Skip to content

AA abundance per position plot #37

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
mzueva wants to merge 3 commits into
base: main
Choose a base branch
from
Open

AA abundance per position plot #37

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
cfee4ea
MILAB-5490 Add AA abundance per position plot
mzueva Mar 27, 2026
62e55b7
MILAB-5490 sdk update
mzueva Apr 14, 2026
848d79e
MILAB-5490 missing file
mzueva Apr 14, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions .changeset/eighty-coats-cheer.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
---
"@platforma-open/milaboratories.cdr3-spectratype.model": patch
"@platforma-open/milaboratories.cdr3-spectratype.ui": patch
---

Add AA abundance per position plot
74 changes: 69 additions & 5 deletions model/src/index.ts
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ export type UiState = {
weightedFlag: boolean;
vStackedBarPlotState: GraphMakerState;
cdr3StackedBarPlotState: GraphMakerState;
aaPositionPlotState: GraphMakerState;
};

export const model = BlockModel.create()
Expand Down Expand Up @@ -47,6 +48,11 @@ export const model = BlockModel.create()
template: 'stackedBar',
currentTab: null,
},
aaPositionPlotState: {
title: 'CDR3 AA Position',
template: 'stackedBar',
currentTab: null,
},
})

.argsValid((ctx) => {
Expand Down Expand Up @@ -120,17 +126,75 @@ export const model = BlockModel.create()
);
})

.outputWithStatus('aaPositionPf', (ctx) => {
const datasetRef = ctx.args.datasetRef;
if (datasetRef === undefined) return undefined;

const pCols = ctx.resultPool.getAnchoredPColumns(
{ main: datasetRef },
[{
axes: [
{ anchor: 'main', idx: 0 },
{ anchor: 'main', idx: 1 },
{ name: 'pl7.app/vdj/chain' },
{ name: 'pl7.app/vdj/numberingPosition' },
],
}],
);

if (!pCols || pCols.length === 0) return undefined;
return ctx.createPFrame(pCols);
})

.output('aaPositionPCols', (ctx) => {
const datasetRef = ctx.args.datasetRef;
if (datasetRef === undefined) return undefined;

const pCols = ctx.resultPool.getAnchoredPColumns(
{ main: datasetRef },
[{
axes: [
{ anchor: 'main', idx: 0 },
{ anchor: 'main', idx: 1 },
{ name: 'pl7.app/vdj/chain' },
{ name: 'pl7.app/vdj/numberingPosition' },
],
}],
);

if (!pCols || pCols.length === 0) return undefined;
return pCols.map((c) => ({ columnId: c.id, spec: c.spec } satisfies PColumnIdAndSpec));
})

.output('isRunning', (ctx) => ctx.outputs?.getIsReadyOrError() === false)

.title(() => 'CDR3 Spectratype')

.subtitle((ctx) => ctx.args.customBlockLabel || ctx.args.defaultBlockLabel)

.sections((_) => [
{ type: 'link', href: '/', label: 'Bubble Plot' },
{ type: 'link', href: '/vStackedBarPlot', label: 'V Spectratype' },
{ type: 'link', href: '/cdr3StackedBarPlot', label: 'CDR3 Spectratype' },
])
.sections((ctx) => {
const datasetRef = ctx.args?.datasetRef;
const hasAaPositions = datasetRef
? (ctx.resultPool.getAnchoredPColumns(
{ main: datasetRef },
[{
axes: [
{ anchor: 'main', idx: 0 },
{ anchor: 'main', idx: 1 },
{ name: 'pl7.app/vdj/chain' },
{ name: 'pl7.app/vdj/numberingPosition' },
],
}],
) ?? []).length > 0
: false;

return [
{ type: 'link', href: '/', label: 'Bubble Plot' },
{ type: 'link', href: '/vStackedBarPlot', label: 'V Spectratype' },
{ type: 'link', href: '/cdr3StackedBarPlot', label: 'CDR3 Spectratype' },
...(hasAaPositions ? [{ type: 'link' as const, href: '/aaPositionPlot' as const, label: 'AA Position' }] : []),
];
})
Comment on lines +129 to +197

@gemini-code-assist gemini-code-assist Bot Mar 27, 2026

Copy link
Copy Markdown

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

medium

The call to ctx.resultPool.getAnchoredPColumns with identical arguments is repeated three times in outputWithStatus('aaPositionPf', ...), output('aaPositionPCols', ...), and sections(...). This is inefficient, especially if getAnchoredPColumns is an expensive operation, and it also leads to code duplication, which can make maintenance more difficult.

A better approach would be to create a single intermediate output to compute the columns once. The result can then be reused in the other outputs and sections, which will improve performance and maintainability.

  .output('internalAaPositionPCols', (ctx) => {
    const datasetRef = ctx.args.datasetRef;
    if (datasetRef === undefined) return undefined;

    const pCols = ctx.resultPool.getAnchoredPColumns(
      { main: datasetRef },
      [{
        axes: [
          { anchor: 'main', idx: 0 },
          { anchor: 'main', idx: 1 },
          { name: 'pl7.app/vdj/chain' },
          { name: 'pl7.app/vdj/numberingPosition' },
        ],
      }],
    );

    return (pCols && pCols.length > 0) ? pCols : undefined;
  })

  .outputWithStatus('aaPositionPf', (ctx) => {
    const pCols = ctx.outputs.internalAaPositionPCols;
    if (pCols === undefined) return undefined;
    return ctx.createPFrame(pCols);
  })

  .output('aaPositionPCols', (ctx) => {
    const pCols = ctx.outputs.internalAaPositionPCols;
    if (pCols === undefined) return undefined;
    return pCols.map((c) => ({ columnId: c.id, spec: c.spec } satisfies PColumnIdAndSpec));
  })

  .output('isRunning', (ctx) => ctx.outputs?.getIsReadyOrError() === false)

  .title(() => 'CDR3 Spectratype')

  .subtitle((ctx) => ctx.args.customBlockLabel || ctx.args.defaultBlockLabel)

  .sections((ctx) => {
    const hasAaPositions = ctx.outputs.internalAaPositionPCols !== undefined;

    return [
      { type: 'link', href: '/', label: 'Bubble Plot' },
      { type: 'link', href: '/vStackedBarPlot', label: 'V Spectratype' },
      { type: 'link', href: '/cdr3StackedBarPlot', label: 'CDR3 Spectratype' },
      ...(hasAaPositions ? [{ type: 'link' as const, href: '/aaPositionPlot' as const, label: 'AA Position' }] : []),
    ];
  })


.done(2);

Expand Down
Loading
Loading