src/hg/instinct/inc/hgStats.h 1.6

Index: src/hg/instinct/inc/hgStats.h
===================================================================
RCS file: src/hg/instinct/inc/hgStats.h
diff -N src/hg/instinct/inc/hgStats.h
--- src/hg/instinct/inc/hgStats.h	24 Jan 2009 00:37:27 -0000	1.5
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,67 +0,0 @@
-#ifndef HGSTATS_H
-#define HGSTATS_H
-
-/* hgStats.h - Include file used by hgStats. 
- * hgStats is collection of routines that set up hgHeatmap data for statistical
- * analysis by cluster 3.0 
- *
- * Much of code in these routines was adapted from cluster 3.0 file "data.c" or "command.c"
- */
-
-#include "cluster.h"
-#include "hgHeatmapLib.h"
-#include "vGfx.h"
-
-struct dataVector
-{
-    struct dataVector *next;    /* linked list for multiple regions */
-    int count;          /*      number of data values   */
-    double value;       /*      array of data values at these positions */
-    double min;         /*      minimum data value in the set   */
-    double max;         /*      maximum data value in the set   */
-    Color color;        /*      color of data point */
-};            
-
-struct pcaData    /* TODO: develop this more fully to keep general summary of PCA results */
-{
-    struct pcaData *next;
-    int numComponents;
-    double *components;
-};
-
-//#define GRAPH_WIDTH     300     /*      actual graphing area size       */
-//#define GRAPH_HEIGHT    300     /*      left and bottom text will add to this */
-#define PLOT_MARGIN     2       /*      around graph and around everything */
-#define DOT_SIZE        2       /*      size of plotted point   */
-
-void getNodeOrderFromTree(Node* tree, int nNodes, const double* order, 
-			  double *nodeorder, int *nodecounts, char metric);
-/* Get new order of genes from Tree for display */
-
-void initializeData(int rows, int columns, struct hash *geneHash, struct slName *genes, 
-		    double **data, int **mask, double *arrayweight, 
-		    double *geneorder, char **genename);
-/* Initialize data structures and fill with hgHeatmap data for cluster routines */
-
-struct slName *clusterGeneSet(struct hash *geneHash, 
-			      struct slName *genes, char method, char metric);
-/* Set up data structures for cluster software, perform hierarchical clustering, and 
- * return a new sorted list of gene names according to clustering */
-
-Node *clusterSamplesByGeneSet(struct hash *geneHash, struct slName *allGenes,
-			      char method, char metric, int transpose, int *nRows, int *nCols);
-/* Performs clustering along samples, returns tree */
-
-void pcaGeneSet(struct hash *geneHash, struct slName *genes, 
-		int rows, int columns, double **data, char **genename, 
-		double **u, double **v, double *w, int *svdorder);
-/* Set up data structures for cluster software and perform PCA on gene set */
-
-struct hash *performPCAandPlot(struct vGfx *vg, int totalWidth, int totalHeight, 
-		    int startX, int startY, struct hash *geneHash, 
-		    struct slName *genes, struct featureColor *fcList); 
-
-struct hash *performPCA(struct hash *geneHash, struct slName *genes);
-/* Simply obtain the statHash containing PCA 1st and 2nd components of input geneset */
- 
-#endif /* HGSTATS_H */