-
Notifications
You must be signed in to change notification settings - Fork 6
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Lots of changes regarding single-cell data
Rename CellTypeLabelling to CellTypeAssignment and perform some related renaming. Add basic VOs for cell type assignment, protocol, etc. Add an explicit dependency on mtj since we use it for parsing MatrixMarket formats.
- Loading branch information
Showing
39 changed files
with
1,008 additions
and
523 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
135 changes: 135 additions & 0 deletions
135
.../main/java/ubic/gemma/core/datastructure/matrix/DoubleSingleCellExpressionDataMatrix.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,135 @@ | ||
| package ubic.gemma.core.datastructure.matrix; | ||
|
|
||
| import no.uib.cipr.matrix.sparse.CompRowMatrix; | ||
| import org.springframework.util.Assert; | ||
| import ubic.gemma.model.common.quantitationtype.QuantitationType; | ||
| import ubic.gemma.model.expression.bioAssayData.SingleCellDimension; | ||
| import ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector; | ||
| import ubic.gemma.model.expression.designElement.CompositeSequence; | ||
| import ubic.gemma.model.expression.experiment.ExpressionExperiment; | ||
| import ubic.gemma.persistence.util.ByteArrayUtils; | ||
|
|
||
| import java.util.*; | ||
|
|
||
| /** | ||
| * @author poirigui | ||
| */ | ||
| public class DoubleSingleCellExpressionDataMatrix implements SingleCellExpressionDataMatrix<Double> { | ||
|
|
||
| private static final Comparator<CompositeSequence> designElementComparator = Comparator.comparing( CompositeSequence::getName ) | ||
| .thenComparing( CompositeSequence::getId ); | ||
|
|
||
| private final ExpressionExperiment expressionExperiment; | ||
| private final QuantitationType quantitationType; | ||
| private final SingleCellDimension singleCellDimension; | ||
| private final CompRowMatrix matrix; | ||
| private final List<CompositeSequence> designElements; | ||
|
|
||
| public DoubleSingleCellExpressionDataMatrix( Collection<SingleCellExpressionDataVector> vectors ) { | ||
| Assert.isTrue( !vectors.isEmpty(), "At least one vector must be supplied. Use EmptyExpressionDataMatrix for empty data matrices instead." ); | ||
| Assert.isTrue( vectors.stream().map( SingleCellExpressionDataVector::getQuantitationType ).distinct().count() == 1, | ||
| "All vectors must have the same quantitation type." ); | ||
| Assert.isTrue( vectors.stream().map( SingleCellExpressionDataVector::getSingleCellDimension ).distinct().count() == 1, | ||
| "All vectors must have the same single-cell dimension." ); | ||
| SingleCellExpressionDataVector vector = vectors.iterator().next(); | ||
| expressionExperiment = vector.getExpressionExperiment(); | ||
| quantitationType = vector.getQuantitationType(); | ||
| singleCellDimension = vector.getSingleCellDimension(); | ||
| // sort vectors by CS | ||
| List<SingleCellExpressionDataVector> sortedVectors = new ArrayList<>( vectors ); | ||
| sortedVectors.sort( Comparator.comparing( SingleCellExpressionDataVector::getDesignElement, designElementComparator ) ); | ||
| int rows = sortedVectors.size(); | ||
| int i = 0; | ||
| int[][] nz = new int[rows][]; | ||
| for ( SingleCellExpressionDataVector v : sortedVectors ) { | ||
| nz[i++] = v.getDataIndices(); | ||
| } | ||
| matrix = new CompRowMatrix( rows, singleCellDimension.getNumberOfCells(), nz ); | ||
| designElements = new ArrayList<>( sortedVectors.size() ); | ||
| i = 0; | ||
| for ( SingleCellExpressionDataVector v : sortedVectors ) { | ||
| designElements.add( v.getDesignElement() ); | ||
| double[] row = ByteArrayUtils.byteArrayToDoubles( v.getData() ); | ||
| int[] indices = v.getDataIndices(); | ||
| for ( int j = 0; j < row.length; j++ ) { | ||
| matrix.set( i, indices[j], row[j] ); | ||
| } | ||
| i++; | ||
| } | ||
| } | ||
|
|
||
| @Override | ||
| public ExpressionExperiment getExpressionExperiment() { | ||
| return expressionExperiment; | ||
| } | ||
|
|
||
| @Override | ||
| public int columns() { | ||
| return matrix.numColumns(); | ||
| } | ||
|
|
||
| @Override | ||
| public Double get( int row, int column ) { | ||
| return matrix.get( row, column ); | ||
| } | ||
|
|
||
| @Override | ||
| public Double[] getColumn( int column ) { | ||
| Double[] vec = new Double[matrix.numRows()]; | ||
| for ( int j = 0; j < matrix.numRows(); j++ ) { | ||
| vec[j] = matrix.get( j, column ); | ||
| } | ||
| return vec; | ||
| } | ||
|
|
||
| @Override | ||
| public List<CompositeSequence> getDesignElements() { | ||
| return designElements; | ||
| } | ||
|
|
||
| @Override | ||
| public CompositeSequence getDesignElementForRow( int index ) { | ||
| return designElements.get( index ); | ||
| } | ||
|
|
||
| @Override | ||
| public Double[] getRow( CompositeSequence designElement ) { | ||
| int ix = getRowIndex( designElement ); | ||
| if ( ix == -1 ) { | ||
| return null; | ||
| } | ||
| return getRow( ix ); | ||
| } | ||
|
|
||
| @Override | ||
| public Double[] getRow( int index ) { | ||
| Double[] vec = new Double[matrix.numColumns()]; | ||
| int[] rowptr = matrix.getRowPointers(); | ||
| int[] colind = matrix.getColumnIndices(); | ||
| double[] data = matrix.getData(); | ||
| for ( int i = rowptr[index]; i < rowptr[index + 1]; i++ ) { | ||
| vec[colind[i]] = data[i]; | ||
| } | ||
| return vec; | ||
| } | ||
|
|
||
| @Override | ||
| public int getRowIndex( CompositeSequence designElement ) { | ||
| return Math.max( Collections.binarySearch( designElements, designElement, designElementComparator ), -1 ); | ||
| } | ||
|
|
||
| @Override | ||
| public int rows() { | ||
| return matrix.numRows(); | ||
| } | ||
|
|
||
| @Override | ||
| public QuantitationType getQuantitationType() { | ||
| return quantitationType; | ||
| } | ||
|
|
||
| @Override | ||
| public SingleCellDimension getSingleCellDimension() { | ||
| return singleCellDimension; | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.