Package ubic.gemma.core.loader.expression.singleCell

Class SingleCellDataLoaderConfig

java.lang.Object
ubic.gemma.core.loader.expression.DataLoaderConfig
ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig
ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig
Direct Known Subclasses:
AnnDataSingleCellDataLoaderConfig, MexSingleCellDataLoaderConfig
public class SingleCellDataLoaderConfig extends SequencingDataLoaderConfig
Basic configuration for loading single-cell data.
Author:
poirigui
See Also:

  • Field Details

    • transformExecutor

      @Nullable public ExecutorService transformExecutor
      Executor service to use to transform single-cell data.

  • Constructor Details

  • Method Details

    • builder

      public static SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder<?,?> builder()

    • isIgnoreSamplesLackingData

      public boolean isIgnoreSamplesLackingData()
      Ignore individual samples that lack or have incomplete data.

      This is only implemented for MEX.

    • getCellTypeAssignmentFile

      @Nullable public Path getCellTypeAssignmentFile()
      A location where cell type can be found in a format covered by GenericMetadataSingleCellDataLoader.

      If null, no cell type assignment will be imported. However, the loader might have other provisions for loading cell types. For example, AnnDataSingleCellDataLoader can import cell types using a factor name.

    • getCellTypeAssignmentName

      @Nullable public String getCellTypeAssignmentName()
      A name to use for the cell type assignment.

      If null, it is left to the specific loader to decide the name.

    • getCellTypeAssignmentDescription

      @Nullable public String getCellTypeAssignmentDescription()
      A description to use for the cell type assignment.

    • getCellTypeAssignmentProtocol

      @Nullable public Protocol getCellTypeAssignmentProtocol()
      A protocol to use for the cell type assignment.

      If non-null, this must be persistent.

    • isReplaceExistingCellTypeAssignment

      public boolean isReplaceExistingCellTypeAssignment()
      If there is already a cell type assignment with the same name, replace it with the new one.

      Note that CTAs with a null name cannot be replaced.

    • isIgnoreExistingCellTypeAssignment

      public boolean isIgnoreExistingCellTypeAssignment()
      If true, ignore existing cell type assignment with the same name.

    • getOtherCellLevelCharacteristicsFile

      @Nullable public Path getOtherCellLevelCharacteristicsFile()
      A location where additional cell-level characteristics can be loaded.

    • getOtherCellLevelCharacteristicsNames

      @Nullable public List<String> getOtherCellLevelCharacteristicsNames()
      Name to use for the cell-level characteristics.

      Must match the number and order of CLCs in otherCellLevelCharacteristicsFile.

    • getOtherCellLevelCharacteristicsDefaultValues

      @Nullable public List<String> getOtherCellLevelCharacteristicsDefaultValues()
      Default values to use for the cell-level characteristics.

      Must match the number and order of CLCs in otherCellLevelCharacteristicsFile.

    • getOtherCellLevelCharacteristicsDefaultValueUris

      @Nullable public List<String> getOtherCellLevelCharacteristicsDefaultValueUris()
      Default value URIs to use for the cell-level characteristics.

      Must match the number and order of CLCs in otherCellLevelCharacteristicsFile.

    • isReplaceExistingOtherCellLevelCharacteristics

      public boolean isReplaceExistingOtherCellLevelCharacteristics()
      If there are already other CLCs with the same names, replace them with the new ones.

      Note that other CLCs with a null name cannot be replaced.

    • isIgnoreExistingOtherCellLevelCharacteristics

      public boolean isIgnoreExistingOtherCellLevelCharacteristics()
      If true, ignore existing other CLCs with the same names.

    • isInferSamplesFromCellIdsOverlap

      public boolean isInferSamplesFromCellIdsOverlap()
      When parsing cellTypeAssignmentFile and otherCellLevelCharacteristicsFile, use the overlap between the cell IDs from the file and those from the SingleCellDimension to infer sample associations.

      When this option is set, the sample ID column must be supplied for this strategy to be applied.

    • isUseCellIdsIfSampleNameIsMissing

      public boolean isUseCellIdsIfSampleNameIsMissing()
      When parsing cellTypeAssignmentFile and otherCellLevelCharacteristicsFile, allow for a missing sample_id column, in which case barcodes are used to infer the sample a cell belongs to. This strategy will not work in the case of a barcode collision.

    • isIgnoreUnmatchedCellIds

      public boolean isIgnoreUnmatchedCellIds()
      When parsing cellTypeAssignmentFile and otherCellLevelCharacteristicsFile, ignore cell IDs that cannot be matched to a sample.

    • isMarkSingleCellTypeAssignmentAsPreferred

      public boolean isMarkSingleCellTypeAssignmentAsPreferred()
      If only one CTA is present, mark it as preferred.

    • getPreferredCellTypeAssignmentName

      @Nullable public String getPreferredCellTypeAssignmentName()
      Name of the CTA to mark as preferred, or null to ignore.

      This setting overrides markSingleCellTypeAssignmentAsPreferred.

    • isRecreateCellTypeFactorIfNecessary

      public boolean isRecreateCellTypeFactorIfNecessary()
      Re-create the cell type factor if necessary.

    • isIgnoreCompatibleCellTypeFactor

      public boolean isIgnoreCompatibleCellTypeFactor()
      When re-creating, ignore a compatible cell type factor that may already exist.

      Requires recreateCellTypeFactorIfNecessary to be set.

    • isPreferSinglePrecision

      public boolean isPreferSinglePrecision()
      Prefer single-precision for storage, even if the data is available with double-precision.

      This reduces the size of vectors and thus the storage requirement.

    • isIgnoreDataVectors

      public boolean isIgnoreDataVectors()
      Skip single-cell data vectors if possible, or at least skip transformation that would normally be applied to them to make them usable.

      When this option is set, SingleCellDataLoader.loadVectors(Collection, SingleCellDimension, QuantitationType) will throw an UnsupportedOperationException.

    • getDiscardEmptyCells

      @Nullable public Boolean getDiscardEmptyCells()
      Discard (or keep) empty cells.

      The default is to discard if empty cells are found. Setting this to false will disable the detection entirely.

      See Also:

    • getTransformExecutor

      @Nullable public ExecutorService getTransformExecutor()
      Executor service to use to transform single-cell data.

    • getConsole

      @Nullable public Console getConsole()
      Console to use for reporting progress.