EDA in WDK: Integrate EDA scatterplot in WDK record page #1325

dmfalke · 2025-02-14T18:17:57Z

This PR builds off of #1314. It integrates an EDA scatterplot into a WDK gene page, for crispr phenotype data.

TODOs

Prototype use of scatterplot on gene page
Refactor ExpressionGraph component to use new record table that will include plot configs per dataset (JB is working on this)

Testing

I am testing it with a local genomics-site dev server, using my dev site, which is configured to use toxo068n, since phenotype data isn't showing up on toxo-inc.

In packages/sites/genomics-site/.env:

BASE_PROXY_URL=https://dfalke-b.toxodb.org
LEGACY_WEB_APP_URL=${BASE_PROXY_URL}/toxo
PROJECT_ID=ToxoDB

Run yarn nx start @veupathdb/genomics-site and navigate to http://localhost:8080/a/app/record/gene/TGGT1_261490#category:phenomics.

param value

… object

dynamically.

* fix for thumnails not rendering * replace mutating state with better check of filters

dynamically.

…ies (#1323)

* added plot annotations functionality * improve scatter annotation story * added histogram annotation story * introduce VEuPathDBAnnotation type * fix annotation types in histogram

dmfalke · 2025-02-14T18:22:40Z

packages/libs/web-common/src/components/eda/EdaScatterPlot.tsx

+        studyId,
+        filters: [],
+        config: {
+          outputEntityId: xAxisVariable.entityId,


@asizemore I'm linking this comment to this pr.

To address your question, I wonder if this should be a part of the plot configuration that we will be getting from the record table. Might be a question for @jbrestel

dmfalke and others added 30 commits January 28, 2025 14:37

checkpoint

d4b68f8

Add type annotations to remove inferred any type.

2d10d9a

Allow an analysis descriptor to be provided to useAnalysis

cdd1672

Only update state if the next param value is different than the previous

f65bf95

param value

Extract useAnalysisState to allow external state tracking of analysis…

3897a70

… object

Use useAnalysisState, add counts, etc

dab2578

Add stubbed question page with custom name

76fd220

Allow hiding starred variable feature

cf7cf3b

fix typo

cebee2c

Use global memoization

13ada9f

Encapsulate creation of eda api clients

9a6c058

Adhere to lastest "api" for GenesByEdaSubset

486270d

Stub in eda scatterplot for phenotype dataset

9aeb81d

Merge remote-tracking branch 'origin/main' into eda-in-wdk/search

f36ebb7

Allow html formatting in search page header

5d4e3f1

Enable override for GenesByEdaSubset and set question page heading

b8b4790

dynamically.

use more specific query name

f78170e

Merge remote-tracking branch 'origin/main' into eda-in-wdk/search

3fa6651

update query name

76d6de3

use dynamic import for plotly, to keep it out of the main bundle

8e7644e

replace "EdaSubsetting" with "EdaSubset"

7db8014

dont wrap sentence

756faaf

fix label in user comment upload form

92a28ce

Fix volcano plot thumbnail out of sync (#1299)

00b5a15

* fix for thumnails not rendering * replace mutating state with better check of filters

Allow html formatting in search page header

78d719d

Enable override for GenesByEdaSubset and set question page heading

6d891e6

dynamically.

use more specific query name

f29a30d

Use alphabetic ordering when displaying a flattened list of eda entit…

fd1c732

…ies (#1323)

only order variable tree entities alphabetically (#1324)

929f835

Add annotations to plotly plots (#1321)

f00a004

* added plot annotations functionality * improve scatter annotation story * added histogram annotation story * introduce VEuPathDBAnnotation type * fix annotation types in histogram

dmfalke added 5 commits February 14, 2025 10:35

update query name

025803f

use dynamic import for plotly, to keep it out of the main bundle

69997dc

replace "EdaSubsetting" with "EdaSubset"

08ef180

Revert to injecting script and link tags in document head

ef8bca8

Merge branch 'eda-in-wdk/search' into eda-in-wdk/record-page

f13da20

dmfalke commented Feb 14, 2025

View reviewed changes

dmfalke changed the title ~~Eda in wdk: record page~~ EDA in WDK: Integrate EDA scatterplot in WDK record page Feb 17, 2025

dmfalke added 13 commits February 18, 2025 14:36

Merge branch 'main' into eda-in-wdk/record-page

be0bbf5

Export type

3d73886

Expand type to include ReactHTML elements

9631fc3

Allow className to be overridden

18b4c8e

Add EdaDatasetGraph component

25d93f8

Use EdaDatasetGraph component with EdaPhenotypeGraphsDataTable

12ba4cc

simplify layout and add warning message for genes not in experiment

655e32e

Merge remote-tracking branch 'origin/main' into eda-in-wdk/record-page

c3f0f56

Add parentheses

4515795

Wire up highlightIds

03ae31d

Highlight graph_ids

b683ff5

Allow arbitrary variable values to be highlighted

82334b0

Specify gene variable values to highlight

eb8a47b

dmfalke merged commit cdf3a33 into main Feb 24, 2025
1 check passed

dmfalke deleted the eda-in-wdk/record-page branch February 24, 2025 18:34

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

EDA in WDK: Integrate EDA scatterplot in WDK record page #1325

EDA in WDK: Integrate EDA scatterplot in WDK record page #1325

dmfalke commented Feb 14, 2025 •

edited

Loading

dmfalke Feb 14, 2025

EDA in WDK: Integrate EDA scatterplot in WDK record page #1325

EDA in WDK: Integrate EDA scatterplot in WDK record page #1325

Conversation

dmfalke commented Feb 14, 2025 • edited Loading

TODOs

Testing

dmfalke Feb 14, 2025

Choose a reason for hiding this comment

dmfalke commented Feb 14, 2025 •

edited

Loading