Extending QTL features

[Don-Isdale]

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Based on users' feedback from use of QTL spreadsheet upload, which is now released, and the types of dataset which users are loading and how they wish to use this data Pretzel, this branch will draw on those ideas to develop the QTL functionality.

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This continues on from the work done in :

• 197

• 233

Related :

• 46

• 256 (of those, cropOntology.org seems most applicable)

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• [x] [6-16H/16H] explorer tab specific to Trait / QTLs : perhaps group by : Trait : Parent (GM) : Scope (Chromosome) trait tab : trait / parent / scope 4986e414: dataset explorer : add Trait tab c85fe714: apply search filter to Trait tab 0199ba31: trait tab : display number of matched traits

• [x] [1-3H/0.5H] hover in Trait table can show features (QTL) list of trait. 5663ea4b

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from meeting 2021Oct07

• trait tab : trait : parent : blocks (datasets) Can move later to be sibling to 'Datasets'.
• API to get a list of all traits in the database
• Ontology browser : discussed requirements; not starting yet. (tree with progressive focus, like https://www.ncbi.nlm.nih.gov/genome/gdv/; select leaf, or a node to filter for its child nodes)

QTL display :

• [x] [2-4H/1.5H] diamond size : default 2-3 times wider than current (noted previously : slider for diamond size) e93e3705 : QTL diamond : 2x default size, and add a view slider to adjust.

• [x] [1H/0.2H] change border colour from block colour to trait colour (same as fill colour). 7abbe1b2

• • [x] [1H/1.5H] for these elements : selected feature / triangle / text / vertical line interval (click, shift-click) if the feature is QTL, use trait colour instead of block colour. 0a5d34e4

• [x] [1-2H/3H+2H] axis ticks : drop ,000,000 where possible, i.e. remove the common factor 80c6e61f: axis tick labels : use SI to avoid ,000 612dd8b9 : axis tick labels : slightly increase the resolution

• [ ] [1H] in workshop introduction : explain the toggles in 'Chart Options'

• [ ] integrate 'Chart Options' into 'Selected Axis Options' and rename to 'View Settings'

• [ ] [1-2H] add a toggle for all paths, because when viewing QTLs they may be a distraction. This can discard the block-adjs components, which saves on computation and API requests.

• [x] [1-2H/4H] lookup cropOntology API to display CO: values in Feature.values.Ontology cbd290e8 : feature table : for Ontology column, lookup from cropOntology API and display name.

• [x] [1H/0.5H] button to copy selected Feature.values.Sequence into Sequence Search input 513f8b58 : sequence search : add arrow button to copy .values.Sequence from the first selected QTL which defines it.

• [ ] [1-2H] upload uses collection.insert which is deprecated

• [6-16H reqs to be defined] create, persist QTL

• • discuss requirements :
• • • persist to database or localStorage;
• • • create dataset and blocks - populate the upload/csv panel
• • • add to existing dataset

• [4-8H] project QTL to adjacent axis : e.g. QTL -> nearest path endpoints (inside or outside the QTL) -> features at other end of paths -> define an interval on the target axis related : #46

• [8-24H depends on requirements] QTL upload : ontology for Trait column (#256, cropOntology.org)

• • possibly controlled in spreadsheet template; or provide an audit & edit dialog in the frontend GUI : highlight (e.g. in features table) the Traits which don't have an ontology, and provide GUI selection for those, and update the database.

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• [x] [/1H] Move QTLs closer to axis. 7f4061b0

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Adjustments to QTL horizontal position and width, discussed 2021Oct29 and earlier

• [ ] [2-3H] making all QTL widths the same regardless of layering / duplicate position
• [x] [2-3H/1.5H] QTL diamond clipping at top of axis 40c7fe37: QTL diamond : prevent clipping at top of axis by raising top of clip rectangle. 1fbf1956 : update clip rect for QTL diamond when diamondWidth changes b758ab19 : QTL diamond clipping : also extend clip rect at bottom of axis
• [ ] [2-4H] GUI toggle for QTL width : compress into a fixed space, or stack them up even if they go over the next axis
• [x] [1-2H/1H] slider to adjust the distance of QTL from axis. aaea3e1b, 45f3468b
• [x] [1-2H/1H] viewing QTL blocks : change task ownership of getBlockFeaturesIntervalTask() to models/block, so each block can make a request in quick succession (currently prevented by .drop()). a20d79f1. cfaae1be 0.5H.

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• [ ] [2-4H] update pulses QTL spreadsheet to make sure it matches the current requirements.
  • • [ ] [1H] include citation to check that metadata handles the requirements.
  • • [x] [2-8H/4H] chickpea QTL file

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not related to QTLs, but probably look at this in the same time-frame :

• investigate to scope out : loading initial display of viewed datasets/blocks from url; this currently shows axes OK; shows paths for some datasets, with possible update required to complete the display

[Don-Isdale]

Some feature developments for consideration

(there will be more detail to add to these, increasing the estimates approx 2x )

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• Use alias instead of direct feature name lookup on QTL flanking markers to determine position on the parent dataset. This would benefit QTLs which are positioned by SSR Flanking Markers. Aliases may produce multiple positions on the parent dataset, so show the range of positions as the QTL interval.

implementation :

• [8-12H] use a variation of pathsAliases between the QTL block and its parent block. Variation is to use QTL flanking markers instead of the QTL block's features. (alternate : could change the flanking markers to be sub-features of the QTL feature; this seems more general, but has more design impact, and that abstraction doesn't seem to have near-term feature benefits)

• this could be enabled by a tag on the dataset (applies when the QTL dataset is loaded), or a GUI checkbox (can re-calculate positions dynamically in response to user action [2H] ).

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moved Ontology items to new sub issue : #273

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• top-level explorer : genome-level - all chromosomes of a dataset. show : qtl-s, feature counts, synteny blocks, no paths, This would probably be like a different mode of draw-map; from the user's perspective this is a new outer-most mode.

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• chromosome / Block heat map (within dataset explorer) : based on the selected Chromosome / Block, show the counts of common (direct) features
  • • [1-3H] api to get the counts of connections between all blocks
  • • [1-2H] show counts as number and/or colour on the Block nodes; could summarise on Dataset nodes also [1-2H]. The purpose of this is to assist in choosing related datasets to add to the display.

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• [3-5H] drag stack sideways to a different position and stay there until add / change stacks

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