Release 13.0.2 (#210)

* Pass drug screen when multiple data types are selected

* Clean up code

* Add additional depletion screen scores

Caleydo/tdp_bi_bioinfodb#1364

* orphan import

* Linting and other fixes

* Linting

* prepare next development version 12.0.1-SNAPSHOT

* Replace `gene_map_ensgs` with idtype mapping

Closes Caleydo/tdp_bi_bioinfodb#419

* Replace `gene_map_ensgs` request with native idtype mapping
* Remove python DB view
* Remove `_id` from typing, as it was not returned by the API and was not used previously

* Remove orphan import

* Fix typo in depletion screen score name

* Allow for the domain of the scores to be auto-inferred (#175)

Co-authored-by: Holger Stitz <holger.stitz@datavisyn.io>

* Fix Typescript compile errors in `selectionChanged` and `parameterCanged` of ranking views (#191)

* Fix TS errors ranking views

The return value of `selectionChanged` and `parameterCanged` has been typed/changed in datavisyn/tdp_core#725

* Fix data type select in welcome tour (#192)

* Fix outdated dist folder (#194)

* Prepare github changes

* Remove circleci

* prepare next dev version

* Update fontawesome

* refactor: Improve Cypress setup and use Cypress commands.js (#169)

Co-authored-by: Florian Engertsberger <florian.engertsberger@datavisyn.io>
Co-authored-by: Holger Stitz <holger.stitz@datavisyn.io>

* Merge visyn_scripts

* prepare next dev version

* Add nowrap to button, add scrollbar to searchbox (#203)

* Show CoExpression messages / errors (#202)

* Fix sorting of chromosomes due to new typings (#206)

* Fix sorting of chromosomes due to new typings

Caused by datavisyn/tdp_core#794

* Add missing dist files

* prepare next dev version

* Fix score domains (#204)

Co-authored-by: Holger Stitz <holger.stitz@datavisyn.io>

* fix: boxplot and matrix domain in aggregated scores (#208)

Fix boxplot and matrix domain in aggregated scores

Fixes Caleydo/tdp_bi_bioinfodb#1402

* fix: domain of gene signature scores (#209)

Caleydo/tdp_bi_bioinfodb#1402

* fix: rename AVANA to Avana

* prepare release 13.0.2

Co-authored-by: oltionchampari <oltion.champari@datavisyn.io>
Co-authored-by: Holger Stitz <holger.stitz@datavisyn.io>
Co-authored-by: Champari Oltion <51322092+oltionchampari@users.noreply.github.com>
Co-authored-by: anita-steiner <>
Co-authored-by: Florian Engertsberger <florian.engertsberger@datavisyn.io>

package.json

@@ -1,7 +1,7 @@
 {
   "name": "tdp_publicdb",
   "description": "",
-  "version": "13.0.1",
+  "version": "13.0.2",
   "author": {
     "name": "The Caleydo Team",
     "email": "contact@caleydo.org",
@@ -62,8 +62,8 @@
     "react-select": "^4.1.0",
     "react-select-async-paginate": "^0.5.3",
     "react-virtualized": "^9.22.3",
-    "tdp_core": "^16.1.0",
-    "visyn_scripts": "^1.0.1"
+    "tdp_core": "^16.2.1",
+    "visyn_scripts": "^1.1.1"
   },
   "optionalDependencies": {
     "ordino": "git+ssh://git@github.com:Caleydo/ordino#semver:^13.0.1"

requirements.txt

@@ -1 +1 @@
-tdp_core>=16.1.0,<17.0.0
+tdp_core>=16.2.1,<17.0.0

src/common/config.ts

@@ -312,7 +312,7 @@ export const expression: IDataTypeConfig = {
       id: 'tpm',
       name: 'Normalized Gene Expression (TPM Values)',
       type: dataSubtypes.number,
-      domain: [null, null], // domain will be auto-inferred
+      domain: [0, null],
       missingValue: NaN,
       constantDomain: true,
       useForAggregation: 'tpm',
@@ -321,7 +321,7 @@ export const expression: IDataTypeConfig = {
       id: 'counts',
       name: 'Raw Counts',
       type: dataSubtypes.number,
-      domain: [null, null],
+      domain: [0, null],
       missingValue: NaN,
       constantDomain: true,
       useForAggregation: 'counts',
@@ -443,7 +443,7 @@ export const depletion: IDataTypeConfig = {
       id: 'ataris',
       name: 'DRIVE ATARiS (ER McDonald III et al., Cell, 2017)',
       type: dataSubtypes.number,
-      domain: [0, null],
+      domain: [null, null],
       missingValue: NaN,
       constantDomain: false,
       useForAggregation: 'ataris',
@@ -453,17 +453,17 @@ export const depletion: IDataTypeConfig = {
       id: 'ceres',
       name: 'Avana CERES (Robin M. Meyers et al., Nature Genetics, 2017)',
       type: dataSubtypes.number,
-      domain: [0, null],
+      domain: [null, null],
       missingValue: NaN,
       constantDomain: false,
       useForAggregation: 'ceres',
       filter: 'Avana',
     },
     {
       id: 'chronos',
-      name: 'AVANA Chronos (DepMap.org)',
+      name: 'Avana Chronos (DepMap.org)',
       type: dataSubtypes.number,
-      domain: [0, null],
+      domain: [null, null],
       missingValue: NaN,
       constantDomain: false,
       useForAggregation: 'chronos',
@@ -473,7 +473,7 @@ export const depletion: IDataTypeConfig = {
       id: 'escore',
       name: 'Sanger E-score (Fiona M. Behan et al., Nature 2019)',
       type: dataSubtypes.number,
-      domain: [0, null],
+      domain: [null, null],
       missingValue: NaN,
       constantDomain: false,
       useForAggregation: 'escore',

src/scores/GeneSignatureScore.ts

@@ -67,7 +67,7 @@ export class GeneSignatureScore implements IScore<number> {
    */
   createDesc() {
     const label = this.options.description;
-    return ColumnDescUtils.numberCol('_gene_signature', -5, 5, { label });
+    return ColumnDescUtils.numberCol('_gene_signature', null, null, { label }); // null, null = infer min/max automatically from the data
   }
 
   /**

src/scores/ScoreUtils.ts

@@ -38,7 +38,7 @@ export class ScoreUtils {
           type: 'boxplot',
           label,
           description,
-          domain: [1, 100],
+          domain: [null, null],
           lazyLoaded: true,
           sort: 'median', // sort by default by median
           missingValue: null,
@@ -48,7 +48,7 @@ export class ScoreUtils {
           type: 'numbers',
           label,
           description,
-          domain: [1, 100],
+          domain: [null, null],
           colorRange: ['white', 'black'],
           lazyLoaded: true,
           dataLength: 10, // initial width