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Adding box plots drawn on std-deviation instead of quartiles #6698

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Merged
merged 21 commits into from
Aug 18, 2023
Merged

Adding box plots drawn on std-deviation instead of quartiles #6698

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7241716
First push
28raining Aug 5, 2023
fe3d2d0
Adding draftlog
28raining Aug 5, 2023
923df18
Create sizemode after fb in pull 6698
28raining Aug 12, 2023
b0868e5
Fix failing translate string
28raining Aug 12, 2023
3e1319e
Updating schema
28raining Aug 12, 2023
0e9d5a6
generate correct baseline. Use .replace to keep var in translated string
28raining Aug 15, 2023
29c813f
re-add whiskers to violin plots
28raining Aug 15, 2023
6ea8d6d
Update src/traces/box/plot.js
28raining Aug 15, 2023
c3f9ea7
reverting jasmine test
28raining Aug 15, 2023
d7e2f1b
Merge branch 'dev-box-sigma-boxes' of https://github.com/28raining/pl…
28raining Aug 15, 2023
4e4b486
Change whisker default if sizemode=='sd'
28raining Aug 15, 2023
b3812f8
add showwhiskers to candlestick
28raining Aug 15, 2023
505a14e
if sizemode === quartiles, don't use boxmean
28raining Aug 16, 2023
3a3b46c
Update description for whisker default behavior
28raining Aug 16, 2023
44e1355
roll back candelstick and violin changes
28raining Aug 16, 2023
edfa543
simplify sizemode usage
28raining Aug 16, 2023
a48f2ce
fix lint
28raining Aug 16, 2023
66dcba7
update schema
28raining Aug 16, 2023
013f4d3
roll back violin further
28raining Aug 16, 2023
1668fe9
rolled back contributing
28raining Aug 17, 2023
f84e93f
selectively coerce sdmultiple
28raining Aug 17, 2023
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8 changes: 7 additions & 1 deletion CONTRIBUTING.md
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Expand Up @@ -118,7 +118,7 @@ npm start

This command bundles up the source files and opens up a tab in your browser.

#### Step 6: Open up the console and start developing
#### Step 6a: Open up the console and start developing

A typical workflow is to make some modifications to the source, update the
test dashboard, inspect and debug the changes, then repeat. The test dashboard
Expand Down Expand Up @@ -146,6 +146,12 @@ Three additional helpers exist that are refreshed every second:
There is also a search bar in the top right of the dashboard. This fuzzy-searches
image mocks based on their file name and trace type.

#### Step 6b: Create a mock to test new features
Create a new JSON inside
`test\image\mocks\`
which you'll then be able to search from the test dashboard
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In several cases adding new image tests are not necessary.
So this step should be optional and it could be part of Step 6.
You may revert changes in CONTRIBUTING.md and possibly submit a separate PR to suggest improvements as well.
Thank you!



#### Step 7: Regenerate plot-schema in "test" folder then review & commit potential changes

```bash
Expand Down
1 change: 1 addition & 0 deletions draftlogs/6697_add.md
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@@ -0,0 +1 @@
- Add [1-6]-sigma (std deviations) box plots as an alternative to quartiles [[#6697](https://github.com/plotly/plotly.js/issues/6697)]
34 changes: 33 additions & 1 deletion src/traces/box/attributes.js
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Expand Up @@ -218,7 +218,30 @@ module.exports = {
'right (left) for vertical boxes and above (below) for horizontal boxes'
].join(' ')
},

sdmultiple: {
valType: 'number',
min: 0,
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Shouldn't the minimum be one instead of zero?

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what if you want 0.5σ? Might be weird but I don't see a reason to prohibit it.

editType: 'calc',
dflt: 1,
description: [
'Scales the box size when sizemode=sd',
'Allowing boxes to be drawn across any stddev range',
'For example 1-stddev, 3-stddev, 5-stddev',
].join(' ')
},
sizemode: {
valType: 'enumerated',
values: ['quartiles', 'sd'],
editType: 'calc',
dflt: 'quartiles',
description: [
'Sets the upper and lower bound for the boxes',
'quartiles means box is drawn between Q1 and Q3',
'SD means the box is drawn between Mean +- Standard Deviation',
'Argument sdmultiple (default 1) to scale the box size',
'So it could be drawn 1-stddev, 3-stddev etc',
].join(' ')
},
boxmean: {
valType: 'enumerated',
values: [true, 'sd', false],
Expand Down Expand Up @@ -378,6 +401,15 @@ module.exports = {
].join(' ')
},

showwhiskers: {
valType: 'boolean',
editType: 'calc',
description: [
'Determines whether or not whiskers are visible.',
'Defaults to true for `sizemode` *quartiles*, false for *sd*.'
].join(' ')
},

offsetgroup: barAttrs.offsetgroup,
alignmentgroup: barAttrs.alignmentgroup,

Expand Down
6 changes: 4 additions & 2 deletions src/traces/box/calc.js
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Expand Up @@ -221,7 +221,7 @@ module.exports = function calc(gd, trace) {
cdi.min = boxVals[0];
cdi.max = boxVals[N - 1];
cdi.mean = Lib.mean(boxVals, N);
cdi.sd = Lib.stdev(boxVals, N, cdi.mean);
cdi.sd = Lib.stdev(boxVals, N, cdi.mean) * trace.sdmultiple;
cdi.med = Lib.interp(boxVals, 0.5);

if((N % 2) && (usesExclusive || usesInclusive)) {
Expand Down Expand Up @@ -286,7 +286,9 @@ module.exports = function calc(gd, trace) {
q1: _(gd, 'q1:'),
q3: _(gd, 'q3:'),
max: _(gd, 'max:'),
mean: trace.boxmean === 'sd' ? _(gd, 'mean ± σ:') : _(gd, 'mean:'),
mean: (trace.boxmean === 'sd') || (trace.sizemode === 'sd') ?
_(gd, 'mean ± σ:').replace('σ', trace.sdmultiple === 1 ? 'σ' : (trace.sdmultiple + 'σ')) : // displaying mean +- Nσ whilst supporting translations
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This line is getting too long.
How about adding agetMean(gd, trace) and move & revise this logic there?

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Putting the code into a function would make the code less readable - if readability is the concern here.

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I agree - if it's only going to be used here, extracting to a function just means it takes another jump to read and understand the code. @archmoj if your concern is just line length we can break this onto more lines. Or leave it for now and sometime add prettier to our toolchain like we have in various other projects 😉

_(gd, 'mean:'),
lf: _(gd, 'lower fence:'),
uf: _(gd, 'upper fence:')
}
Expand Down
7 changes: 6 additions & 1 deletion src/traces/box/defaults.js
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Expand Up @@ -40,9 +40,14 @@ function supplyDefaults(traceIn, traceOut, defaultColor, layout) {
if(sd && sd.length) boxmeanDflt = 'sd';
}
}
coerce('boxmean', boxmeanDflt);

coerce('whiskerwidth');
var sizemode = coerce('sizemode');
if(sizemode === 'quartiles') {
coerce('boxmean', boxmeanDflt);
}
coerce('showwhiskers', sizemode === 'quartiles');
coerce('sdmultiple');
coerce('width');
coerce('quartilemethod');

Expand Down
4 changes: 2 additions & 2 deletions src/traces/box/hover.js
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Expand Up @@ -140,7 +140,7 @@ function hoverOnBoxes(pointData, xval, yval, hovermode) {
pointData.spikeDistance = dxy(di) * spikePseudoDistance / hoverPseudoDistance;
pointData[spikePosAttr] = pAxis.c2p(di.pos, true);

var hasMean = trace.boxmean || (trace.meanline || {}).visible;
var hasMean = trace.boxmean || (trace.sizemode === 'sd') || (trace.meanline || {}).visible;
var hasFences = trace.boxpoints || trace.points;

// labels with equal values (e.g. when min === q1) should still be presented in the order they have when they're unequal
Expand Down Expand Up @@ -179,7 +179,7 @@ function hoverOnBoxes(pointData, xval, yval, hovermode) {
// clicked point from a box during click-to-select
pointData2.hoverOnBox = true;

if(attr === 'mean' && ('sd' in di) && trace.boxmean === 'sd') {
if(attr === 'mean' && ('sd' in di) && ((trace.boxmean === 'sd') || (trace.sizemode === 'sd'))) {
pointData2[vLetter + 'err'] = di.sd;
}

Expand Down
34 changes: 22 additions & 12 deletions src/traces/box/plot.js
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Expand Up @@ -54,6 +54,7 @@ function plotBoxAndWhiskers(sel, axes, trace, t, isStatic) {
var wdPos = t.wdPos || 0;
var bPosPxOffset = t.bPosPxOffset || 0;
var whiskerWidth = trace.whiskerwidth || 0;
var showWhiskers = (trace.showwhiskers !== false);
var notched = trace.notched || false;
var nw = notched ? 1 - 2 * trace.notchwidth : 1;

Expand Down Expand Up @@ -94,12 +95,15 @@ function plotBoxAndWhiskers(sel, axes, trace, t, isStatic) {

var posm0 = posAxis.l2p(lcenter - bdPos0 * nw) + bPosPxOffset;
var posm1 = posAxis.l2p(lcenter + bdPos1 * nw) + bPosPxOffset;
var q1 = valAxis.c2p(d.q1, true);
var q3 = valAxis.c2p(d.q3, true);
var sdmode = trace.sizemode === 'sd';
var q1 = valAxis.c2p(sdmode ? d.mean - d.sd : d.q1, true);
var q3 = sdmode ? valAxis.c2p(d.mean + d.sd, true) :
valAxis.c2p(d.q3, true);
// make sure median isn't identical to either of the
// quartiles, so we can see it
var m = Lib.constrain(
valAxis.c2p(d.med, true),
sdmode ? valAxis.c2p(d.mean, true) :
valAxis.c2p(d.med, true),
Math.min(q1, q3) + 1, Math.max(q1, q3) - 1
);

Expand All @@ -109,7 +113,7 @@ function plotBoxAndWhiskers(sel, axes, trace, t, isStatic) {
// - box always has d.lf, but boxpoints can be anything
// - violin has d.lf and should always use it (boxpoints is undefined)
// - candlestick has only min/max
var useExtremes = (d.lf === undefined) || (trace.boxpoints === false);
var useExtremes = (d.lf === undefined) || (trace.boxpoints === false) || sdmode;
var lf = valAxis.c2p(useExtremes ? d.min : d.lf, true);
var uf = valAxis.c2p(useExtremes ? d.max : d.uf, true);
var ln = valAxis.c2p(d.ln, true);
Expand All @@ -127,10 +131,13 @@ function plotBoxAndWhiskers(sel, axes, trace, t, isStatic) {
'V' + pos0 + // right edge
(notched ? 'H' + un + 'L' + m + ',' + posm0 + 'L' + ln + ',' + pos0 : '') + // bottom notched edge
'Z' + // end of the box
'M' + q1 + ',' + posc + 'H' + lf + 'M' + q3 + ',' + posc + 'H' + uf + // whiskers
(whiskerWidth === 0 ?
'' : // whisker caps
'M' + lf + ',' + posw0 + 'V' + posw1 + 'M' + uf + ',' + posw0 + 'V' + posw1
(showWhiskers ?
'M' + q1 + ',' + posc + 'H' + lf + 'M' + q3 + ',' + posc + 'H' + uf + // whiskers
(whiskerWidth === 0 ?
'' : // whisker caps
'M' + lf + ',' + posw0 + 'V' + posw1 + 'M' + uf + ',' + posw0 + 'V' + posw1
) :
''
)
);
} else {
Expand All @@ -148,10 +155,13 @@ function plotBoxAndWhiskers(sel, axes, trace, t, isStatic) {
''
) + // notched left edge
'Z' + // end of the box
'M' + posc + ',' + q1 + 'V' + lf + 'M' + posc + ',' + q3 + 'V' + uf + // whiskers
(whiskerWidth === 0 ?
'' : // whisker caps
'M' + posw0 + ',' + lf + 'H' + posw1 + 'M' + posw0 + ',' + uf + 'H' + posw1
(showWhiskers ?
'M' + posc + ',' + q1 + 'V' + lf + 'M' + posc + ',' + q3 + 'V' + uf + // whiskers
(whiskerWidth === 0 ?
'' : // whisker caps
'M' + posw0 + ',' + lf + 'H' + posw1 + 'M' + posw0 + ',' + uf + 'H' + posw1
) :
''
)
);
}
Expand Down
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156 changes: 156 additions & 0 deletions test/image/mocks/box_sizemode_sd.json
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@@ -0,0 +1,156 @@
{
"data": [
{
"y": [
0.4995, 0.3786, 0.5188, 0.4505, 0.5805, 0.5539, 0.7341, 0.3303, 0.6202, 0.4754, 0.4814, 0.6103, 0.5157, 0.3841, 0.6166, 0.4917, 0.5646, 0.4532, 0.5983,
0.5079, 0.5227, 0.5483, 0.3081, 0.5172, 0.4127, 0.3871, 0.4703, 0.5331, 0.4573, 0.6187, 0.5718, 0.4474, 0.5349, 0.4614, 0.3096, 0.4411, 0.7143, 0.5956,
0.5171, 0.5515, 0.4234, 0.4589, 0.4289, 0.417, 0.4229, 0.5039, 0.4726, 0.5382, 0.261, 0.5326, 0.4472, 0.54, 0.4998, 0.5513, 0.3891, 0.4821, 0.5006,
0.4362, 0.4184, 0.3632, 0.5182, 0.5229, 0.5493, 0.507, 0.4528, 0.4836, 0.5009, 0.49, 0.5757, 0.5408, 0.4246, 0.511, 0.5216, 0.3817, 0.4471, 0.4935,
0.5668, 0.3187, 0.3633, 0.5964, 0.637, 0.4701, 0.4292, 0.4921, 0.439, 0.5846, 0.4502, 0.44, 0.3057, 0.4756, 0.4867, 0.502, 0.438, 0.6819, 0.2607,
0.5233, 0.3291, 0.5555, 0.5397, 0.5068
],
"line": {
"color": "#1c9099"
},
"type": "box",
"boxpoints": "all",
"pointpos": 0,
"name": "1-sigma",
"sizemode": "sd",
"showwhiskers": false
},
{
"y": [
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0.4362, 0.4184, 0.3632, 0.5182, 0.5229, 0.5493, 0.507, 0.4528, 0.4836, 0.5009, 0.49, 0.5757, 0.5408, 0.4246, 0.511, 0.5216, 0.3817, 0.4471, 0.4935,
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0.5233, 0.3291, 0.5555, 0.5397, 0.5068
],
"line": {
"color": "#1c9099"
},
"boxpoints": "all",
"pointpos": 0,
"type": "box",
"name": "2-sigma",
"sdmultiple" : 2,
"sizemode": "sd",
"showwhiskers": false
},
{
"y": [
0.4995, 0.3786, 0.5188, 0.4505, 0.5805, 0.5539, 0.7341, 0.3303, 0.6202, 0.4754, 0.4814, 0.6103, 0.5157, 0.3841, 0.6166, 0.4917, 0.5646, 0.4532, 0.5983,
0.5079, 0.5227, 0.5483, 0.3081, 0.5172, 0.4127, 0.3871, 0.4703, 0.5331, 0.4573, 0.6187, 0.5718, 0.4474, 0.5349, 0.4614, 0.3096, 0.4411, 0.7143, 0.5956,
0.5171, 0.5515, 0.4234, 0.4589, 0.4289, 0.417, 0.4229, 0.5039, 0.4726, 0.5382, 0.261, 0.5326, 0.4472, 0.54, 0.4998, 0.5513, 0.3891, 0.4821, 0.5006,
0.4362, 0.4184, 0.3632, 0.5182, 0.5229, 0.5493, 0.507, 0.4528, 0.4836, 0.5009, 0.49, 0.5757, 0.5408, 0.4246, 0.511, 0.5216, 0.3817, 0.4471, 0.4935,
0.5668, 0.3187, 0.3633, 0.5964, 0.637, 0.4701, 0.4292, 0.4921, 0.439, 0.5846, 0.4502, 0.44, 0.3057, 0.4756, 0.4867, 0.502, 0.438, 0.6819, 0.2607,
0.5233, 0.3291, 0.5555, 0.5397, 0.5068
],
"line": {
"color": "#1c9099"
},
"type": "box",
"boxpoints": "all",
"pointpos": 0,
"name": "3-sigma",
"sdmultiple" : 3,
"sizemode": "sd",
"showwhiskers": false
},
{
"y": [
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0.5079, 0.5227, 0.5483, 0.3081, 0.5172, 0.4127, 0.3871, 0.4703, 0.5331, 0.4573, 0.6187, 0.5718, 0.4474, 0.5349, 0.4614, 0.3096, 0.4411, 0.7143, 0.5956,
0.5171, 0.5515, 0.4234, 0.4589, 0.4289, 0.417, 0.4229, 0.5039, 0.4726, 0.5382, 0.261, 0.5326, 0.4472, 0.54, 0.4998, 0.5513, 0.3891, 0.4821, 0.5006,
0.4362, 0.4184, 0.3632, 0.5182, 0.5229, 0.5493, 0.507, 0.4528, 0.4836, 0.5009, 0.49, 0.5757, 0.5408, 0.4246, 0.511, 0.5216, 0.3817, 0.4471, 0.4935,
0.5668, 0.3187, 0.3633, 0.5964, 0.637, 0.4701, 0.4292, 0.4921, 0.439, 0.5846, 0.4502, 0.44, 0.3057, 0.4756, 0.4867, 0.502, 0.438, 0.6819, 0.2607,
0.5233, 0.3291, 0.5555, 0.5397, 0.5068
],
"line": {
"color": "#1c9099"
},
"type": "box",
"boxpoints": "all",
"pointpos": 0,
"name": "1-sigma + whiskers",
"sizemode": "sd",
"showwhiskers": true
},
{
"y": [
0.4995, 0.3786, 0.5188, 0.4505, 0.5805, 0.5539, 0.7341, 0.3303, 0.6202, 0.4754, 0.4814, 0.6103, 0.5157, 0.3841, 0.6166, 0.4917, 0.5646, 0.4532, 0.5983,
0.5079, 0.5227, 0.5483, 0.3081, 0.5172, 0.4127, 0.3871, 0.4703, 0.5331, 0.4573, 0.6187, 0.5718, 0.4474, 0.5349, 0.4614, 0.3096, 0.4411, 0.7143, 0.5956,
0.5171, 0.5515, 0.4234, 0.4589, 0.4289, 0.417, 0.4229, 0.5039, 0.4726, 0.5382, 0.261, 0.5326, 0.4472, 0.54, 0.4998, 0.5513, 0.3891, 0.4821, 0.5006,
0.4362, 0.4184, 0.3632, 0.5182, 0.5229, 0.5493, 0.507, 0.4528, 0.4836, 0.5009, 0.49, 0.5757, 0.5408, 0.4246, 0.511, 0.5216, 0.3817, 0.4471, 0.4935,
0.5668, 0.3187, 0.3633, 0.5964, 0.637, 0.4701, 0.4292, 0.4921, 0.439, 0.5846, 0.4502, 0.44, 0.3057, 0.4756, 0.4867, 0.502, 0.438, 0.6819, 0.2607,
0.5233, 0.3291, 0.5555, 0.5397, 0.5068
],
"line": {
"color": "#1c9099"
},
"boxpoints": "all",
"pointpos": 0,
"type": "box",
"name": "3-sigma + whiskers",
"sdmultiple" : 3,
"sizemode": "sd",
"showwhiskers": true
},
{
"y": [
0.4995, 0.3786, 0.5188, 0.4505, 0.5805, 0.5539, 0.7341, 0.3303, 0.6202, 0.4754, 0.4814, 0.6103, 0.5157, 0.3841, 0.6166, 0.4917, 0.5646, 0.4532, 0.5983,
0.5079, 0.5227, 0.5483, 0.3081, 0.5172, 0.4127, 0.3871, 0.4703, 0.5331, 0.4573, 0.6187, 0.5718, 0.4474, 0.5349, 0.4614, 0.3096, 0.4411, 0.7143, 0.5956,
0.5171, 0.5515, 0.4234, 0.4589, 0.4289, 0.417, 0.4229, 0.5039, 0.4726, 0.5382, 0.261, 0.5326, 0.4472, 0.54, 0.4998, 0.5513, 0.3891, 0.4821, 0.5006,
0.4362, 0.4184, 0.3632, 0.5182, 0.5229, 0.5493, 0.507, 0.4528, 0.4836, 0.5009, 0.49, 0.5757, 0.5408, 0.4246, 0.511, 0.5216, 0.3817, 0.4471, 0.4935,
0.5668, 0.3187, 0.3633, 0.5964, 0.637, 0.4701, 0.4292, 0.4921, 0.439, 0.5846, 0.4502, 0.44, 0.3057, 0.4756, 0.4867, 0.502, 0.438, 0.6819, 0.2607,
0.5233, 0.3291, 0.5555, 0.5397, 0.5068
],
"line": {
"color": "#1c9099"
},
"boxpoints": "all",
"pointpos": 0,
"type": "box",
"name": "diamond 1-sigma",
"boxmean": "sd",
"showwhiskers": false
},
{
"y": [
0.4995, 0.3786, 0.5188, 0.4505, 0.5805, 0.5539, 0.7341, 0.3303, 0.6202, 0.4754, 0.4814, 0.6103, 0.5157, 0.3841, 0.6166, 0.4917, 0.5646, 0.4532, 0.5983,
0.5079, 0.5227, 0.5483, 0.3081, 0.5172, 0.4127, 0.3871, 0.4703, 0.5331, 0.4573, 0.6187, 0.5718, 0.4474, 0.5349, 0.4614, 0.3096, 0.4411, 0.7143, 0.5956,
0.5171, 0.5515, 0.4234, 0.4589, 0.4289, 0.417, 0.4229, 0.5039, 0.4726, 0.5382, 0.261, 0.5326, 0.4472, 0.54, 0.4998, 0.5513, 0.3891, 0.4821, 0.5006,
0.4362, 0.4184, 0.3632, 0.5182, 0.5229, 0.5493, 0.507, 0.4528, 0.4836, 0.5009, 0.49, 0.5757, 0.5408, 0.4246, 0.511, 0.5216, 0.3817, 0.4471, 0.4935,
0.5668, 0.3187, 0.3633, 0.5964, 0.637, 0.4701, 0.4292, 0.4921, 0.439, 0.5846, 0.4502, 0.44, 0.3057, 0.4756, 0.4867, 0.502, 0.438, 0.6819, 0.2607,
0.5233, 0.3291, 0.5555, 0.5397, 0.5068
],
"line": {
"color": "#1c9099"
},
"boxpoints": "all",
"pointpos": 0,
"type": "box",
"name": "diamond 3-sigma",
"sdmultiple" : 3,
"boxmean": "sd",
"showwhiskers": false
}
],
"layout": {
"showlegend": false,
"yaxis": {
"title": { "text": "Random Variable" },
"type": "linear",
"range":[-0.2, 1.2]
},
"title": { "text": "Box plots drawn on std deviation instead of quartiles" },
"xaxis": {
"type": "category"
},
"height": 598,
"width": 1080,
"autosize": true
}
}
22 changes: 22 additions & 0 deletions test/plot-schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16594,6 +16594,13 @@
"editType": "calc",
"valType": "data_array"
},
"sdmultiple": {
"description": "Scales the box size when sizemode=sd Allowing boxes to be drawn across any stddev range For example 1-stddev, 3-stddev, 5-stddev",
"dflt": 1,
"editType": "calc",
"min": 0,
"valType": "number"
},
"sdsrc": {
"description": "Sets the source reference on Chart Studio Cloud for `sd`.",
"editType": "none",
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"editType": "style",
"valType": "boolean"
},
"showwhiskers": {
"description": "Determines whether or not whiskers are visible. Defaults to true for `sizemode` *quartiles*, false for *sd*.",
"editType": "calc",
"valType": "boolean"
},
"sizemode": {
"description": "Sets the upper and lower bound for the boxes quartiles means box is drawn between Q1 and Q3 SD means the box is drawn between Mean +- Standard Deviation Argument sdmultiple (default 1) to scale the box size So it could be drawn 1-stddev, 3-stddev etc",
"dflt": "quartiles",
"editType": "calc",
"valType": "enumerated",
"values": [
"quartiles",
"sd"
]
},
"stream": {
"editType": "calc",
"maxpoints": {
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