Fix heatmap bug in representing deletions. #183
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ashsny
reviewed
May 2, 2024
| export function parseSimpleProVariant(variant: string): SimpleProteinVariation | null { | ||
| const match = variant.match(proVariantRegex) | ||
| if (!match) { | ||
| // console.log(`WARNING: Unrecognized pro variant: ${variant}`) |
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should probably be un-commented or deleted
src/components/ScoreSetHeatmap.vue
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| // .tickFormat(n => String.fromCharCode('A'.charCodeAt(0) + n - 1)) | ||
| .tickFormat((n) => { | ||
| // Get the row's amino acid code or variation symbol. | ||
| const label = HEATMAP_ROWS[HEATMAP_ROWS.length - 1 - n] |
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repeating this logic to reverse the HEATMAP_ROWS gets very confusing to the reader.
I think there are a few options here.
- reverse heatmap_rows
- use a d3 scalePoint as in this notebook to combine the flipping and translation of letter to axis position: https://observablehq.com/@mbostock/phases-of-the-moon
- to eliminate the backwards iteration below, use a data structure for each heatmap_rows entry with style and label attributes that have defaults, so we have entries like {'symbol': '-', 'style': 'mave-heatmap-y-axis-tick-label-lg'} and {'symbol': '*', 'label': '\uff0a'}
src/lib/heatmap.ts
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| * @return The one-character code representing the same amino acid or change, or null if the input was not a supported | ||
| * amino acid or change. | ||
| */ | ||
| export function singleLetterAminoAcidOrHgvsCode(aaCodeOrChange: string) { |
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let's do explicit return types for ts in this project
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This fixes issue #139, in which it was reported that deletions appear in the top row of the heatmap, normally reserved for substitutions by Ala.
In addition:
@PlushZ provided a useful example in score set tmp:540c9d47-9e0c-4c56-839c-3b1249a957df. To test the bug fix using this example, you may change the ownership of that score set in a development instance of MaveDB.
The heatmap for this score set should now look like this:
The heatmap for score set urn:mavedb:00000001-a-1 is a good check against regressions, and it should look like this:
