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Dataframe, part deux - add varData and summarize() (#608)

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* initial dataframe commit

* initial dataframe port of core app

* rename variables for clarity

* remove unused import

* comment out unused code

* fix array handling bug in crossfilter dimension creation

* allow creation of empty dataframes

* handle non-existent columns

* handle non-existent columns

* revise tests for new dataframe

* comments for clarity

* comments for clarity

* generate bulk add placeholder with real gene names

* fix bug in gene name adding

* more dataframe unit tests

* fix bug - subset from current world, not universe

* put cut and pasted code into a single function

* improve caching of crossfilter

* remove cascading update bug from graph

* more performance work

* improve state handling for scatterplot

* performance optimization of critical path

* add column summarization

* dataframe utils

* add callOnceLazy

* fix tests

* minor updates found during review

* fix misspelling

* remove RESTv02 from function names

* comment cleanup

* cut/icut col parameter defaults to null

* break up large test

* improve tests and comments on dataframe at/has functions

* add Dataframe withCol/dropCol

* expression varData now stored in a dataframe

* dead code cleanup

* use dataframe.summarize()

* test cases for Dataframe.col.summarize

* update test cases for new dataframe summarize

* improve naming

* use new hasCol API

* add comments

* add more Dataframe.withCol tests

* add ability to specify row index in cut operation

* retire subsetVarData function

* correctly handle expression subsetting

* lint and improve comments

* rename cut to subset

* changes based on PR review
This commit is contained in:
Bruce Martin
2019-02-28 08:34:22 -08:00
committed by GitHub
parent 2bae696986
commit ffd6273419
21 changed files with 910 additions and 1140 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/src/components/brushableHistogram/index.js
+7 -16
View File
@@ -10,7 +10,6 @@ import { Button, ButtonGroup, Tooltip } from "@blueprintjs/core";
import { connect } from "react-redux";
import * as d3 from "d3";
import memoize from "memoize-one";
import { kvCache } from "../../util/stateManager";
import * as globals from "../../globals";
import actions from "../../actions";
import finiteExtent from "../../util/finiteExtent";
@@ -21,7 +20,6 @@ import finiteExtent from "../../util/finiteExtent";
scatterplotYYaccessor: state.controls.scatterplotYYaccessor,
crossfilter: state.controls.crossfilter,
differential: state.differential,
initializeRanges: _.get(state.controls.world, "summary.obs"),
colorAccessor: state.controls.colorAccessor,
colorScale: state.controls.colorScale,
obsAnnotations: _.get(state.controls.world, "obsAnnotations", null)
@@ -35,7 +33,7 @@ class HistogramBrush extends React.Component {
.scaleLinear()
.range([this.height - this.marginBottom, 0]);
if (obsAnnotations.col(field)) {
if (obsAnnotations.hasCol(field)) {
// recalculate expensive stuff
const allValuesForContinuousFieldAsArray = obsAnnotations
.col(field)
@@ -52,9 +50,8 @@ class HistogramBrush extends React.Component {
.thresholds(40)(allValuesForContinuousFieldAsArray);
histogramCache.numValues = allValuesForContinuousFieldAsArray.length;
} else if (kvCache.get(world.varDataCache, field)) {
/* it's not in observations, so it's a gene, but let's check to make sure */
const varValues = kvCache.get(world.varDataCache, field);
} else if (world.varData.hasCol(field)) {
const varValues = world.varData.col(field).asArray();
histogramCache.x = d3
.scaleLinear()
@@ -143,21 +140,15 @@ class HistogramBrush extends React.Component {
}
handleColorAction() {
const {
obsAnnotations,
dispatch,
field,
world,
initializeRanges
} = this.props;
const { obsAnnotations, dispatch, field, world, ranges } = this.props;
if (obsAnnotations.col(field)) {
if (obsAnnotations.hasCol(field)) {
dispatch({
type: "color by continuous metadata",
colorAccessor: field,
rangeMaxForColorAccessor: initializeRanges[field].range.max
rangeMaxForColorAccessor: ranges.max
});
} else if (kvCache.get(world.varDataCache, field)) {
} else if (world.varData.hasCol(field)) {
dispatch(actions.requestSingleGeneExpressionCountsForColoringPOST(field));
}
}
client/src/components/continuous/continuous.js
+26 -21
View File
@@ -9,7 +9,7 @@ import * as globals from "../../globals";
import HistogramBrush from "../brushableHistogram";
@connect(state => ({
ranges: _.get(state.controls.world, "summary.obs", null),
obsAnnotations: _.get(state.controls.world, "obsAnnotations", null),
colorAccessor: state.controls.colorAccessor,
colorScale: state.controls.colorScale,
selectionUpdate: _.get(state.controls, "crossfilter.updateTime", null),
@@ -28,17 +28,18 @@ class Continuous extends React.Component {
handleColorAction(key) {
return () => {
const { dispatch, ranges } = this.props;
const { dispatch, obsAnnotations } = this.props;
const summary = obsAnnotations.col(key).summarize();
dispatch({
type: "color by continuous metadata",
colorAccessor: key,
rangeMaxForColorAccessor: ranges[key].range.max
rangeMaxForColorAccessor: summary.max
});
};
}
render() {
const { ranges, schema } = this.props;
const { obsAnnotations, schema } = this.props;
if (schema && !this.continuousChecked) {
this.hasContinuous = _.some(
schema.annotations.obs,
@@ -62,23 +63,27 @@ class Continuous extends React.Component {
Continuous metadata
</p>
) : null}
{_.map(ranges, (value, key) => {
const isColorField = key.includes("color") || key.includes("Color");
zebra += 1;
if (value.range && key !== "name" && !isColorField) {
return (
<HistogramBrush
key={key}
field={key}
isObs
zebra={zebra % 2 === 0}
ranges={value.range}
handleColorAction={this.handleColorAction(key).bind(this)}
/>
);
}
return null;
})}
{obsAnnotations
? _.map(obsAnnotations.colIndex.keys(), key => {
const summary = obsAnnotations.col(key).summarize();
const isColorField =
key.includes("color") || key.includes("Color");
zebra += 1;
if (!summary.categorical && key !== "name" && !isColorField) {
return (
<HistogramBrush
key={key}
field={key}
isObs
zebra={zebra % 2 === 0}
ranges={summary}
handleColorAction={this.handleColorAction(key).bind(this)}
/>
);
}
return null;
})
: null}
</div>
);
}
client/src/components/geneExpression/cellSetButtons.js
+5 -1
View File
@@ -14,7 +14,11 @@ class CellSetButton extends React.Component {
eitherCellSetOneOrTwo
} = this.props;
const set = World.getSelectedByIndex(crossfilter);
// Reducer and components assume that value will be null if
// no selection made. World..getSelectedByIndex() returns a
// zero length TypedArray when nothing is selected.
let set = World.getSelectedByIndex(crossfilter);
if (set.length === 0) set = null;
if (!differential.diffExp) {
/* diffexp needs to be cleared before we store a new set */
client/src/components/geneExpression/index.js
+7 -9
View File
@@ -56,12 +56,8 @@ const filterGenes = (query, genes) =>
});
@connect(state => {
const ranges = _.get(state.controls.world, "summary.obs", null);
const initializeRanges = _.get(state.controls.world, "summary.obs");
return {
ranges,
initializeRanges,
obsAnnotations: _.get(state.controls.world, "obsAnnotations", null),
userDefinedGenes: state.controls.userDefinedGenes,
userDefinedGenesLoading: state.controls.userDefinedGenesLoading,
world: state.controls.world,
@@ -293,16 +289,17 @@ class GeneExpression extends React.Component {
) : null}
{world && userDefinedGenes.length > 0
? _.map(userDefinedGenes, (geneName, index) => {
const values = world.varDataCache[geneName];
const values = world.varData.col(geneName);
if (!values) {
return null;
}
const summary = values.summarize();
return (
<HistogramBrush
key={geneName}
field={geneName}
zebra={index % 2 === 0}
ranges={finiteExtent(values)}
ranges={summary}
isUserDefined
/>
);
@@ -322,16 +319,17 @@ class GeneExpression extends React.Component {
{differential.diffExp
? _.map(differential.diffExp, (value, index) => {
const name = world.varAnnotations.at(value[0], "name");
const values = world.varDataCache[name];
const values = world.varData.col(name);
if (!values) {
return null;
}
const summary = values.summarize();
return (
<HistogramBrush
key={name}
field={name}
zebra={index % 2 === 0}
ranges={finiteExtent(values)}
ranges={summary}
isDiffExp
logFoldChange={value[1]}
pval={value[2]}
client/src/components/scatterplot/scatterplot.js
+8 -5
View File
@@ -19,7 +19,6 @@ import _drawPoints from "./drawPointsRegl";
import scaleLinear from "../../util/scaleLinear";
import { margin, width, height } from "./util";
import { kvCache } from "../../util/stateManager";
import finiteExtent from "../../util/finiteExtent";
@connect(state => {
@@ -30,12 +29,16 @@ import finiteExtent from "../../util/finiteExtent";
scatterplotYYaccessor
} = state.controls;
const expressionX =
world && scatterplotXXaccessor
? kvCache.get(world.varDataCache, scatterplotXXaccessor)
world &&
scatterplotXXaccessor &&
world.varData.hasCol(scatterplotXXaccessor)
? world.varData.col(scatterplotXXaccessor).asArray()
: null;
const expressionY =
world && scatterplotYYaccessor
? kvCache.get(world.varDataCache, scatterplotYYaccessor)
world &&
scatterplotYYaccessor &&
world.varData.hasCol(scatterplotYYaccessor)
? world.varData.col(scatterplotYYaccessor).asArray()
: null;
return {