From 647a9ed6a67ea13ad68dd3f2bdf24cdf18bfe9ce Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Sun, 9 Oct 2022 09:36:06 -0700 Subject: [PATCH] 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 --- README.md | 2 +- package.json | 4 +-- src/components/Analysis/index.js | 55 +++++++++++++++++++++++++++++--- 3 files changed, 54 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 80efc982..f3eb69f2 100644 --- 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 index a728eb7d..828404bb 100644 --- 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 index cb7bed2b..e3d9dd26 100644 --- 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} > - } /> - } /> + + + + } /> @@ -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 = ({
  • Matrix Market - *.mtx or *.mtx.gz
  • features or genes, *.tsv or *.tsv.gz
    • -
  • HDF5 (10x or h5ad) - *.h5 or *.hdf5 or *.h5ad
    • +
  • HDF5 (10X or H5AD) - *.h5 or *.hdf5 or *.h5ad
    • +
  • RDS - *.rds
Note: Names of dataset must be unique! @@ -1977,6 +2017,13 @@ const AnalysisDialog = ({ We will also try to guess which field in the obs annotation contains gene symbols.

+

+ A SummarizedExperiment object saved in the RDS (*.rds) format. + 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. +

+

Batch correction: 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.