ba8ffb877e7fa5eb507334b772c88528b4ecadfe
kate
  Thu Feb 11 11:52:18 2016 -0800
Finishing touches to GTEx gene details page.  Added link to hgGeneand bent knownGene queries for gene description to handle both hg38 and hg19 conventions. refs #15645

diff --git src/hg/hgc/gtexClick.c src/hg/hgc/gtexClick.c
index 9152616..c2aeee6 100644
--- src/hg/hgc/gtexClick.c
+++ src/hg/hgc/gtexClick.c
@@ -1,211 +1,232 @@
 /* Details pages for GTEx tracks */
 
 /* Copyright (C) 2015 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "hdb.h"
 #include "hvGfx.h"
 #include "trashDir.h"
 #include "hgc.h"
+#include "hCommon.h"
 
 #include "gtexGeneBed.h"
 #include "gtexTissue.h"
 #include "gtexSampleData.h"
 #include "gtexUi.h"
 #include "gtexInfo.h"
 
 struct tissueSampleVals
 /* RPKM expression values for multiple samples */
     {
     struct tissueSampleVals *next;
     char *name;         /* GTEx tissue name */
     char *description;  /* GTEx tissue description */
     int color;          /* GTEx tissue color */
     int count;          /* number of samples */
     double *vals;       /* RPKM values */
     double min, max;    /* minimum, maximum value */
     double q1, median, q3;      /* quartiles */
     struct slDouble *valList;   /* used to create val array */
     };
 
 /********************************************************/
 /* R implementation.  Invokes R script */
 
 void drawGtexRBoxplot(struct gtexGeneBed *gtexGene, struct tissueSampleVals *tsvList,
                         boolean doLogTransform, char *version)
 /* Draw a box-and-whiskers plot from GTEx sample data, using R boxplot */
 {
 /* Create R data frame.  This is a tab-sep file, one row per sample, 
  * with columns for sample, tissue, rpkm */
 struct tempName dfTn;
 trashDirFile(&dfTn, "hgc", "gtexGene", ".df.txt");
 FILE *f = fopen(dfTn.forCgi, "w");
 if (f == NULL)
     errAbort("can't create temp file %s", dfTn.forCgi);
 fprintf(f, "sample\ttissue\trpkm\n");
 struct tissueSampleVals *tsv;
 int sampleId=1;
 int i;
 for (tsv = tsvList; tsv != NULL; tsv = tsv->next)
     {
     int count = tsv->count;
     for (i=0; i<count; i++)
         fprintf(f, "%d\t%s\t%0.3f\n", sampleId++, tsv->name, tsv->vals[i]);
     }
 fclose(f);
 
 // Plot to PNG file
 struct tempName pngTn;
 trashDirFile(&pngTn, "hgc", "gtexGene", ".png");
 char cmd[256];
 
 /* Exec R in quiet mode, without reading/saving environment or workspace */
 safef(cmd, sizeof(cmd), "Rscript --vanilla --slave hgcData/gtexBoxplot.R %s %s %s %s %s",  
                                 gtexGene->name, dfTn.forCgi, pngTn.forHtml, 
                                 doLogTransform ? "log=TRUE" : "log=FALSE", version);
 int ret = system(cmd);
 if (ret == 0)
     {
     printf("<IMG SRC = \"%s\" BORDER=1><BR>\n", pngTn.forHtml);
     //printf("<IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d><BR>\n",
                     //pngTn.forHtml, imageWidth, imageHeight);
                     //pngTn.forHtml, 900, 500);
     }
 }
 
 struct gtexGeneBed *getGtexGene(char *item, char *table)
 /* Retrieve gene info for this item from the main track table */
 {
 struct gtexGeneBed *gtexGene = NULL;
 struct sqlConnection *conn = hAllocConn(database);
 char **row;
 char query[512];
 struct sqlResult *sr;
 if (sqlTableExists(conn, table))
     {
     sqlSafef(query, sizeof(query), "select * from %s where name = '%s'", table, item);
     sr = sqlGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row != NULL)
         {
         gtexGene = gtexGeneBedLoad(row);
         }
     sqlFreeResult(&sr);
     }
 hFreeConn(&conn);
 return gtexGene;
 }
 
 struct tissueSampleVals *getTissueSampleVals(struct gtexGeneBed *gtexGene, boolean doLogTransform,
                                                 char *version, double *maxValRet)
 /* Get sample data for the gene.  Optionally log10 it. Return maximum value seen */
 {
 // TODO: support version table name.  Likely move to lib.
 struct hash *tsHash = hashNew(0);
 struct tissueSampleVals *tsv;
 struct hashEl *hel;
 struct slDouble *val;
 double maxVal = 0;
 struct gtexSampleData *sd = NULL;
 char query[256];
 char **row;
 char buf[256];
 char *sampleDataTable = "gtexSampleData";
 safef(buf, sizeof(buf), "%s%s", sampleDataTable, version);
 struct sqlConnection *conn = hAllocConn("hgFixed");
 assert(sqlTableExists(conn, buf));
 sqlSafef(query, sizeof(query), "select * from %s where geneId='%s'", 
                 buf, gtexGene->geneId);
 struct sqlResult *sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     sd = gtexSampleDataLoad(row);
     if ((hel = hashLookup(tsHash, sd->tissue)) == NULL)
         {
         AllocVar(tsv);
         hashAdd(tsHash, sd->tissue, tsv);
         }
     else
         tsv = (struct tissueSampleVals *)hel->val;
     maxVal = max(maxVal, sd->score);
     val = slDoubleNew(sd->score);
     slAddHead(&tsv->valList, val);
     }
 /*  Fill in tissue descriptions, fill values array and calculate stats for plotting
         Then make a list, suitable for sorting by tissue or score
     NOTE: Most of this not needed for R implementation */
 struct gtexTissue *tis = NULL, *tissues = gtexGetTissues();
 struct tissueSampleVals *tsList = NULL;
 int i;
 if (doLogTransform)
     maxVal = log10(maxVal+1.0);
 for (tis = tissues; tis != NULL; tis = tis->next)
     {
     tsv = hashFindVal(tsHash, tis->name);
     if (tsv == NULL)
         {
         /* no non-zero values for this tissue/gene */
         AllocVar(tsv);
         val = slDoubleNew(0.0);
         slAddHead(&tsv->valList, val);
         }
     tsv->name = tis->name;
     tsv->description = tis->description;
     tsv->color = tis->color;
     int count = tsv->count = slCount(tsv->valList);
     double *vals = AllocArray(tsv->vals, count);
     for (i=0; i<count; i++)
         {
         val = slPopHead(&tsv->valList);
         if (doLogTransform)
             vals[i] = log10(val->val+1.0);
         else
             vals[i] = val->val;
         }
     doubleBoxWhiskerCalc(tsv->count, tsv->vals, 
                                 &tsv->min, &tsv->q1, &tsv->median, &tsv->q3, &tsv->max);
     slAddHead(&tsList, tsv);
     }
 if (maxValRet != NULL)
     *maxValRet = maxVal;
 return tsList;
 }
 
+char *getGeneDescription(struct gtexGeneBed *gtexGene)
+/* Get description for gene. Needed because knownGene table semantics have changed in hg38 */
+{
+char query[256];
+if (sameString(database, "hg38"))
+    {
+    char *geneId = cloneString(gtexGene->geneId);
+    chopSuffix(geneId);
+    sqlSafef(query, sizeof(query), 
+        "select kgXref.description from kgXref, knownCanonical where knownCanonical.protein like '%%%s%%' and knownCanonical.transcript=kgXref.kgID", geneId);
+    }
+else
+    {
+    sqlSafef(query, sizeof(query), 
+                "select kgXref.description from kgXref where geneSymbol='%s'", gtexGene->name);
+    }
+struct sqlConnection *conn = hAllocConn(database);
+char *desc = sqlQuickString(conn, query);
+hFreeConn(&conn);
+return desc;
+}
+
 void doGtexGeneExpr(struct trackDb *tdb, char *item)
 /* Details of GTEx gene expression item */
 {
 struct gtexGeneBed *gtexGene = getGtexGene(item, tdb->table);
 if (gtexGene == NULL)
     errAbort("Can't find gene %s in GTEx gene table %s\n", item, tdb->table);
 
 genericHeader(tdb, item);
 // TODO: link to UCSC gene
-printf("<b>Gene:</b> %s<br>", gtexGene->name);
-char query[256];
-char *transcriptId = cloneString(gtexGene->transcriptId);
-chopSuffix(transcriptId);
-sqlSafef(query, sizeof(query), 
-        "select kgXref.description from kgXref, knownToEnsembl where knownToEnsembl.value like '%%%s%%' and knownToEnsembl.name=kgXref.kgID", transcriptId);
-struct sqlConnection *conn = hAllocConn(database);
-char *desc = sqlQuickString(conn, query);
-hFreeConn(&conn);
+printf("<b>Gene: </b><a target='_blank' href='%s?db=%s&hgg_gene=%s'>%s</a><br>", 
+                        hgGeneName(), database, gtexGene->name, gtexGene->name);
+char *desc = getGeneDescription(gtexGene);
 if (desc != NULL)
     printf("<b>Description:</b> %s<br>\n", desc);
 printf("<b>Ensembl Gene ID:</b> %s<br>\n", gtexGene->geneId);
-printf("<b>Ensembl Transcript ID:</b> %s<br>\n", transcriptId);
+printf("<b>Ensembl Transcript ID:</b> %s<br>\n", gtexGene->transcriptId);
+printf("<b>Genomic Position: </b><a href='%s&db=%s&position=%s%%3A%d-%d'>%s:%d-%d</a><br>", 
+                        hgTracksPathAndSettings(), database, 
+                        gtexGene->chrom, gtexGene->chromStart+1, gtexGene->chromEnd,
+                        gtexGene->chrom, gtexGene->chromStart+1, gtexGene->chromEnd);
 printf("<a target='_blank' href='http://www.gtexportal.org/home/gene/%s'>View at GTEx portal</a><br>\n", gtexGene->geneId);
 puts("<p>");
 
 boolean doLogTransform = cartUsualBooleanClosestToHome(cart, tdb, FALSE, GTEX_LOG_TRANSFORM,
                                                 GTEX_LOG_TRANSFORM_DEFAULT);
 double maxVal = 0.0;
 char *versionSuffix = gtexVersionSuffix(tdb->table);
 struct tissueSampleVals *tsvs = getTissueSampleVals(gtexGene, doLogTransform, 
                                                         versionSuffix, &maxVal);
 char *version = gtexVersion(tdb->table);
 drawGtexRBoxplot(gtexGene, tsvs, doLogTransform, version);
 
 printTrackHtml(tdb);
 }