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Initial support for Nimble/Append and TCR/Append to Seurat objects
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6 files changed

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‎singlecell/resources/chunks/AppendTcr.R‎

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if (!file.exists('/homeDir/.netrc')) {
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print(list.files('/homeDir'))
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stop('Unable to find file: /homeDir/.netrc')
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}
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invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = '/homeDir/.netrc'))
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Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
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for (datasetId in names(seuratObjects)) {
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printName(datasetId)
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seuratObj <- readRDS(seuratObjects[[datasetId]])
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seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = allowMissing)
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saveData(seuratObj, datasetId)
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# Cleanup
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rm(seuratObj)
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gc()
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}

‎singlecell/resources/chunks/NimbleAppend.R‎

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if (!file.exists('/homeDir/.netrc')) {
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print(list.files('/homeDir'))
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stop('Unable to find file: /homeDir/.netrc')
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}
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invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = '/homeDir/.netrc'))
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Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
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for (datasetId in names(seuratObjects)) {
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printName(datasetId)
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seuratObj <- readRDS(seuratObjects[[datasetId]])
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for (genomeId in names(nimbleGenomes)) {
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#TODO: dropAmbiguousFeatures
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seuratObj <- Rdiscvr::DownloadAndAppendNimble(seuratObject = seuratObj, allowableGenomes = genomeId, targetAssayName = nimbleGenomes[[genomeId]], enforceUniqueFeatureNames = TRUE)
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}
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saveData(seuratObj, datasetId)
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# Cleanup
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rm(seuratObj)
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gc()
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}

‎singlecell/resources/web/singlecell/panel/NimbleAppendPanel.js‎

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Ext4.define('SingleCell.panel.NimbleAppendPanel', {
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extend: 'Ext.form.FieldSet',
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alias: 'widget.singlecell-nimbleappendpanel',
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title: 'Nimble Genomes',
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genomeField: Ext4.widget({
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xtype: 'sequenceanalysis-genomefield',
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allowBlank: false
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}),
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initComponent: function(){
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Ext4.apply(this, {
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style: 'padding: 10px;margins: 5px;',
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minWidth: 650,
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border: true,
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items: [{
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html: 'This step will first run cellranger using the primary genome (selected above). The resulting BAM will be passed to nimble, which will align using each of the genomes selected below, creating supplemental feature counts. By default, the original cellranger output is discarded.',
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maxWidth: 600,
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border: false,
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style: 'padding-bottom: 10px;'
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},{
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xtype: 'ldk-gridpanel',
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clicksToEdit: 1,
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width: 600,
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tbar: [{
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text: 'Add',
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handler: function(btn){
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var grid = btn.up('grid');
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var store = grid.store;
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var recs = store.add(store.createModel({
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genomeId: null,
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targetAssay: 'Nimble'
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}));
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var idx = store.indexOf(recs[0]);
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var cellEditing = grid.getPlugin(grid.editingPluginId);
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cellEditing.completeEdit();
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var jexlIdx = this.showFilterName ? 1 : 0;
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cellEditing.startEditByPosition({row: idx, column: jexlIdx});
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}
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},LABKEY.ext4.GRIDBUTTONS.DELETERECORD()],
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store: {
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type: 'array',
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fields: ['genomeId', 'targetAssay']
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},
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columns: [{
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dataIndex: 'genomeId',
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width: 200,
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header: 'Genome',
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editor: this.genomeField,
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renderer: function(val){
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const store = this.up('singlecell-nimblealignpanel').genomeField.store
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if (val && store) {
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const recIdx = store.find('rowid', val);
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return store.getAt(recIdx).get('name');
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}
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else if (val) {
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return '[' + val + ']';
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}
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else {
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return '[None]';
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}
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}
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},{
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dataIndex: 'targetAssay',
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width: 200,
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header: 'Target Assay',
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editor: {
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xtype: 'textfield',
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allowBlank: false
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}
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}]
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}]
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});
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this.callParent(arguments);
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},
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getValue: function(){
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var ret = [];
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this.down('ldk-gridpanel').store.each(function(r, i) {
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ret.push([r.data.genomeId, r.data.targetAssay]);
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}, this);
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return Ext4.isEmpty(ret) ? null : JSON.stringify(ret);
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},
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getErrors: function(){
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var msgs = [];
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this.down('ldk-gridpanel').store.each(function(r, i){
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if (!r.data.genomeId){
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msgs.push('Missing genome for one or more rows');
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}
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if (!r.data.targetAssay){
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msgs.push('Missing target assay for one or more rows');
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}
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}, this);
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if (!this.down('ldk-gridpanel').store.getCount()){
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msgs.push('Must provide at least one genome for nimble');
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}
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return msgs;
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},
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setValue: function(val){
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var grid = this.down('ldk-gridpanel');
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if (val){
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if (!Ext4.isArray(val)){
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val = Ext4.JSON.decode(val);
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}
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Ext4.Array.forEach(val, function(row){
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var rec = grid.store.createModel({
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genomeId: row[0],
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targetAssay: row[1]
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});
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grid.store.add(rec);
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}, this);
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}
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else {
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grid.store.removeAll();
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}
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}
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});

‎singlecell/src/org/labkey/singlecell/SingleCellModule.java‎

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SequencePipelineService.get().registerPipelineStep(new CheckExpectations.Provider());
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SequencePipelineService.get().registerPipelineStep(new CommonFilters.Provider());
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SequencePipelineService.get().registerPipelineStep(new RunVision.Provider());
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SequencePipelineService.get().registerPipelineStep(new NimbleAppend.Provider());
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SequencePipelineService.get().registerPipelineStep(new AppendTcr.Provider());
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SequenceAnalysisService.get().registerFileHandler(new NimbleHandler());
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}

‎singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendTcr.java‎

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package org.labkey.singlecell.pipeline.singlecell;
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import org.json.JSONObject;
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import org.labkey.api.pipeline.PipelineJobException;
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import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
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import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
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import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
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import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
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import org.labkey.api.singlecell.pipeline.SingleCellStep;
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import java.util.Arrays;
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import java.util.List;
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public class AppendTcr extends AbstractRDiscvrStep
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{
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public AppendTcr(PipelineContext ctx, AppendTcr.Provider provider)
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{
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super(provider, ctx);
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}
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public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
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{
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public Provider()
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{
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super("AppendTcr", "Append TCR Data", "RDiscvr", "This uses Rdiscvr::DownloadAndAppendTcrClonotypes to append TCR data.", Arrays.asList(
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SeuratToolParameter.create("allowMissing", "Allow Missing Data", "If checked, an error will be thrown if any sample lacks TCR data", "checkbox", new JSONObject(){{
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put("checked", true);
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}}, true)
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), null, null);
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}
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@Override
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public AppendTcr create(PipelineContext ctx)
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{
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return new AppendTcr(ctx, this);
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}
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}
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@Override
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public String getFileSuffix()
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{
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return "tcr";
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}
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@Override
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protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWrapper> inputObjects, String outputPrefix) throws PipelineJobException
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{
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Chunk ret = super.createParamChunk(ctx, inputObjects, outputPrefix);
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ret.bodyLines.add("serverBaseUrl <- '" + getPipelineCtx().getJob().getParameters().get("serverBaseUrl") + "'");
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ret.bodyLines.add("defaultLabKeyFolder <- '" + getPipelineCtx().getJob().getParameters().get("labkeyFolderPath") + "'");
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return ret;
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}
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}
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‎singlecell/src/org/labkey/singlecell/pipeline/singlecell/NimbleAppend.java‎

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package org.labkey.singlecell.pipeline.singlecell;
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import org.json.JSONArray;
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import org.json.JSONObject;
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import org.labkey.api.pipeline.PipelineJobException;
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import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
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import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
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import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
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import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
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import org.labkey.api.singlecell.pipeline.SingleCellStep;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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public class NimbleAppend extends AbstractRDiscvrStep
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{
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public NimbleAppend(PipelineContext ctx, NimbleAppend.Provider provider)
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{
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super(provider, ctx);
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}
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public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
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{
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public Provider()
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{
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super("AppendNimble", "Append Nimble Data", "Nimble/Rdiscvr", "The seurat object will be subset based on the expression below, which is passed directly to Seurat's subset(subset = X).", Arrays.asList(
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ToolParameterDescriptor.create("nimbleGenomes", "Genomes", "Genomes to include", "singlecell-nimbleappendpanel", new JSONObject(){{
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put("allowBlank", false);
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}}, null)
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), Arrays.asList("sequenceanalysis/field/GenomeField.js", "/singlecell/panel/NimbleAppendPanel.js"), null);
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}
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@Override
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public NimbleAppend create(PipelineContext ctx)
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{
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return new NimbleAppend(ctx, this);
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}
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}
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@Override
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public Collection<String> getRLibraries()
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{
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Set<String> ret = new HashSet<>();
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ret.add("Seurat");
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ret.addAll(super.getRLibraries());
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return ret;
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}
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@Override
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protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWrapper> inputObjects, String outputPrefix) throws PipelineJobException
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{
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Chunk ret = super.createParamChunk(ctx, inputObjects, outputPrefix);
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ret.bodyLines.add("serverBaseUrl <- '" + getPipelineCtx().getJob().getParameters().get("serverBaseUrl") + "'");
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ret.bodyLines.add("defaultLabKeyFolder <- '" + getPipelineCtx().getJob().getParameters().get("labkeyFolderPath") + "'");
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ret.bodyLines.add("nimbleGenomes <- list(");
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String genomeStr = getPipelineCtx().getJob().getParameters().get("nimbleGenomes");
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JSONArray json = new JSONArray(genomeStr);
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for (int i = 0; i < json.length(); i++)
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{
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JSONArray arr = json.getJSONArray(i);
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if (arr.length() != 2)
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{
70+
throw new PipelineJobException("Unexpected value: " + json.getString(i));
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}
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int genomeId = arr.getInt(0);
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String targetAssay = arr.getString(1);
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ret.bodyLines.add("\t" + genomeId + " = " + targetAssay);
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}
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ret.bodyLines.add(")");
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return ret;
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}
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@Override
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public String getFileSuffix()
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{
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return "nimble";
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}
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}

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