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Gene sets UI, right sidebar refactor (#2097)

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* prototyping

* render histos on open gene set

* prototyping

* render histos on open gene set

* factor out add genes to own component

* remove unused import

* mock reducer

* color by geneset stub

* menus and buttons

* geneset dialogue stub

* remove heatmap mock

* componetize histogram

* reenable add genes

* re-add isuserdefined

* test data

* remove have fetched

* add isExpanded state to gene, and pass to histogram

* expand button

* toggleable

* mini

* bump number of genes to 50

* don't clear diffexp on subset

* move create category to top

* render diffexp as geneset

* geneset show mean expression

* gene set reducer

* add geneset UI reducer

* wire e2e gene set loading prototype

* fix sniffing bug

* fix typo

* add gene modals

* client/src/actions/

* add autosave

* rename data-dir cli param

* add geneset, add gene, delete set

* prototype: remove csv upload placeholder

* handle delete gene from set

* prepopulate geneset with genes from modal

* add geneset: rename action

* icons, language consistency

* chevron after

* handle empty string case on genes for create geneset

* edit geneset

* fix language on create

* copy correction

* add popper2
upgrade react popper
upgrade react popper
adding popover2 package

* truncate uses tooltip2

* gene set button text typo

* remove logging

* moving server over

* remove test imports

* don't try to destructure map, use array.from

* fix add gene map datastructure error

* Revert "fix add gene map datastructure error"

This reverts commit b0eed45952.

* name --> genesetName, genes --> geneSymbols

* add gene to geneset, temporary format

* handle empty case, clear form input

* lint -- genesets wasn't passed via props

* userinfo

* move genes string to object conversion to action

* remove tmp gene description

* emptystring default for description

* remove empty string

* remove top level package json

* remove package lock as well

* remove flag for feature toggle

* remove comments in geneset

* comment cleanup

* remove comment

* revert diffexp genes to 10

* color by gene set

* disable color by gene set

* Gene menus are now inline, remove dead prototype code

* remove todo, magic number to variable

* remove jshint in rightsidebar

Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>

* remove unused geneset validation code

* tmp format pending geneset description

* move magic number into variable

* reorganize genesetsUI reducer pending tests

* rewire edit given new action name

* add basic validation and feedback for geneset name uniqueness

* mv annoDialog

* mv label, repair paths

* Update client/src/components/brushableHistogram/header.js

Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>

* add imports for icon in histo

* update jest snapshots given blueprint/tooltip2 usage of index -1

* ensure no empty paragraph

* intent from blueprint

* remove remainder of jshint references

* do not push undo when autosave fires

* fix autosave bugs

* remove todos

* clamp to util

* scient to util

* revert clearing diffexp

* rename value to be more specific stacked bar

* clean up logging and commetns

* remove gene entry tests pending rewrite

* tab index -1

* update jest snapshot, blueprint tooltip 2

* caret margin

* snapshot update

* ensure histogram is centered

* add geneset actions to config

* comment maybeScientific

* comment clamp

* comment ui reducer

* remove prototype code

* remove error log

* remove references to bl.ocks

* componetize parseBulkGeneString

* catch case where geneset rename same name

* genesetui reducer tests

* add geneset ui to index reducer config

Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
This commit is contained in:
Colin Megill
2021-03-24 16:33:26 -04:00
committed by GitHub
co-authored by Severiano Badajoz bkmartinjr
parent 5335c39184
commit e6e358ddc8
66 changed files with 1926 additions and 905 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/src/components/geneExpression/index.js
+62 -43
View File
@@ -1,59 +1,78 @@
/* rc slider https://www.npmjs.com/package/rc-slider */
import React from "react";
import _ from "lodash";
import { connect } from "react-redux";
import HistogramBrush from "../brushableHistogram";
import * as globals from "../../globals";
import AddGenes from "./addGenes";
import { Button } from "@blueprintjs/core";
import GeneSet from "./geneSet";
import CreateGenesetDialogue from "./menus/createGenesetDialogue";
import EditGenesetNameDialogue from "./menus/editGenesetNameDialogue";
@connect((state) => {
return {
userDefinedGenes: state.controls.userDefinedGenes,
differential: state.differential,
genesets: state.genesets.genesets,
};
})
class GeneExpression extends React.Component {
renderGeneSets = () => {
const sets = [];
const { genesets } = this.props;
for (const [name, genes] of genesets) {
sets.push(
<GeneSet
key={name}
setGenes={Array.from(genes.genes.keys())}
setName={name}
/>
);
}
return sets;
};
renderDiffexpGeneSets = () => {
const { differential } = this.props;
const setGenes = [];
if (differential.diffExp) {
differential.diffExp.forEach((diffexpGene) => {
setGenes.push(diffexpGene[0]);
});
}
return differential.diffExp ? (
<GeneSet
key="Temp DiffExp Set"
setGenes={setGenes}
isDiffexp
setName="Temp DiffExp Set"
/>
) : null;
};
handleActivateCreateGenesetMode = () => {
const { dispatch } = this.props;
dispatch({ type: "geneset: activate add new geneset mode" });
};
render() {
const { userDefinedGenes, differential } = this.props;
return (
<div
style={{
borderBottom: `1px solid ${globals.lighterGrey}`,
}}
>
<div>
<div>
<AddGenes />
{userDefinedGenes.length > 0
? _.map(userDefinedGenes, (geneName, index) => {
return (
<HistogramBrush
key={geneName}
field={geneName}
zebra={index % 2 === 0}
isUserDefined
/>
);
})
: null}
</div>
<div>
{differential.diffExp
? _.map(differential.diffExp, (value, index) => {
return (
<HistogramBrush
key={value[0]}
field={value[0]}
zebra={index % 2 === 0}
isDiffExp
logFoldChange={value[1]}
pval={value[2]}
pvalAdj={value[3]}
/>
);
})
: null}
<div style={{ marginBottom: 10, position: "relative", top: -2 }}>
<Button
data-testid="open-create-geneset-dialog"
onClick={this.handleActivateCreateGenesetMode}
intent="primary"
>
Create new <strong>gene set</strong>
</Button>
</div>
<CreateGenesetDialogue />
<EditGenesetNameDialogue />
</div>
<div>{this.renderDiffexpGeneSets()}</div>
<div>{this.renderGeneSets()}</div>
</div>
);
}