPositionHorizontal": "right", - "axisLabelFormatting": "normal", + "color": "#808080", + "stroke": "#ffffff", + "fontSize": 12, + "fontIsLeftAligned": false, + "showMousePosition": false, + "mousePositionColor": "#000000" + }, + "filetype": "chromsizes-tsv", + "tilesetUid": "NyITQvZsS_mOFNlz5C2LJg" + }, + { + "uid": "fastaex", + "data": { + "type": "fasta", + "faiUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.fa.fai", + "fastaUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.fa", + "chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes" + }, + "type": "horizontal-sequence", + "width": 768, + "height": 25, + "options": { + "name": "hg38", + "barBorder": true, "colorScale": [ "#08519c", "#6baed6", @@ -92,34 +150,83 @@ "#808080", "#DCDCDC" ], - "outlineReadOnHover": false, - "showMousePosition": false, - "showCoverage": false, - "coverageHeight": 10, - "name": "https://genomeark.s3.amazonaws.com/species/Gorilla_gorilla/mGorGor1/assembly_curated/mapping/bwa.analysis-dip.illumina.bam", - "outlineMateOnHover": true, - "maxTileWidth": 200000, - "collapseWhenMaxTileWidthReached": false, - "minMappingQuality": 0, - "highlightReadsBy": [], - "largeInsertSizeThreshold": 1000, - "viewAsPairs": false - }, - "width": 774, - "height": 317 + "labelColor": "black", + "valueScaling": "linear", + "labelPosition": "topLeft", + "barBorderColor": "white", + "backgroundColor": "white", + "labelTextOpacity": 0.4, + "sortLargestOnTop": true, + "trackBorderColor": "white", + "trackBorderWidth": 0, + "extendedPreloading": false, + "colorAggregationMode": "none", + "notificationText": "Zoom in to see nucleotides...", + "fontSize": 16, + "fontFamily": "Arial", + "fontColor": "white", + "textOption": { + "fontSize": "32px", + "fontFamily": "Arial", + "fill": 16777215, + "fontWeight": "bold" + } + } }, { - "type": "top-axis", - "local": true, - "orientation": "1d-horizontal", - "thumbnail": {}, - "defaultOptions": {}, - "server": "", - "tilesetUid": "JYQIW1hmQAWH-K0APqZq-A", - "uid": "HHTqfZfqQF-FjCdGTESZ9A", - "options": {}, - "width": 461, - "height": 20 + "type": "pileup", + "options": { + "axisPositionHorizontal": "right", + "axisLabelFormatting": "normal", + "outlineReadOnHover": "yes", + "groupBy": "strand", + "minusStrandColor": "#ffd1d4", + "plusStrandColor": "#cfd0ff", + "showCoverage": true, + "colorScale": [ + // A T G C N Other + "#08519c", + "#6baed6", + "#993404", + "#fe9929", + "#808080", + "#DCDCDC" + ] + }, + "height": 500, + "uid": "FylkvVBTSumoJ959HT4-5B", + "data": { + "type": "bam", + + // Caution: Example does not fit to the sequence track above. + // "url": "https://pkerp.s3.amazonaws.com/public/bamfile_test/SRR1770413.sorted.bam", + // "chromSizesUrl": "https://pkerp.s3.amazonaws.com/public/bamfile_test/GCF_000005845.2_ASM584v2_genomic.chrom.sizes", + + // Variant + Soft Clipping (left) + "bamUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr9_22004085.bam", + "baiUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr9_22004085.bam.bai", + "chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes", + + // Insertions + Soft Clipping both sides + // "bamUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr1_105806_S_I.bam", + // "baiUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr1_105806_S_I.bam.bai", + // "chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes", + + // Hard Clipping (left and both sides) + // "bamUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr1_145209_H.bam", + // "baiUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr1_145209_H.bam.bai", + // "chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes", + + // Deletions + // "bamUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr1_128970_D.bam", + // "baiUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr1_128970_D.bam.bai", + // "chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes", + + "options": { + "maxTileWidth": 30000 + } + }, + "width": 470 } ], "left": [], @@ -131,11 +238,11 @@ }, "layout": { "w": 12, - "h": 12, + "h": 6, "x": 0, "y": 0 }, - "uid": "cz2sOeJgRIWJ5J0wYZu4fw" + "uid": "WdlA7F8aTY2gXQzPGiBlwQ" } ], "zoomLocks": {