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Support Summarized Experiment derivatives (RDS file) (#145)
* feat: Load any single-cell dataset stored as a `SummarizedExperiment` or `SingleCellExperiment` derivative * docs: update documentation Co-authored-by: LTLA <[email protected]>
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‎README.md

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@@ -24,7 +24,7 @@ Our client-side approach has a number of advantages:
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## For users
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If you have a Matrix Market (`.mtx`) file or HDF5 (tenx V3 or AnnData representation stored as h5ad), you're ready to go.
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If you have a Matrix Market (`.mtx`) file or HDF5 (tenx V3 or `AnnData` representation stored as h5ad), or `SummarizedExperiment` (or derivatives like `SingleCellExperiment`) stored as an RDS file, you're ready to go.
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1. Launch the application by clicking [**here**](https://www.jkanche.com/kana/).
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2. Select the Matrix Market file (this may be Gzip-compressed).

‎package.json

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@@ -1,7 +1,7 @@
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{
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"name": "kana",
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"description": "Single cell data analysis in the browser",
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"version": "2.3.1",
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"version": "2.4.0",
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"private": true,
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"author": {
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"name": "Jayaram Kancherla",
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"@testing-library/jest-dom": "^5.16.5",
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"@testing-library/react": "^11.1.0",
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"@testing-library/user-event": "^12.1.10",
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"bakana": "^0.5.0",
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"bakana": "^0.6.0",
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"d3": "^7.1.1",
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"epiviz.gl": "^1.0.2",
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"epiviz.scatter.gl": "^0.0.5",

‎src/components/Analysis/index.js

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@@ -46,6 +46,7 @@ const AnalysisDialog = ({
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genes: "Choose feature/gene file",
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annotations: "Choose barcode/annotation file",
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file: "Choose file...",
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rds: "Choose file..."
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});
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let [stmpInputFiles, ssetTmpInputFiles] = useState({
@@ -218,9 +219,19 @@ const AnalysisDialog = ({
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) {
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all_valid = false;
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}
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if (
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x?.rds && !(
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inputText[ix]?.rds.toLowerCase().endsWith("rds")
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)
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) {
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all_valid = false;
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}
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if (x.format === "MatrixMarket") {
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if (!x.mtx) all_valid = false;
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} else if (x.format === "SummarizedExperiment") {
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if (!x.rds) all_valid = false;
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} else {
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if (!x.h5) all_valid = false;
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}
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}
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if (!x.h5 && (sinputText?.file !== "Choose file...")) all_valid = false;
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} else if (
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x.format === "SummarizedExperiment") {
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if (x?.rds && !(
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sinputText?.rds.toLowerCase().endsWith("rds")
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)
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) {
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all_valid = false;
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}
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if (!x.rds && (sinputText?.file !== "Choose file...")) all_valid = false;
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}
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// setTmpInputValid(all_valid);
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ssetTmpInputValid(all_valid);
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}
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}
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}, [stmpInputFiles]);
@@ -1103,7 +1123,7 @@ const AnalysisDialog = ({
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}}
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defaultSelectedTabId={newImportFormat}
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>
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<Tab id="MatrixMarket" title="Matrix Market file" panel={
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<Tab id="MatrixMarket" title="Matrix Market" panel={
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<div className="row"
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>
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<Label className="row-input">
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</Label>
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</div>
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} />
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<Tab id="10X" title="10x HDF5 matrix" panel={
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<Tab id="10X" title="10X HDF5 Matrix" panel={
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<div className="row"
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>
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<Label className="row-input">
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</Label>
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</div>
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} />
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<Tab id="SummarizedExperiment" title="SummarizedExperiment (RDS)" panel={
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<div className="row"
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>
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<Label className="row-input">
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<FileInput style={{
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marginTop: '5px'
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}}
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text={sinputText.rds}
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onInputChange={(msg) => {
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if (msg.target.files) {
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ssetInputText({ ...sinputText, "rds": msg.target.files[0].name });
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ssetTmpInputFiles({ ...stmpInputFiles, "rds": msg.target.files[0] })
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}
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}} />
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</Label>
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</div>
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} />
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</Tabs>
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</div>
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</div>
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if (row.annotations) {
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tname += ` annotations: ${row.annotations.name} `;
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}
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} else if (row["format"] === "SummarizedExperiment") {
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tname += ` file: ${row.rds.name} `;
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} else {
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tname += ` file: ${row.h5.name} `;
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}
@@ -1948,7 +1987,8 @@ const AnalysisDialog = ({
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<ul>
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<li>Matrix Market - <code>*.mtx</code> or <code>*.mtx.gz</code></li>
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<li>features or genes, <code>*.tsv</code> or <code>*.tsv.gz</code></li>
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<li>HDF5 (10x or h5ad) - <code>*.h5</code> or <code>*.hdf5</code> or <code>*.h5ad</code></li>
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<li>HDF5 (10X or H5AD) - <code>*.h5</code> or <code>*.hdf5</code> or <code>*.h5ad</code></li>
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<li>RDS - <code>*.rds</code></li>
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</ul>
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Note: Names of dataset must be unique!
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We will also try to guess which field in the <code>obs</code> annotation contains gene symbols.
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</p>
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<p>
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<strong>A SummarizedExperiment object saved in the RDS (<code>*.rds</code>) format. </strong>
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We support any SummarizedExperiment subclass containing a dense or sparse count matrix
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(identified as any assay with name starting with "counts", or if none exist, just the first assay).
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For a SingleCellExperiment, any alternative experiment with name starting with "hto", "adt" or "antibody" is assumed to represent CITE-seq data.
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</p>
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<p><strong>Batch correction:</strong> you can now import more than one file to integrate and analyze datasets.
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If you only import a single dataset, specify the annotation column that contains the batch information.</p>
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</Callout>

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