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java.lang.Object
|
+--MJAbase
|
+--MJAcluster
MAExplorer Open Java API class to access MJAcluster methods and data structures. Access cluster data structures and support methods.
List of methods available to Plugin-writers
get_useCorrelationCoefficientFlag() - get gene-gene distance metric flag. set_hierClusterUnWeightedAvgFlag() - hier-clustering averaging method flag get_clusterOnFilteredGenesFlag() - to show cluster on Filtered genes get_useSimilarGeneClusterDisplayFlag() - if similar genes clustering method is active get_useClusterCountsDisplayFlag() - if gene cluster counts of # similar genes is active get_normHierClusterByRatioHPFlag() - to norm hierarchical cluster by ratio HP get_useMedianForKmeansClusteringFlag() - use K-median else default K-means get_useHierClusterDisplayFlag() - if hierarchical clustering method is active get_useKmeansClusterCountsDispFlag() - show K-means clusters counts get_useLSQmagnitudeNormalizationFlag() - to normalize cluster expression get_useClusterDistanceCacheFlag() - to use cluster distance cache get_useShortClusterDistanceCacheFlag() - use short[] cluster dist cache getKmeansClusters() - list of K-means clustering data. getClusterOfSimilarGenes() - list of gene cluster similar to seed gene. getHierClusterOfGenes() - get Hashtable list of hierarchical gene cluster addr1D() - lookup lower-diagonal addr1D(x,y) [y' + x'*(x'+1)/2] computeGeneGeneDistanceMatri() - return gene-gene cluster distance matrix. calcNormGeneVectors() - calc HP-E intensity vector for genes to normalize findGeneWithLeastSumDistances() - find gene with minimum cluster distance
This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.
| Method Summary | |
int |
addr1D(int x,
int y)
addr1D() - lookup lower-diagonal addr1D(x,y) [y' + x'*(x'+1)/2] |
float[][] |
calcNormGeneVectors(java.lang.String geneListToNormalize)
calcNormGeneVectors() - compute HP-E intensity vector for geneList To Normalize. |
float[] |
computeGeneGeneDistanceMatrix(java.lang.String geneListToUse)
computeGeneGeneDistanceMatrix() - return gene-gene cluster distance matrix. |
int |
findGeneWithLeastSumDistances(float[] ccDist1D,
int nGenes)
findGeneWithLeastSumDistances() - find gene with minimum cluster distance to all other genes. |
boolean |
get_clusterOnFilteredGenesFlag()
get_clusterOnFilteredGenesFlag() - get flag to cluster on Filtered genes else All genes. |
boolean |
get_normHierClusterByRatioHPFlag()
get_normHierClusterByRatioHPFlag() - get flag to that normalizing each HP-E gene expression vector dataV[1:nHP] by the ratio of HP-X dataV[HP-X]. |
boolean |
get_useClusterCountsDisplayFlag()
get_useClusterCountsDisplayFlag() - get flag to show if gene cluster counts cluster method is active. |
boolean |
get_useClusterDistanceCacheFlag()
get_useClusterDistanceCacheFlag() - get flag to use cluster distance cache to speed up computations. |
boolean |
get_useCorrelationCoefficientFlag()
get_useCorrelationCoefficientFlag() - get gene-gene distance metric flag. |
boolean |
get_useHierClusterDisplayFlag()
get_useHierClusterDisplayFlag() - get flag show hierarchical clusters in the pseudoarray image for All Filtered genes. |
boolean |
get_useKmeansClusterCountsDispFlag()
get_useKmeansClusterCountsDispFlag() - get flag show K-means cluster counts for all Filtered genes in the pseudoarray image. |
boolean |
get_useLSQmagnitudeNormalizationFlag()
get_useLSQmagnitudeNormalizationFlag() - get flag to normalize cluster expression vector geneEPvect[] to 1.0 for clustering |
boolean |
get_useMedianForKmeansClusteringFlag()
get_useMedianForKmeansClusteringFlag() - get flag for K-median else K-means clustering |
boolean |
get_useShortClusterDistanceCacheFlag()
get_useShortClusterDistanceCacheFlag() - get flag t ouse short[] cluster distance cache to save memory |
boolean |
get_useSimilarGeneClusterDisplayFlag()
get_useSimilarGeneClusterDisplayFlag() - get flag to show if similar genes cluster method is active. |
java.util.Hashtable |
getClusterOfSimilarGenes(java.lang.String geneListToCluster,
float curGeneDistanceThr,
int initialSeedGeneMID)
getClusterOfSimilarGenes() - get Hashtable list of gene cluster similar to seed gene. |
java.util.Hashtable |
getHierClusterOfGenes(java.lang.String geneListToCluster)
getHierClusterOfGenes() - get Hashtable list of hierarchical gene cluster of genes. |
java.util.Hashtable |
getKmeansClusters(java.lang.String geneListToCluster,
int nbrOfClusters,
int initialSeedGeneMID)
getKmeansClusters() - get Hashtable list of K-means clustering data. |
void |
set_hierClusterUnWeightedAvgFlag(boolean value)
set_hierClusterUnWeightedAvgFlag() - set hier-clustering averaging method flag. |
| Methods inherited from class MJAbase |
cvtHashtable2SimpleTable, cvtTable2Hashtable |
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Method Detail |
public final boolean get_useCorrelationCoefficientFlag()
public final void set_hierClusterUnWeightedAvgFlag(boolean value)
value - to set flagpublic final boolean get_clusterOnFilteredGenesFlag()
public final boolean get_useSimilarGeneClusterDisplayFlag()
public final boolean get_useClusterCountsDisplayFlag()
public final boolean get_normHierClusterByRatioHPFlag()
public final boolean get_useMedianForKmeansClusteringFlag()
public final boolean get_useHierClusterDisplayFlag()
public final boolean get_useKmeansClusterCountsDispFlag()
public final boolean get_useLSQmagnitudeNormalizationFlag()
public final boolean get_useClusterDistanceCacheFlag()
public final boolean get_useShortClusterDistanceCacheFlag()
public final java.util.Hashtable getKmeansClusters(java.lang.String geneListToCluster,
int nbrOfClusters,
int initialSeedGeneMID)
The Hashtable list returned is defined as:
nAme - Value
"NbrClusters" - int number of clusters
"NbrSamples" - int number of HP-E samples
"NbrGenes" - int number of Genes clustered
"NameGeneListToCluster" - String name of GeneList set to cluster
"InitialSeedGeneMID" - int initial seed gene MID to start cluster 1
"maxGlobalDist" - float max Global cluster distance for
all genes
"kMeansDist" - float[1:NbrClusters] distance between K-means
clusters
"kMeansMaxDist" - float[1:NbrClusters] max distance within each
K-means cluster
"mnWithinClusterDist" - float[1:NbrClusters] mean within-cluster
distance between K-means clusters
"sdWithinClusterDist" - float[1:NbrClusters] StdDev within-cluster
distance between K-means clusters
"kMeansList" - int[1:NbrClusters] index of gene as K-means
cluster center
"hpDataNbrA" - int [0:NbrClusters-1] opt # genes/K-means
cluster for HP-E samples
"hpDataMnA" - float[0:NbrClusters-1][0:NbrSamples-1] opt
Mean HP-E quant data
"hpDataSDA" - float[0:NbrClusters-1][0:NbrSamples-1] opt.
StdDev HP-E quant data
"nClustersFound" - int # of unique K-means clusters
actually found
"maxKmeansNodes" - int max # of K-means clusters set by
thresholding slider
"geneEPvector" - float[0:NbrGenes-1][0:NbrSamples-1]
normalized quantified gene vector
"ClusterMeansGeneList" - Hashtable list GeneList of means of clusters
"CurClusterGeneList" - Hashtable list GeneList of genes in current
cluster
geneListToCluster - name of gene list with genes to clusternbrOfClusters - # of clusters to generateinitialSeedGeneMID - initial seed gene specified by MIDnull if error.
public final java.util.Hashtable getClusterOfSimilarGenes(java.lang.String geneListToCluster,
float curGeneDistanceThr,
int initialSeedGeneMID)
The Hashtable list returned is defined as:
Name - Value
"NbrSamples" - int number of HP-E samples
"NbrGenes" - int number of Genes clustered
"NameGeneListToCluster" - String name of GeneList set to cluster
"InitialSeedGeneMID" - int initial seed gene MID to start cluster
"maxGlobalDist" - float max Global cluster distance for all
genes
"curGeneDistanceThr" - float threshold distance for similar genes
"NbrSimilarGenesInCluster" - int # genes in cluster simiar to seed gene
"CurClusterGeneList" - Hashtable of GeneList of genes in current
cluster
geneListToCluster - name of gene list with genes to clustercurGeneDistanceThr - threshold distance for similar genesinitialSeedGeneMID - initial seed gene specified by MIDnull if not found or error,
else return Hashtable list.public final java.util.Hashtable getHierClusterOfGenes(java.lang.String geneListToCluster)
The Hashtable list returned is defined as:
Name - Value
"NbrSamples" - int number of HP-E samples
"NbrGenes" - int number of Genes clustered
"NameGeneListToCluster" - String name of GeneList set to cluster
"NormByRatioHPflag" - boolean flag: normalize EP data before
cluster by "HP-X Sample data/gene"
else "HP max intensities data"
"HierClusterUnWtAvgFlag" - boolean flag: "unweighted-avg"
else "weighted-avg"
"HierClusterMode" - int cluster linkage mode. Either
HIER_CLUST_NEXT_MIN_LNKG,
HIER_CLUST_PGMA_LNKG or HIER_CLUST_PGMC_LNKG
"CurClusterGeneList" - Hashtable list GeneList of genes in current
cluster in order of hierarchical cluster.
"NbrNodes" - int number of nodes in the cluster
(2*NbrGenes-1)
"MaxDistLR" - float max distance (squared) between any
Left and Right found between all nodes
"TreeEnumeration" - Hashtable enumeration of the hierarchical
cluster
The TreeEnumeration Hashtable list is returned an enumeration
of the cluster tree and is defined as:
Name - Value
"GeneMID" - int Gene MID index if it is a terminal
node else -1
"NodeID" - int unique cluster node #
"EnumOrder" - float enumeration order in range
[0:NbrNodes-1].
Intermediate nodes may be fractional eg.
(LeftChildNode.enumOrder +
RightChildNode.enumOrder)/2.0
"ParentNodeID" - int if not -1, then parent node
"LeftChildNodeID" - int if not -1, then left node
"RightChildNodeID" - int distance between left and right
children nodes
"MeanEPdataForNode" - mean vector float [0:NbrSamples-1] of left
and right
"NbrChildren" - int # of children of Node
geneListToCluster - name of gene list with genes to clusternull if not found or error,
else return Hashtable list.
public final int addr1D(int x,
int y)
where:
x' = (x>y) ? x : y,
y' = (x>y) ? y : x.
x - coordinatey - coordinatepublic final float[] computeGeneGeneDistanceMatrix(java.lang.String geneListToUse)
addr1D(x,y) = [y' + x'*(x'+1)/2]
where:
x' = (x>y) ? x : y,
y' = (x>y) ? y : x.
geneListToUse - is the name of the genelist to filter bypublic final float[][] calcNormGeneVectors(java.lang.String geneListToNormalize)
geneListToNormalize - gene list to normalize.
public final int findGeneWithLeastSumDistances(float[] ccDist1D,
int nGenes)
ccDist1D - gene-gene distance computed with
computeGeneGeneDistanceMatrix()nGenes - is the # of genes in gene-gene matrix.computeGeneGeneDistanceMatrix(java.lang.String)
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