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Enable FastMNN #246

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merged 10 commits into from
May 14, 2021
Merged

Enable FastMNN #246

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4b6f2ed
Enable FastMNN
JuanluOnieva-biomage May 10, 2021
10b0c7f
Add noIntegration
JuanluOnieva-biomage May 10, 2021
ecfadd9
Change value to unisample and fastmnn
JuanluOnieva-biomage May 10, 2021
452d5b0
Add option classes
JuanluOnieva-biomage May 11, 2021
738b707
Update snapshot
JuanluOnieva-biomage May 11, 2021
cc6f3a5
Minor refactoring
May 11, 2021
b1540f5
Tipo achive
JuanluOnieva-biomage May 12, 2021
86fb84d
Grammar change
JuanluOnieva-biomage May 12, 2021
f3c96b8
rephrase sentenced
JuanluOnieva-biomage May 12, 2021
942f6d8
Vicky's comment
JuanluOnieva-biomage May 13, 2021
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8 changes: 8 additions & 0 deletions src/__test__/redux/reducers/__snapshots__/experimentSettingsReducer.test.js.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -149,10 +149,18 @@ Object {
"dataIntegration": Object {
"method": "seuratv4",
"methodSettings": Object {
"fastmnn": Object {
"normalization": "logNormalize",
"numGenes": 2000,
},
"seuratv4": Object {
"normalization": "logNormalize",
"numGenes": 2000,
},
"unisample": Object {
"normalization": "logNormalize",
"numGenes": 2000,
},
},
},
"dimensionalityReduction": Object {
Expand Down
8 changes: 8 additions & 0 deletions src/__test__/test-utils/experimentSettings.mock.js
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,14 @@ const testableProcessingConfig = {
numGenes: 2000,
normalization: 'logNormalize',
},
fastmnn: {
numGenes: 2000,
normalization: 'logNormalize',
},
unisample: {
numGenes: 2000,
normalization: 'logNormalize',
},
},
},
dimensionalityReduction: {
Expand Down
33 changes: 28 additions & 5 deletions src/components/data-processing/DataIntegration/CalculationConfig.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,8 @@ import {
import _ from 'lodash';

import SeuratV4Options from './SeuratV4Options';
import FastMNNOptions from './FastMNNOptions';
import UnisampleOptions from './UnisampleOptions';

import { updateProcessingSettings } from '../../../redux/actions/experimentSettings';
import generateDataProcessingPlotUuid from '../../../utils/generateDataProcessingPlotUuid';
Expand Down Expand Up @@ -52,6 +54,16 @@ const CalculationConfig = (props) => {
text: 'Seurat v4',
disabled: false,
},
{
value: 'fastmnn',
text: 'Fast MNN',
disabled: false,
},
{
value: 'unisample',
text: 'No integration',
disabled: false,
},
{
value: 'seuratv3',
text: 'Seurat v3',
Expand All @@ -72,11 +84,6 @@ const CalculationConfig = (props) => {
text: 'Liger',
disabled: true,
},
{
value: 'fastMNN',
text: 'Fast MNN',
disabled: true,
},
];

const [numPCs, setNumPCs] = useState(dimensionalityReduction.numPCs);
Expand Down Expand Up @@ -105,6 +112,22 @@ const CalculationConfig = (props) => {
disabled={disabled}
/>
),
fastmnn: () => (
<FastMNNOptions
config={dataIntegration.methodSettings.fastmnn}
onUpdate={updateSettings}
onChange={() => setChangesOutstanding(true)}
disabled={disabled}
/>
),
unisample: () => (
<UnisampleOptions
config={dataIntegration.methodSettings.unisample}
onUpdate={updateSettings}
onChange={() => setChangesOutstanding(true)}
disabled={disabled}
/>
),
};

const roundedVariationExplained = () => {
Expand Down
129 changes: 129 additions & 0 deletions src/components/data-processing/DataIntegration/FastMNNOptions.jsx
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Original file line number Diff line number Diff line change
@@ -0,0 +1,129 @@
import React, { useState } from 'react';
import PropTypes from 'prop-types';
import { Form, InputNumber, Select, Tooltip, Typography } from 'antd';

import {
QuestionCircleOutlined,
} from '@ant-design/icons';

const { Option } = Select;
const { Text } = Typography;

const FastMNNOptions = (props) => {
ivababukova marked this conversation as resolved.
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const {
config, onUpdate, onChange, disabled,
} = props;

const [numGenes, setNumGenes] = useState(config.numGenes);

return (
<>
<Form.Item label='# of HGV genes'>
<InputNumber
value={numGenes}
step={100}
min={1}
onChange={(value) => {
onChange();
setNumGenes(value);
}}
onPressEnter={(e) => e.preventDefault()}
onStep={(value) => onUpdate({
dataIntegration: {
methodSettings: {
fastmnn: {
numGenes: value,
},
},
},
})}
onBlur={(e) => onUpdate({
dataIntegration: {
methodSettings: {
fastmnn: {
numGenes: parseInt(e.target.value, 0),
},
},
},
})}
disabled={disabled}
/>
{' '}
<Tooltip overlay={(
<span>
Number of genes to mark as top highly variable genes (HGV).
Integration as well as PCA is based on a sensible selection of HGV.
Here, this number selects the top variable genes based on the "vst" method.
The default 2000 has been found to be a sensible for many cases.
Further info can be found
<a
href='https://satijalab.org/seurat/articles/integration_introduction.html'
target='_blank'
rel='noreferrer'
>
{' '}
<code>here</code>
</a>
</span>
)}
>
<QuestionCircleOutlined />
</Tooltip>
</Form.Item>
<Form.Item label={(
<span>
Normalization&nbsp;
<Tooltip overlay={(
<span>
Normalization aims to remove technical factors including sequencing depth.
There are several methods to achive normalization.
"sctransform" claims to recover sharper biological distinction compared to log-normalization.
Normalization is applied to each sample before integration.
Further info can be found
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Sounds like a nice message, but it will be better if you are more explicit and say Cellscope uses "sctransform".' after sentence There are several methods to achive normalization.`

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also a typo in achive -- it is achieve and there should be a comma just after factors on the first line (I think :D ). It would read better if you rephrased the first sentence to Normalization aims to remove technical factors, like sequencing depth for example.

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Also, it is worth to point out that I personally have no idea what technical factors mean. That can just as well be because of my lack of biology/bioinformatics background. I am noting it, because if biologists might not know this, we will need to rephrase it. @vickymorrison any thoughts?

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Thanks for the review @ivababukova! For this PR I looked at what was already in place in SeuratV4Options to create the counterpart to FastMNN and Unisample. In the new commit Martin has done a great job of refactoring. Regarding technical errors, I guess it refers to possible biases that occur when sequencing or in the lab in the sample preparation.

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For the first sentence, how about: "Normalization aims to remove technical variation that is not biologically relevant, e.g. sequencing depth." ?

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I like it

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The thing is that we could add as covariates for the normalization the mt-content, so I guess we should not especify biologically relevant. For the current version we cannot add covariates but I think that we will support it.

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I would argue that 'not biologically relevant' still stands - if the user chooses to exclude specific gene categories that is because they believe those genes are not biologically relevant to the question they are trying to answer.

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It makes sense! I'll change!

<a
href='https://satijalab.org/seurat/articles/sctransform_vignette.html'
target='_blank'
rel='noreferrer'
>
{' '}
<code>here</code>
</a>
</span>
)}
>
<QuestionCircleOutlined />
</Tooltip>
</span>
)}
>
<Select
value={config.normalization}
onChange={(val) => onUpdate({
dataIntegration: {
methodSettings: {
fastmnn: { normalization: val },
},
},
})}
disabled={disabled}
>
<Option value='logNormalize'>LogNormalize</Option>
<Option value='scTransform'>SCTransform</Option>
</Select>

</Form.Item>
</>
);
};

FastMNNOptions.propTypes = {
config: PropTypes.object.isRequired,
onUpdate: PropTypes.func.isRequired,
onChange: PropTypes.func,
};

FastMNNOptions.defaultProps = {
onChange: null,
};

export default FastMNNOptions;
129 changes: 129 additions & 0 deletions src/components/data-processing/DataIntegration/UnisampleOptions.jsx
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Original file line number Diff line number Diff line change
@@ -0,0 +1,129 @@
import React, { useState } from 'react';
import PropTypes from 'prop-types';
import { Form, InputNumber, Select, Tooltip, Typography } from 'antd';

import {
QuestionCircleOutlined,
} from '@ant-design/icons';

const { Option } = Select;
const { Text } = Typography;

const UnisampleOptions = (props) => {
const {
config, onUpdate, onChange, disabled,
} = props;

const [numGenes, setNumGenes] = useState(config.numGenes);

return (
<>
<Form.Item label='# of HGV genes'>
<InputNumber
value={numGenes}
step={100}
min={1}
onChange={(value) => {
onChange();
setNumGenes(value);
}}
onPressEnter={(e) => e.preventDefault()}
onStep={(value) => onUpdate({
dataIntegration: {
methodSettings: {
unisample: {
numGenes: value,
},
},
},
})}
onBlur={(e) => onUpdate({
dataIntegration: {
methodSettings: {
unisample: {
numGenes: parseInt(e.target.value, 0),
},
},
},
})}
disabled={disabled}
/>
{' '}
<Tooltip overlay={(
<span>
Number of genes to mark as top highly variable genes (HGV).
Integration as well as PCA is based on a sensible selection of HGV.
Here, this number selects the top variable genes based on the "vst" method.
The default 2000 has been found to be a sensible for many cases.
Further info can be found
<a
href='https://satijalab.org/seurat/articles/integration_introduction.html'
target='_blank'
rel='noreferrer'
>
{' '}
<code>here</code>
</a>
</span>
)}
>
<QuestionCircleOutlined />
</Tooltip>
</Form.Item>
<Form.Item label={(
<span>
Normalization&nbsp;
<Tooltip overlay={(
<span>
Normalization aims to remove technical factors including sequencing depth.
There are several methods to achive normalization.
"sctransform" claims to recover sharper biological distinction compared to log-normalization.
Normalization is applied to each sample before integration.
Further info can be found
<a
href='https://satijalab.org/seurat/articles/sctransform_vignette.html'
target='_blank'
rel='noreferrer'
>
{' '}
<code>here</code>
</a>
</span>
)}
>
<QuestionCircleOutlined />
</Tooltip>
</span>
)}
>
<Select
value={config.normalization}
onChange={(val) => onUpdate({
dataIntegration: {
methodSettings: {
unisample: { normalization: val },
},
},
})}
disabled={disabled}
>
<Option value='logNormalize'>LogNormalize</Option>
<Option value='scTransform'>SCTransform</Option>
</Select>

</Form.Item>
</>
);
};

UnisampleOptions.propTypes = {
config: PropTypes.object.isRequired,
onUpdate: PropTypes.func.isRequired,
onChange: PropTypes.func,
};

UnisampleOptions.defaultProps = {
onChange: null,
};

export default UnisampleOptions;