Prototype genotype backend API

[Don-Isdale]

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Comments with open items :

• :construction: 2022Jun17 (Don-Isdale)

• 2022Aug01

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MVP

• [x] use bcftools, on vcf file; [/4H] [feature/genotypeApi b7c81d11] Add vcfGenotypeLookup API 130c68e9 : increase height of textarea
• • later can integrate into Pretzel db
• [x] just 1A of the first file (of 3, on dataverse) 'wheat LD'. b7c81d11
• [x] [/4H] request : get a list of samples. 0e5ca585
• • • [x] [/2H] select samples for request (using copy/paste instead of multi-select)
• [x] enable request when zoomed in to 1Mb. b7c81d11

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• [x] [/0.5H] vcfGenotypeLookup : increase height of textarea. 130c68e9

• [x] [/3H] move vcfGenotypeLookup to added Genotypes tab. 8ec6922d, 66d3f8aa

• [x] [/5H] show results in table 4ebd8b2e : vcfGenotypeLookup : show result in features table

• • [x] [1-2H/1H] feature positions in the table are OK, but it is using the location of the last feature in the vcf result to position the yellow circles of all features assign .id to created features. a1f86df2
• • [x] [/8H] matrix-view (ref/alt coloured triangles). 6e6ee748

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From comment 2

:construction:

2022Jun17

• [x] [1-2H/4H] change bcftools view format to request just GT (0/1) be95f036 vcfGenotype : request alternate formats, display TGT using CATGRenderer
  • • [x] [/4H] try alternate data Renderer-s (CATG, AB, numericalData). be95f036
• • [x] [1-2H/4H] coloured triangles for distinct alleles. cf1ac392
  • • • [x] AB. implemented A/B comparison. enabled by options=gtSelectColumn

  related : #47

• [x] re-try column heading rotate. 1d505a4e : genotype table : rotate column headers to vertical, noted in #324

• [x] [2-3H/3H] add replace checkbox to remove previous results from feature table. added button : be95f036,

• • [x] 739825b3 : VCF lookup : implement replaceResults : remove features of block from selectedFeatures (Jun20 2H15, tested Aug01)

• [x] [2-3H/10H] retain samples & selected samples when changing between tabs (e.g. feature table & genotype tab) retain samples & selected samples when changing between tabs. 0d5cb0ee genotype table : filter features when re-displaying. 95ca3678

• show list of vcf data blocks in brushed axes, with checkboxes to select which are requested (default true)

• pass samples via array

• option off block long name from column header (col_name_fn)

• pass ._meta.vcfFilename - optional, default is datasetId.id

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From comment 3, Jun17

MVP screenshots

Illustration of completion of items in MVP comment above

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• request : get a list of samples. 0e5ca585
• • • select samples for request (using copy/paste instead of multi-select)

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• show results in table 4ebd8b2e : vcfGenotypeLookup : show result in features table

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• • matrix-view (ref/alt coloured triangles). 6e6ee748

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From comment 4, Aug01

2022Aug01

• [x] [/2H] test these Jun20 changes : VCF lookup : implement replaceResults : remove features of block from selectedFeatures. 739825b3
• [x] [/1H] matrix-view : increase table height. f1785538

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• [x] 666dc763 update genotype display in response to brush change

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• [x] [/8H] matrix-view : show yellow in axis circles, as in feature table - highlightFeature. d1230296 these changes supported that : 4d7d8bd2 [/2H] : feature table : use feature data in row 8724be3e [/3H] : ensure that axis menu can be shown.

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• [x] [/4H] changes related to axis-1d replacing .axis. 0dcca1bd
• [x] [/2H] dataset explorer : improve performance when switching between server tabs. 2c14d8c5

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• [x] vcf lookup : support multiple vcf datasets. 75eda1c4
  • • [x] handle repeated requests and same SNPs in another VCF dataset result. 2f2b2da1 [/2H]

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Aug29 - Sep02

• [x] 93d5e100 vcf lookup : handle various white-space in samples request list
• [x] 0133e675 genotype table : preserve user settings / selections through tab switch.

vcf lookup :

• [x] 6194081a : map cr/lf in sample names list to a single newline.
• [x] f695335d : update selection list when a data block is viewed.

genotype table :

• [x] fcd460ef : enable multiple blocks
• [x] 6c466ac5 : show sample column for each block, 95d93cd0 re-indent
• [x] d383d1a8 : respond to block .visible

vcf lookup :

• [x] f42d7aeb : add sliders for intervalLimit and rowLimit
• [x] 3be2b146 : apply row limit to truncate query result in server, 1a2ee854 re-indent

genotype table :

• [x] cafad54d : replace A/A with A
• [x] 7a2635d7 : sort by feature start value
• [x] 4c1fee16 : prepend Position column
• [x] f92f29ae : re-enable yellow circle

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Sep05

• [x] [/6H] vcf lookup : wrap inputs and select in dialog. e125b870
• [x] [/4H] vcf lookup : indicate result size, minimise by default. b2e930f2

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from meeting 2022Aug11

• to show aligment of axes with genotype table : generate a dynamic 'view' dataset+block which is parallel to the genotype table (matrix-view) horizontal position at right edge, abutting the table

• row hover can also highlight in axis tracks - split axis.

• possible genotype table actions :

• • click to create a axis annotation (as with feature triangles, but different shape)
• • brush to create an interval annotation

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• [x] [/7H] A/B comparison is set up so far is to select A and all others become B - i.e. they are expressed relative to A (difference) instead : keep it anchored relative to the genome sequence, so ACGT rather than A/B but maybe it colours it instead keeps the nucleotide but the colours indicate different/same 5175cb46 : colour relative to selected sample column - indicate different/same

• check feature a

• maybe server selector

• ? genotype table : add chromosome column ?

• limit on samples, or POST, because CORS "missing allow-origin" (related POST in #216 : 09f6fb8a)

• preserve samples of block, e.g. Map and status selected:boolean of sample

• button 'Show combined results'

• vcf blocks list : if no brush, use selected or selected dataBlocks

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from meeting 2022Sep06 :

• [ ] 1. [8H] merge when match position (option) merge feature name with comma if different names at equal position. pass displayDataRows and columnNames to matrix-view which can then use displayDataRows directly instead of converting in dataByRow() use position as row index (sparse array) column index : continue to use datasetId + block scope/name + sampleName cell attributes may be single or an array : string value, feature Symbol reference where value is an array, use feature block colour to indicate the block of each part merging columns (same sample name) probably not needed atm, add to the arrays.

• [x] [/1H] drop dataset name in left column 42f7624e. genotype table : abbreviate dataset name in left column

• [x] [/3H] load remainder of chr vcf for the 2 vcf.

  • [x] [/2H] Add description of getting datasets from Harvard Dataverse. a2491c60
  • [x] smooth the process of addition of multiple vcf files (document in pretzel-hosting) [/1H] add more detail to VCF description in blast.md. pretzel-hosting : 6204b97

• [x] [/2H] block colour column (when overlaps) a62e7984. genotype table : add block colour column.

• [x] showing differerence from reference genome : standard colours : 0 : orange, 2 : blue, 1 : white [/8H] add colouring by copy#, used in ABRenderer dependiing on column selection, support select all features and clearing column selection, etc. e9df33e8 [/2H] connect mouse click to selectBlock for genotype table, handle more cases in cell colour. 7d348208, 4c9908c8 [/0.5H] genotype table : reduce x/y or x|y copy# %GT differently to CATG %TGT. 0cd58b28

• [x] [/2.5H] bcftools options : request extra columns : ref/alt vcf lookup : request extra columns : ref/alt from bcftools, and display them in genotype table. e043ccac

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• display vcf lookup errors in GUI

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2022Sep09

• [x] thin white gap between Alt column and sample columns [/3H] genotype table : add a white border between Alt and first sample column. e22720a9

• [ ] sample column headings : omit dataset name

  • colour by block

• [x] performance of dataset explorer when many datasets caused by dataset with 1000s of traits - removed. worked on using progressive rendering of long lists in explorer and View : Trait & Ontology (@html-next/vertical-collection, ember-in-viewport) - can use those later as lists get larger.

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2022Sep12

• [ ] 2. [/2H] when in the 012 view, it would make sense to also colour the ref/alt on the left side with the 2 colours used for the rest of the genotypes

• [x] [/2H] use class-based rule for table cell colours. e3fc9b8d, 0435f4ba

• [x] [/1H] vcf lookup : fix condition for closing dialog. 606227f9

• [x] [/0.5H] display features from VCF lookup in axis tracks. 88438cdc

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[Don-Isdale]

[moved content to comment 1 : Jun10]

[Don-Isdale]

[moved content to comment 1 : Jun10]

[Don-Isdale]

[moved content to comment 1 : Jun10]

[Don-Isdale]

Ideas for genotype & haplotype views

To prompt a variety of ideas on visualising the genotype & haplotype data, these pages and papers have diagrams with different views. These are mostly beyond the immediate requirements, but as always the approach is to look as far forward as possible, to provide a linear and staged process to those long-term goals.

• figure 5 Haplotype structure across 12 wheat varieties obtained from The 10 + Wheat Genome Project Muqaddasi et al 2020 Prospects of GWAS and predictive breeding for European winter wheat’s grain protein content, grain starch content, and grain hardness

• WhatsHap User Guide

IGV : Integrative Genomics Viewer

• Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration paper - Semantic Scholar

• IGV Default Display

• IGV multilocus view in Pretzel : fairly easy to implement multiple selected regions ("brushes") per axis.

Sequence tube maps

• figure 1
• Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
• github : vgteam/sequenceTubeMap

SNiPlay :

• paper
• LD scores figure 9
• CGI page
• github
• Dockerfile
• Genotype Investigator for Genome Wide Analyses Gigwa

Various

• MoMI-G: modular multi-scale integrated genome graph browser paper github

• A Detailed View of KIR Haplotype Structures and Gene Families as Provided by a New Motif-Based Multiple Sequence Alignment paper

• Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit paper

• A Detailed View of KIR Haplotype Structures and Gene Families as Provided by a New Motif-Based Multiple Sequence Alignment paper

• figure 2

• Natural Genetic Diversity in Tomato Flavor Genes paper

• HaploSWEEP : Haplotype-based genotyping designed for polyploid species github

• inPHAP: Interactive visualization of genotype and phased haplotype data github

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• circular haplotype tree, linked to Phylum / cMAG / Isolate Figure 1

[Don-Isdale]

draft diagrams

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2022Sep06

• [ ] add ref/alt columns, request ref/alt from bcftools
• [ ] (lower priority) create lines aligning genotype table to adjacent axis : add a virtual axis adjacent the table, with constant-spaced features matching row positions; update when table scroll

• [ ] drop the dataset name from the left column, add an adjacent column showing a coloured rectangle with block colour

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