AG-1344 scaling bug fix and refactor of gene evidence box plots #1281

sagely1 · 2024-02-05T18:41:54Z

No description provided.

sagely1 · 2024-02-05T18:42:53Z

src/app/features/charts/components/box-plot-chart/box-plot-chart.component.ts

@@ -34,6 +34,7 @@ export class BoxPlotComponent extends BaseChartComponent {
  @Input() yAxisLabel = 'LOG 2 FOLD CHANGE';
  @Input() yAxisMin: number | undefined;
  @Input() yAxisMax: number | undefined;
+  @Input() yAxisPadding = 0.2;


now the chart has the ability to have a padding specified

...app/features/genes/components/gene-evidence-proteomics/gene-evidence-proteomics.component.ts

src/app/features/charts/components/box-plot-chart/box-plot-chart.component.ts

src/app/models/ChartRange.ts

...app/features/genes/components/gene-evidence-proteomics/gene-evidence-proteomics.component.ts

hallieswan

These changes look good!

While looking at the examples in the ticket, I noticed that the TMT plot for MDK still isn't shown, even though there is data available. I think this may be related to this code , where selectedUniProtId is determined using the uniprotids from both proteomics_LFQ and proteomics_TMT. For MDK, proteomics_LFQ has E9PPJ5 and P21741 as uniprotids, but proteomics_TMT only has P21741 as uniprotid. E9PPJ5 is set as the selectedUniProtId, but is only found in the LFQ data, so no data is displayed for the TMT plot. Would you mind taking a look? Up to you whether to make the fix here or open a new ticket to track!

sagely1 · 2024-02-23T23:33:06Z

These changes look good!

While looking at the examples in the ticket, I noticed that the TMT plot for MDK still isn't shown, even though there is data available. I think this may be related to this code , where selectedUniProtId is determined using the uniprotids from both proteomics_LFQ and proteomics_TMT. For MDK, proteomics_LFQ has E9PPJ5 and P21741 as uniprotids, but proteomics_TMT only has P21741 as uniprotid. E9PPJ5 is set as the selectedUniProtId, but is only found in the LFQ data, so no data is displayed for the TMT plot. Would you mind taking a look? Up to you whether to make the fix here or open a new ticket to track!

Good observation. The nature of the data is that there are times that data for LFQ or TMT may not exist. In that case, we can allow the plots to show as 'no data is currently available'.

sagely1 · 2024-02-23T23:35:31Z

...app/features/genes/components/gene-evidence-proteomics/gene-evidence-proteomics.component.ts

@@ -54,10 +54,6 @@ export class GeneEvidenceProteomicsComponent {
  init() {
    this.reset();

-    if (!this._gene?.proteomics_LFQ && this._gene?.proteomics_TMT) {


Original code is confusing and these props are always defined.

hallieswan · 2024-02-23T23:45:08Z

Good observation. The nature of the data is that there are times that data for LFQ or TMT may not exist. In that case, we can allow the plots to show as 'no data is currently available'.

Oh I see! I didn't notice the dropdown for selecting the uniprotid of interest, which determines which data to show. Thanks for helping me understand!

AG-1344 scaling bug fix and refactor of gene evidence box plots

0c19150