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Add boxplots for cell-level data
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@arteymix
arteymix committed Feb 26, 2025
1 parent 25418b0 commit fc6cbe5
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Showing 24 changed files with 935 additions and 112 deletions.
15 changes: 7 additions & 8 deletions gemma-cli/src/main/java/ubic/gemma/core/util/EntityLocatorImpl.java
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Expand Up @@ -221,20 +221,19 @@ public CellTypeAssignment locateCellTypeAssignment( ExpressionExperiment express
Assert.isTrue( StringUtils.isNotBlank( cta ), "Cell type assignment name must not be blank." );
cta = StringUtils.strip( cta );
try {
Optional<CellTypeAssignment> c = singleCellExpressionExperimentService.getCellTypeAssignment( expressionExperiment, qt, Long.parseLong( cta ) );
if ( c.isPresent() ) {
return c.get();
CellTypeAssignment c = singleCellExpressionExperimentService.getCellTypeAssignment( expressionExperiment, qt, Long.parseLong( cta ) );
if ( c != null ) {
return c;
}
} catch ( NumberFormatException e ) {
// ignore
}
String finalCta = cta;

return singleCellExpressionExperimentService.getCellTypeAssignment( expressionExperiment, qt, cta )
.orElseThrow( () -> {
List<CellTypeAssignment> possibleValues = singleCellExpressionExperimentService.getCellTypeAssignments( expressionExperiment, qt );
return new NullPointerException( "Could not locate any cell type assignment with identifier or name matching " + finalCta + "." + formatPossibleValues( possibleValues, true ) );
} );
return requireNonNull( singleCellExpressionExperimentService.getCellTypeAssignment( expressionExperiment, qt, cta ), () -> {
List<CellTypeAssignment> possibleValues = singleCellExpressionExperimentService.getCellTypeAssignments( expressionExperiment, qt );
return "Could not locate any cell type assignment with identifier or name matching " + finalCta + "." + formatPossibleValues( possibleValues, true );
} );
}

@Override
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53 changes: 52 additions & 1 deletion ...ain/java/ubic/gemma/core/analysis/preprocess/convert/QuantitationTypeConversionUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@
import cern.colt.matrix.DoubleMatrix1D;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.beans.BeanUtils;
import ubic.basecode.dataStructure.matrix.DoubleMatrix;
import ubic.basecode.math.MatrixStats;
import ubic.gemma.core.analysis.preprocess.detect.InferredQuantitationMismatchException;
Expand All @@ -30,11 +31,15 @@
import ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter;
import ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix;
import ubic.gemma.model.common.quantitationtype.*;
import ubic.gemma.model.expression.bioAssayData.DataVector;
import ubic.gemma.model.expression.biomaterial.BioMaterial;
import ubic.gemma.model.expression.designElement.CompositeSequence;

import javax.annotation.CheckReturnValue;
import java.util.List;
import java.beans.PropertyDescriptor;
import java.util.*;
import java.util.function.BiConsumer;
import java.util.function.Function;
import java.util.stream.Collectors;

import static ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtils.detectSuspiciousValues;
Expand Down Expand Up @@ -278,4 +283,50 @@ private static boolean isHeterogeneous( ExpressionDataDoubleMatrix expressionDat
return false;
}

/**
* Convert a collection of vectors.
* @param createQtFunc a function to create a converted {@link QuantitationType}
* @param doToVector a consumer to post-process the created vector (first argument) given the original vector
* (second argument)
* @param vectorType the type of vector to produce
*/
public static <T extends DataVector> Collection<T> convertVectors( Collection<T> vectors, Function<QuantitationType, QuantitationType> createQtFunc, BiConsumer<T, T> doToVector, Class<T> vectorType ) {
ArrayList<T> result = new ArrayList<>( vectors.size() );
Map<QuantitationType, QuantitationType> convertedQts = new HashMap<>();
String[] ignoredProperties = getDataVectorIgnoredProperties( vectorType );
for ( T vector : vectors ) {
QuantitationType convertedQt = convertedQts.computeIfAbsent( vector.getQuantitationType(), createQtFunc );
result.add( createVector( vector, vectorType, convertedQt, doToVector, ignoredProperties ) );
}
return result;
}


/**
* Convert a single vector.
*/
public static <T extends DataVector> T convertVector( T vector, Function<QuantitationType, QuantitationType> createQtFunc, BiConsumer<T, T> doToVector, Class<T> vectorType ) {
return createVector( vector, vectorType, createQtFunc.apply( vector.getQuantitationType() ), doToVector, getDataVectorIgnoredProperties( vectorType ) );
}

private static <T extends DataVector> T createVector( T vector, Class<T> vectorType, QuantitationType convertedQt, BiConsumer<T, T> doToVector, String[] ignoredProperties ) {
T convertedVector = BeanUtils.instantiate( vectorType );
BeanUtils.copyProperties( vector, convertedVector, ignoredProperties );
convertedVector.setQuantitationType( convertedQt );
doToVector.accept( convertedVector, vector );
return convertedVector;
}

/**
* List of properties to copy over when converting a vector to a different QT.
*/
private static String[] getDataVectorIgnoredProperties( Class<? extends DataVector> vectorType ) {
List<String> ignoredPropertiesList = new ArrayList<>();
for ( PropertyDescriptor pd : BeanUtils.getPropertyDescriptors( vectorType ) ) {
if ( pd.getName().equals( "quantitationType" ) || ( pd.getName().startsWith( "data" ) && !pd.getName().equals( "dataIndices" ) ) ) {
ignoredPropertiesList.add( pd.getName() );
}
}
return ignoredPropertiesList.toArray( new String[0] );
}
}
62 changes: 15 additions & 47 deletions .../main/java/ubic/gemma/core/analysis/preprocess/convert/RepresentationConversionUtils.java
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Original file line number Diff line number Diff line change
@@ -1,18 +1,16 @@
package ubic.gemma.core.analysis.preprocess.convert;

import org.apache.commons.lang3.StringUtils;
import org.springframework.beans.BeanUtils;
import ubic.gemma.model.common.quantitationtype.PrimitiveType;
import ubic.gemma.model.common.quantitationtype.QuantitationType;
import ubic.gemma.model.expression.bioAssayData.DataVector;

import java.beans.PropertyDescriptor;
import java.util.*;
import java.util.Collection;

import static ubic.gemma.persistence.util.ByteArrayUtils.doubleArrayToBytes;

/**
* Convert {@link ubic.gemma.model.expression.bioAssayData.DataVector} from different representations.
* Convert {@link DataVector} to different {@link PrimitiveType}.
* @author poirigui
*/
public class RepresentationConversionUtils {
Expand All @@ -21,51 +19,21 @@ public class RepresentationConversionUtils {
* Convert a collection of vectors to a desired representation.
*/
public static <T extends DataVector> Collection<T> convertVectors( Collection<T> vectors, PrimitiveType toRepresentation, Class<T> vectorType ) {
ArrayList<T> result = new ArrayList<>( vectors.size() );
Map<QuantitationType, QuantitationType> convertedQts = new HashMap<>();
List<String> ignoredPropertiesList = new ArrayList<>();
for ( PropertyDescriptor pd : BeanUtils.getPropertyDescriptors( vectorType ) ) {
if ( pd.getName().equals( "quantitationType" ) || ( pd.getName().startsWith( "data" ) && !pd.getName().equals( "dataIndices" ) ) ) {
ignoredPropertiesList.add( pd.getName() );
}
}
String[] ignoredProperties = ignoredPropertiesList.toArray( new String[0] );
for ( T vector : vectors ) {
QuantitationType qt = vector.getQuantitationType();
QuantitationType convertedQt = convertedQts.computeIfAbsent( qt, qt2 -> {
QuantitationType quantitationType = QuantitationType.Factory.newInstance( qt2 );
String description;
if ( StringUtils.isNotBlank( qt.getDescription() ) ) {
description = StringUtils.appendIfMissing( StringUtils.strip( qt.getDescription() ), "." ) + " ";
} else {
description = "";
}
description += "Data was converted from " + qt.getRepresentation() + " to " + toRepresentation + ".";
quantitationType.setDescription( description );
quantitationType.setRepresentation( toRepresentation );
return quantitationType;
} );
T convertedVector = BeanUtils.instantiate( vectorType );
BeanUtils.copyProperties( vector, convertedVector, ignoredProperties );
convertedVector.setQuantitationType( convertedQt );
convertedVector.setData( convertData( vector, toRepresentation ) );
result.add( convertedVector );
}
return result;
return QuantitationTypeConversionUtils.convertVectors( vectors, qt -> getConvertedQuantitationType( qt, toRepresentation ), ( vec, origVec ) -> vec.setData( convertData( origVec, toRepresentation ) ), vectorType );
}

/**
* Convert a single vector to a desired representation.
*/
public static <T extends DataVector> T convertVector( T vector, PrimitiveType toRepresentation, Class<T> vectorType ) {
QuantitationType qt = vector.getQuantitationType();
QuantitationType convertedQt = QuantitationType.Factory.newInstance( qt );
convertedQt.setRepresentation( toRepresentation );
T convertedVector = BeanUtils.instantiate( vectorType );
BeanUtils.copyProperties( vector, convertedVector );
convertedVector.setQuantitationType( convertedQt );
convertedVector.setData( convertData( vector, toRepresentation ) );
return convertedVector;
private static QuantitationType getConvertedQuantitationType( QuantitationType qt, PrimitiveType toRepresentation ) {
QuantitationType quantitationType = QuantitationType.Factory.newInstance( qt );
String description;
if ( StringUtils.isNotBlank( qt.getDescription() ) ) {
description = StringUtils.appendIfMissing( StringUtils.strip( qt.getDescription() ), "." ) + " ";
} else {
description = "";
}
description += "Data was converted from " + qt.getRepresentation() + " to " + toRepresentation + ".";
quantitationType.setDescription( description );
quantitationType.setRepresentation( toRepresentation );
return quantitationType;
}

private static byte[] convertData( DataVector vector, PrimitiveType to ) {
Expand Down
59 changes: 41 additions & 18 deletions ...e/src/main/java/ubic/gemma/core/analysis/preprocess/convert/ScaleTypeConversionUtils.java
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Original file line number Diff line number Diff line change
@@ -1,14 +1,18 @@
package ubic.gemma.core.analysis.preprocess.convert;

import org.apache.commons.lang3.StringUtils;
import ubic.gemma.model.common.quantitationtype.PrimitiveType;
import ubic.gemma.model.common.quantitationtype.QuantitationType;
import ubic.gemma.model.common.quantitationtype.ScaleType;
import ubic.gemma.model.common.quantitationtype.StandardQuantitationType;
import ubic.gemma.model.expression.bioAssayData.DataVector;

import java.util.Collection;

/**
* Utilities for converting data vectors to different scales and representations.
* Convert {@link DataVector} to different {@link ScaleType}.
* <p>
* For now, all conversions produce doubles
* For now, all conversions produce {@link PrimitiveType#DOUBLE}.
* @author poirigui
*/
public class ScaleTypeConversionUtils {
Expand All @@ -18,6 +22,25 @@ public class ScaleTypeConversionUtils {
private static final ThreadLocal<float[]> ONE_FLOAT_VALUE = ThreadLocal.withInitial( () -> new float[1] );
private static final ThreadLocal<double[]> ONE_DOUBLE_VALUE = ThreadLocal.withInitial( () -> new double[1] );

public static <T extends DataVector> Collection<T> convertVectors( Collection<T> vectors, ScaleType toScale, Class<T> vectorType ) {
return QuantitationTypeConversionUtils.convertVectors( vectors, qt -> getConvertedQuantitationType( qt, toScale ), ( vec, origVec ) -> vec.setDataAsDoubles( convertData( origVec, toScale ) ), vectorType );
}

private static QuantitationType getConvertedQuantitationType( QuantitationType qt, ScaleType toScale ) {
QuantitationType quantitationType = QuantitationType.Factory.newInstance( qt );
String description;
if ( StringUtils.isNotBlank( qt.getDescription() ) ) {
description = StringUtils.appendIfMissing( StringUtils.strip( qt.getDescription() ), "." ) + " ";
} else {
description = "";
}
description += "Data was converted from " + qt.getScale() + " to " + toScale + ".";
quantitationType.setDescription( description );
quantitationType.setScale( toScale );
quantitationType.setRepresentation( PrimitiveType.DOUBLE );
return quantitationType;
}

/**
* Convert a single number.
* <p>
Expand All @@ -31,19 +54,19 @@ public static double convertScalar( Number val, QuantitationType qt, ScaleType s
if ( val instanceof Float ) {
float[] vec = ONE_FLOAT_VALUE.get();
vec[0] = val.floatValue();
return convertVector( vec, qt, scaleType )[0];
return convertData( vec, qt, scaleType )[0];
} else if ( val instanceof Double ) {
double[] vec = ONE_DOUBLE_VALUE.get();
vec[0] = val.doubleValue();
return convertVector( vec, qt, scaleType )[0];
return convertData( vec, qt, scaleType )[0];
} else if ( val instanceof Integer ) {
int[] vec = ONE_INT_VALUE.get();
vec[0] = val.intValue();
return convertVector( vec, scaleType )[0];
return convertData( vec, scaleType )[0];
} else if ( val instanceof Long ) {
long[] vec = ONE_LONG_VALUE.get();
vec[0] = val.longValue();
return convertVector( vec, scaleType )[0];
return convertData( vec, scaleType )[0];
} else {
throw new UnsupportedOperationException( "Cannot convert " + val.getClass().getSimpleName() + " to " + scaleType + " scale." );
}
Expand All @@ -65,16 +88,16 @@ public static void clearScalarConversionThreadLocalStorage() {
* @throws IllegalArgumentException if the conversion is not possible
* @throws UnsupportedOperationException if the conversion is not supported
*/
public static double[] convertVector( DataVector vec, ScaleType scaleType ) {
public static double[] convertData( DataVector vec, ScaleType scaleType ) {
switch ( vec.getQuantitationType().getRepresentation() ) {
case FLOAT:
return convertVector( vec.getDataAsFloats(), vec.getQuantitationType(), scaleType );
return convertData( vec.getDataAsFloats(), vec.getQuantitationType(), scaleType );
case DOUBLE:
return convertVector( vec.getDataAsDoubles(), vec.getQuantitationType(), scaleType );
return convertData( vec.getDataAsDoubles(), vec.getQuantitationType(), scaleType );
case INT:
return convertVector( vec.getDataAsInts(), scaleType );
return convertData( vec.getDataAsInts(), scaleType );
case LONG:
return convertVector( vec.getDataAsLongs(), scaleType );
return convertData( vec.getDataAsLongs(), scaleType );
default:
throw new UnsupportedOperationException( "Conversion of " + vec.getQuantitationType().getRepresentation() + " is not supported." );
}
Expand All @@ -83,23 +106,23 @@ public static double[] convertVector( DataVector vec, ScaleType scaleType ) {
/**
* Convert a vector of float data to the target scale.
*/
public static double[] convertVector( float[] vec, QuantitationType quantitationType, ScaleType scaleType ) {
return convertVector( float2double( vec ), quantitationType.getType(), quantitationType.getScale(), scaleType );
public static double[] convertData( float[] vec, QuantitationType quantitationType, ScaleType scaleType ) {
return convertData( float2double( vec ), quantitationType.getType(), quantitationType.getScale(), scaleType );
}

/**
* Convert a vector of double data to the target scale.
*/
public static double[] convertVector( double[] vec, QuantitationType quantitationType, ScaleType scaleType ) {
return convertVector( vec, quantitationType.getType(), quantitationType.getScale(), scaleType );
public static double[] convertData( double[] vec, QuantitationType quantitationType, ScaleType scaleType ) {
return convertData( vec, quantitationType.getType(), quantitationType.getScale(), scaleType );
}

/**
* Convert a vector of counting data to the target scale.
* <p>
* The type and scale are assumed to be counts.
*/
public static double[] convertVector( int[] vec, ScaleType scaleType ) {
public static double[] convertData( int[] vec, ScaleType scaleType ) {
if ( scaleType == ScaleType.LINEAR || scaleType == ScaleType.COUNT ) {
return int2double( vec );
}
Expand Down Expand Up @@ -129,7 +152,7 @@ public static double[] convertVector( int[] vec, ScaleType scaleType ) {
* <p>
* The type and scale are assumed to be counts.
*/
public static double[] convertVector( long[] vec, ScaleType scaleType ) {
public static double[] convertData( long[] vec, ScaleType scaleType ) {
if ( scaleType == ScaleType.LINEAR || scaleType == ScaleType.COUNT ) {
return long2double( vec );
}
Expand All @@ -154,7 +177,7 @@ public static double[] convertVector( long[] vec, ScaleType scaleType ) {
return result;
}

public static double[] convertVector( double[] vec, StandardQuantitationType fromType, ScaleType fromScale, ScaleType scaleType ) {
public static double[] convertData( double[] vec, StandardQuantitationType fromType, ScaleType fromScale, ScaleType scaleType ) {
if ( fromScale == scaleType ) {
return vec;
}
Expand Down
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