d09b392333a2f5d2f943f2f36dad4be0a477381e
kate
  Thu Sep 14 13:55:37 2017 -0700
Add pvalue and TSS distance for each eQTL. Input from Casey Brown, U Penn. refs #15646

diff --git src/hg/hgc/gtexEqtlClusterClick.c src/hg/hgc/gtexEqtlClusterClick.c
index f25be1f..7152e66 100644
--- src/hg/hgc/gtexEqtlClusterClick.c
+++ src/hg/hgc/gtexEqtlClusterClick.c
@@ -1,186 +1,188 @@
 /* Details page for GTEx eQTL Clusters */
 
 /* Copyright (C) 2017 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "hCommon.h"
 #include "web.h"
 #include "gtexTissue.h"
 #include "gtexInfo.h"
 #include "gtexEqtlCluster.h"
 #include "hgc.h"
 
 static struct gtexEqtlCluster *getGtexEqtl(char *item, char *chrom, int start, int end, char *table)
 /* Retrieve this item from the track table */
 {
 char *gene = firstWordInLine(cloneString(item));
 struct sqlConnection *conn = hAllocConn(database);
 struct gtexEqtlCluster *eqtls = NULL, *eqtl;
 char **row;
 int offset;
 char where[512];
 sqlSafefFrag(where, sizeof(where), "target='%s'", gene);
 struct sqlResult *sr = hRangeQuery(conn, table, chrom, start, end, where, &offset); 
 while ((row = sqlNextRow(sr)) != NULL)
     {
     eqtl = gtexEqtlClusterLoad(row+offset);
     slAddHead(&eqtls, eqtl);
     }
 slReverse(&eqtls);
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return eqtls;
 }
 
 static char *getGeneDescription(struct sqlConnection *conn, char *geneName)
 /* Return description from KnownGenes track */
 {
 char query[256];
 sqlSafef(query, sizeof query,
                 "SELECT kgXref.description FROM kgXref WHERE geneSymbol='%s'", geneName);
 return sqlQuickString(conn, query);
 }
 
 static void printMinorAlleleFreq(char *rsId, struct sqlConnection *conn)
 /* Print minor allele frequency for a SNP (from UCSC dbSNP table) */
 {
 #define SNP_COMMON_SUFFIX       "Common"
 #define MAX_ALLELE_COUNT 10
 char *snpTable = hFindLatestSnpTableConn(conn, SNP_COMMON_SUFFIX);
 if (!snpTable)
     return;
 char query[256];
 sqlSafef(query, sizeof query, "SELECT alleleFreqs FROM %s WHERE name='%s'", snpTable, rsId);
 double freqs[MAX_ALLELE_COUNT];
 int count = sqlDoubleArray(sqlQuickString(conn, query), freqs, MAX_ALLELE_COUNT);
 doubleSort(count, freqs);
 printf("<br><b>Minor allele frequency (1000 Genomes):</b> %.0f%%\n", 100.0 * freqs[count-2]);
 }
 
 static void printGwasCatalogTrait(char *rsId, struct sqlConnection *conn)
 /* Print trait/disease for a SNP (from UCSC gwasCatalog table) */
 {
 char query[256];
 sqlSafef(query, sizeof query, "SELECT count(*) FROM gwasCatalog WHERE name='%s'", rsId);
 int count = sqlQuickNum(conn, query);
 if (count)
     {
     sqlSafef(query, sizeof query, "SELECT trait FROM gwasCatalog WHERE name='%s' LIMIT 1", rsId);
     char *trait = sqlQuickString(conn, query);
     printf("<br><b>GWAS disease or trait");
     if (count > 1)
         printf(" (1 of %d)", count);
     printf(": </b>%s <a target='_blank' href='https://www.ebi.ac.uk/gwas/search?query=%s'>"
                     "GWAS Catalog</a>\n", trait, rsId);
     }
 }
 
 static void printEqtlRegion(struct gtexEqtlCluster *eqtl, char *table, struct sqlConnection *conn)
 /* Print position of region encompassing all identified eQTL's for this gene */
 {
 #define FLANK  1000 
 char query[256];
 sqlSafef(query, sizeof query, "SELECT MIN(chromStart) from %s WHERE target='%s'", 
             table, eqtl->target);
 int start = sqlQuickNum(conn, query) - FLANK;
 sqlSafef(query, sizeof query, "SELECT MAX(chromEnd) from %s WHERE target='%s'", 
             table, eqtl->target);
 int end = sqlQuickNum(conn, query) + FLANK;
 char posLink[1024];
 safef(posLink, sizeof posLink,"<a href='%s&db=%s&position=%s%%3A%d-%d'>%s:%d-%d</a>",
         hgTracksPathAndSettings(), database,
             eqtl->chrom, start+1, end,
             eqtl->chrom, start+1, end);
 printf("<br><b>Region containing eQTLs for this gene:</b> %s (%d bp, including +-%dbp flank)\n", 
         posLink, end-start, FLANK);
 }
 
 static void printClusterDetails(struct gtexEqtlCluster *eqtl, char *table)
 /* Print details of an eQTL cluster */
 {
 webNewSection("eQTL Cluster Details");
 char *version = gtexVersion(table);
 struct gtexTissue *tissues = gtexGetTissues(version);
 struct hash *tissueHash = hashNew(0);
 struct gtexTissue *tis = NULL;
 for (tis = tissues; tis != NULL; tis = tis->next)
     hashAdd(tissueHash, tis->name, tis);
 printf("<table id='eqtls' cellspacing=1 cellpadding=3>\n");
 printf("<style>#eqtls th {text-align: left; background-color: #F3E0BE;}</style>");
-printf("<tr><th>&nbsp;&nbsp;&nbsp;</th><th>Tissue</th><th>Effect &nbsp;&nbsp;</th><th>Probability </th></tr>\n");
+printf("<tr><th>&nbsp;&nbsp;&nbsp;</th><th>Tissue</th><th>Effect &nbsp;&nbsp;</th><th>P-Value (-log10)</th><th>Probability </th></tr>\n");
 int i;
 for (i=0; i<eqtl->expCount; i++)
     {
     double effect = eqtl->expScores[i];
+    double pval = eqtl->expPvals[i];
     double prob = eqtl->expProbs[i];
     struct gtexTissue *tis = (struct gtexTissue *)hashFindVal(tissueHash, eqtl->expNames[i]);
     unsigned color = tis ? tis->color : 0;       // BLACK
     char *name = tis ? tis->description : "Unknown";
-    printf("<tr><td bgcolor=#%06X></td><td>%s</td><td>%s%0.2f</td><td>%0.2f</td></tr>\n", 
-                                color, name, effect < 0 ? "" : "+", effect, prob); 
+    printf("<tr><td bgcolor=#%06X></td><td>%s</td><td>%s%0.2f</td><td>%0.2f</td><td>%0.2f</td></tr>\n", 
+                                color, name, effect < 0 ? "" : "+", effect, pval, prob); 
     }
 printf("</table>");
 webEndSection();
 }
 
 void doGtexEqtlDetails(struct trackDb *tdb, char *item)
 /* Details of GTEx eQTL item */
 {
 char *chrom = cartString(cart, "c");
 int start = cartInt(cart, "o");
 int end = cartInt(cart, "t");
 struct gtexEqtlCluster *eqtl = getGtexEqtl(item, chrom, start, end, tdb->table);
 char *geneName = eqtl->target;
 
 
 genericHeader(tdb, item);
 printf("<b>Gene: </b>");
 struct sqlConnection *conn = hAllocConn(database);
 char *desc = getGeneDescription(conn, geneName);
 if (desc == NULL)
     printf("%s\n", geneName);
 else
     {
     printf("<a target='_blank' href='%s?db=%s&hgg_gene=%s'>%s</a><br>\n",
                         hgGeneName(), database, geneName, geneName);
     printf("<b>Description:</b> %s\n", desc);
     }
 
 // TODO: Consider adding Ensembl gene ID, GENCODE biotype and class (as in gtexGene track)
 printf("<br><b>Variant: </b>%s ", eqtl->name);
 if (startsWith("rs", eqtl->name))
     {
     printDbSnpRsUrl(eqtl->name, "dbSNP");
     printMinorAlleleFreq(eqtl->name, conn);
     printGwasCatalogTrait(eqtl->name, conn);
     }
 else
     printf("%s\n", eqtl->name);
+printf("<br><b>Distance from TSS:</b> %d\n", eqtl->distance);
 
 char posLink[1024];
 safef(posLink, sizeof posLink,"<a href='%s&db=%s&position=%s%%3A%d-%d'>%s:%d-%d</a>",
         hgTracksPathAndSettings(), database,
             eqtl->chrom, eqtl->chromStart+1, eqtl->chromEnd,
             eqtl->chrom, eqtl->chromStart+1, eqtl->chromEnd);
 printf("<br><b>Position:</b> %s\n", posLink);
 
 printf("<br><b>Score:</b> %d\n", eqtl->score);
 
 printEqtlRegion(eqtl, tdb->table, conn);
 printf("<br><b>Number of tissues with this eQTL:</b> %d\n", eqtl->expCount);
 
 // print link to GTEx portal
 printf("<br><a target='_blank' href='https://www.gtexportal.org/home/bubbleHeatmapPage/%s'>"
         "View eQTL Visualizer for this gene at the GTEx Portal<a>\n", 
                 geneName);
 hFreeConn(&conn);
 
 printClusterDetails(eqtl, tdb->table);
 
 webNewEmptySection();
 printTrackHtml(tdb);
 }