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]>
kanaverse · Oct 9, 2022 · 647a9ed · 647a9ed
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diff --git a/README.md b/README.md
@@ -24,7 +24,7 @@ Our client-side approach has a number of advantages:
 
 ## For users
 
-If you have a Matrix Market (`.mtx`) file or HDF5 (tenx V3 or AnnData representation stored as h5ad), you're ready to go.
+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.
 
 1. Launch the application by clicking [**here**](https://www.jkanche.com/kana/).
 2. Select the Matrix Market file (this may be Gzip-compressed).

diff --git a/package.json b/package.json
@@ -1,7 +1,7 @@
 {
  "name": "kana",
  "description": "Single cell data analysis in the browser",
- "version": "2.3.1",
+ "version": "2.4.0",
  "private": true,
  "author": {
  "name": "Jayaram Kancherla",
@@ -32,7 +32,7 @@
  "@testing-library/jest-dom": "^5.16.5",
  "@testing-library/react": "^11.1.0",
  "@testing-library/user-event": "^12.1.10",
- "bakana": "^0.5.0",
+ "bakana": "^0.6.0",
  "d3": "^7.1.1",
  "epiviz.gl": "^1.0.2",
  "epiviz.scatter.gl": "^0.0.5",

diff --git a/src/components/Analysis/index.js b/src/components/Analysis/index.js
@@ -46,6 +46,7 @@ const AnalysisDialog = ({
  genes: "Choose feature/gene file",
  annotations: "Choose barcode/annotation file",
  file: "Choose file...",
+ rds: "Choose file..."
  });
 
  let [stmpInputFiles, ssetTmpInputFiles] = useState({
@@ -218,9 +219,19 @@ const AnalysisDialog = ({
  ) {
  all_valid = false;
  }
+
+ if (
+ x?.rds && !(
+ inputText[ix]?.rds.toLowerCase().endsWith("rds")
+ )
+ ) {
+ all_valid = false;
+ }
 
  if (x.format === "MatrixMarket") {
  if (!x.mtx) all_valid = false;
+ } else if (x.format === "SummarizedExperiment") {
+ if (!x.rds) all_valid = false;
  } else {
  if (!x.h5) all_valid = false;
  }
@@ -323,11 +334,20 @@ const AnalysisDialog = ({
  }
 
  if (!x.h5 && (sinputText?.file !== "Choose file...")) all_valid = false;
+ } else if (
+ x.format === "SummarizedExperiment") {
+ if (x?.rds && !(
+ sinputText?.rds.toLowerCase().endsWith("rds")
+ )
+ ) {
+ all_valid = false;
+ }
+
+ if (!x.rds && (sinputText?.file !== "Choose file...")) all_valid = false;
  }
 
  // setTmpInputValid(all_valid);
  ssetTmpInputValid(all_valid);
-
  }
  }
  }, [stmpInputFiles]);
@@ -1103,7 +1123,7 @@ const AnalysisDialog = ({
  }}
  defaultSelectedTabId={newImportFormat}
  >
- <Tab id="MatrixMarket" title="Matrix Market file" panel={
+ <Tab id="MatrixMarket" title="Matrix Market" panel={
  <div className="row"
  >
  <Label className="row-input">
@@ -1132,7 +1152,7 @@ const AnalysisDialog = ({
  </Label>
  </div>
  } />
- <Tab id="10X" title="10x HDF5 matrix" panel={
+ <Tab id="10X" title="10X HDF5 Matrix" panel={
  <div className="row"
  >
  <Label className="row-input">
@@ -1166,6 +1186,23 @@ const AnalysisDialog = ({
  </Label>
  </div>
  } />
+ <Tab id="SummarizedExperiment" title="SummarizedExperiment (RDS)" panel={
+ <div className="row"
+ >
+ <Label className="row-input">
+ <FileInput style={{
+ marginTop: '5px'
+ }}
+ text={sinputText.rds}
+ onInputChange={(msg) => {
+ if (msg.target.files) {
+ ssetInputText({ ...sinputText, "rds": msg.target.files[0].name });
+ ssetTmpInputFiles({ ...stmpInputFiles, "rds": msg.target.files[0] })
+ }
+ }} />
+ </Label>
+ </div>
+ } />
  </Tabs>
  </div>
  </div>
@@ -1490,6 +1527,8 @@ const AnalysisDialog = ({
  if (row.annotations) {
  tname += ` annotations: ${row.annotations.name} `;
  }
+ } else if (row["format"] === "SummarizedExperiment") {
+ tname += ` file: ${row.rds.name} `;
  } else {
  tname += ` file: ${row.h5.name} `;
  }
@@ -1948,7 +1987,8 @@ const AnalysisDialog = ({
  <ul>
  <li>Matrix Market - <code>*.mtx</code> or <code>*.mtx.gz</code></li>
  <li>features or genes, <code>*.tsv</code> or <code>*.tsv.gz</code></li>
- <li>HDF5 (10x or h5ad) - <code>*.h5</code> or <code>*.hdf5</code> or <code>*.h5ad</code></li>
+ <li>HDF5 (10X or H5AD) - <code>*.h5</code> or <code>*.hdf5</code> or <code>*.h5ad</code></li>
+ <li>RDS - <code>*.rds</code></li>
  </ul>
 
  Note: Names of dataset must be unique!
@@ -1977,6 +2017,13 @@ const AnalysisDialog = ({
  We will also try to guess which field in the <code>obs</code> annotation contains gene symbols.
  </p>
 
+ <p>
+ <strong>A SummarizedExperiment object saved in the RDS (<code>*.rds</code>) format. </strong>
+ We support any SummarizedExperiment subclass containing a dense or sparse count matrix 
+ (identified as any assay with name starting with "counts", or if none exist, just the first assay).
+ For a SingleCellExperiment, any alternative experiment with name starting with "hto", "adt" or "antibody" is assumed to represent CITE-seq data.
+ </p>
+
  <p><strong>Batch correction:</strong> you can now import more than one file to integrate and analyze datasets.
  If you only import a single dataset, specify the annotation column that contains the batch information.</p>
  </Callout>