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/lib/gtexUi.c src/hg/lib/gtexUi.c
index 5e7e6fb..76cfa0d 100644
--- src/hg/lib/gtexUi.c
+++ src/hg/lib/gtexUi.c
@@ -1,610 +1,610 @@
 /* GTEx (Genotype Tissue Expression) track controls */
 
 /* Copyright (C) 2015 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "cheapcgi.h"
 #include "cart.h"
 #include "hui.h"
 #include "trackDb.h"
 #include "jsHelper.h"
 #include "hCommon.h"
 #include "gtexTissue.h"
 #include "gtexInfo.h"
 #include "gtexUi.h"
 
 #define SYSTEM_BRAIN            "Brain"
 #define SYSTEM_REPRODUCTIVE     "Reproductive"
 #define SYSTEM_GASTRO           "Digestive"
 
 #define SYSTEM_ENDOCRINE        "Endocrine"
 #define SYSTEM_CARDIO           "Cardiovascular"
 #define SYSTEM_OTHER            "Other"
 
 
 /* Restrict features on right-click (popup) version */
 static boolean isPopup = FALSE;
 
 /* Path to Body Map-based track configuration */
 static char *_hgGtexTrackSettingsName = "../cgi-bin/hgGtexTrackSettings"; 
 
 boolean gtexIsGeneTrack(char *trackName)
 /* Identify GTEx gene track so custom trackUi CGI can be launched */
 {
 return startsWith(GTEX_GENE_TRACK_BASENAME, trackName);
 }
 
 boolean gtexIsEqtlTrack(char *trackName)
 /* Identify GTEx eQTL track so custom trackUi CGI can be launched */
 {
 return startsWith(GTEX_EQTL_TRACK_BASENAME, trackName);
 }
 
 char *gtexTrackUiName()
 /* Refer to Body Map CGI if suitable */
 {
 // Display body map configuration page if user is on a browser we've tested
 enum browserType bt = cgiBrowser();
 if (bt == btChrome || bt == btFF || bt == btSafari)
     return(_hgGtexTrackSettingsName);
 return hgTrackUiName();
 }
 
 /* Convenience functions for tissue filter controls */
 
 static char *makeTissueColorPatch(struct gtexTissue *tis)
 /* Display a box colored by defined tissue color */
 {
 char buf[256];
 safef(buf, sizeof(buf), "<td bgcolor=#%06X></td>", tis->color);
 return(cloneString(buf));
 }
 
 static char *makeTissueLabel(struct gtexTissue *tis)
 {
 /* Display tissue color and label */
 char buf[256];
 safef(buf, sizeof(buf), "<td bgcolor=%X></td>"
                         "<td>&nbsp;%s</td>", 
                                 tis->color, tis->description);
 return(cloneString(buf));
 }
 
 static char *getSystem(struct gtexTissue *tis)
 /* Rough categorization of tissues for filter presentation */
 {
 if (startsWith("brain", tis->name))
     return(SYSTEM_BRAIN);
 else if (sameString(tis->name, "uterus") || sameString(tis->name, "testis") ||
         sameString(tis->name, "vagina") || sameString(tis->name, "prostate") ||
         sameString(tis->name, "ovary") ||
         sameString(tis->name, "breastMamTissue") || sameString(tis->name, "ectocervix") ||
         sameString(tis->name, "endocervix") || sameString(tis->name, "fallopianTube"))
     return(SYSTEM_REPRODUCTIVE);
 else if (startsWith("esophagus", tis->name) || startsWith("colon", tis->name) ||
         sameString(tis->name, "stomach") || sameString("smallIntestine", tis->name) ||
         sameString("pancreas", tis->name) || sameString("liver", tis->name))
     return(SYSTEM_GASTRO);
 else if (sameString("adrenalGland", tis->name) || sameString("pituitary", tis->name) ||
         sameString("thyroid", tis->name))
     return(SYSTEM_ENDOCRINE);
 else if (startsWith("heart", tis->name) || startsWith("artery", tis->name))
     return(SYSTEM_CARDIO);
 else
     return(SYSTEM_OTHER);
 }
 
 struct tissueSelect
     {
     struct tissueSelect *next;
     char *name;
     char *label;
     boolean checked;
     };
 
 static void makeGroupCheckboxes(char *name, char *title, struct tissueSelect *tisSelects)
 {
 if (title != NULL)
     printf("<tr><td colspan=10><i><b>%s</b></i></td></tr><tr>\n", title);
 int count = slCount(tisSelects);
 struct tissueSelect **tisArray;
 AllocArray(tisArray, count);
 int i=0;
 struct tissueSelect *tsel;
 for (i=0, tsel = tisSelects; tsel != NULL; tsel = tsel->next, i++)
     tisArray[i] = tsel;
 int col=0;
 int row=0;
 int tableColumns=3;
 for (i=0; i<count; i++)
     {
     int j = row + col*(count/tableColumns+1);
     if (j>=count)
         {
         printf("</tr><tr>");
         row++;
         col = 0;
         }
     j = row + col*(count/tableColumns+1);
     if (!isPopup)
         {
         printf("<td><input type=checkbox name=\"%s\" value=\"%s\" %s></td>" "<td>%s</td>\n",
                name, tisArray[j]->name, tisArray[j]->checked ? "checked" : "", tisArray[j]->label);
         }
     col++;
     }
 if ((i % tableColumns) != 0)
     while ((i++ % tableColumns) != 0)
         printf("<td></td>");
 printf("</tr><tr><td></td></tr>\n");
 }
 
 static void initTissueTableStyle()
 /* Reduce font in tissue table so more rows are visible.
  * Specify some colors.*/
 {
 puts("<style>\n"
         "#tissueTable th, #tissueTable td {font-size: 75%; margin: 0px; border: 0px; padding: 0px}\n"
         "#tissueTable input {margin: 0px .5ex; width: 8px; height: 8px}\n"
         "#gtexGeneControls div {margin-bottom: .3em;}\n"
         ".notSortable {font-color: black;}\n"
     "</style>\n");
 }
 
 static void makeTableTissueCheckboxes(char *name, struct gtexTissue *tissues, 
                         struct slName *checked, struct cart *cart, char *track, char *version)
 {
 initTissueTableStyle();
 char *onClick = "";
 // Sortable table can't be displayed when UI is activated from right-click (popup mode)
 if (!isPopup)
     {
     jsIncludeFile("hui.js", NULL);
     onClick = "'tableSortAtButtonPress(this);";
     }
 struct hash *checkHash = hashNew(0);
 struct slName *sel;
 for (sel = checked; sel != NULL; sel = sel->next)
     hashAdd(checkHash, sel->name, sel->name);
 //puts("<table borderwidth=0><tr>");
 puts("\n<table id='tissueTable' cellspacing='1' cellpadding='0' border='0' class='sortable'>");
 
 /* table header */
 char orderVar[256];
 safef(orderVar, sizeof(orderVar), "%s.sortOrder", name);
 char *sortOrder = cartCgiUsualString(cart, orderVar, "tissue=+ samples=+ organ=+ system=+");
 puts("\n<thead class='sortable'>");
 puts("\n<tr class='sortable'>");
 char *sortableClass = isPopup ? "notSortable" : "sortable";
 printf("\n<th>&nbsp;<input type=hidden name='%s' class='sortOrder' value='%s'></th>\n",
         orderVar, sortOrder);
 puts("<th>&nbsp;&nbsp;&nbsp;&nbsp;</th>");
 printf("<th id='tissue' class='%s sort1' %s align='left'>&nbsp;Tissue</th>", 
                sortableClass, onClick);
 printf("<th id='samples' abbr='use' class='%s sort2' %s align='left'>&nbsp;Samples</th>", 
                sortableClass, onClick);
 printf("<th id='organ' class='%s sort3' %s align='left'>&nbsp;Organ</th>", 
                sortableClass, onClick);
 printf("<th id='system' class='%s sort4' %s align='left'>&nbsp;System</th>", 
                sortableClass, onClick);
 puts("\n</tr>");
 puts("</thead>");
 
 /* table body */
 printf("<tbody class='sortable noAltColors initBySortOrder'>");
 struct hash *tscHash = gtexGetTissueSampleCount(version);
 struct gtexTissue *tis;
 boolean isChecked = FALSE;
 for (tis = tissues; tis != NULL; tis = tis->next)
     {
     puts("\n<tr valign='top'>");
 
     // checkbox
     if (hashNumEntries(checkHash) == 0)
         isChecked = TRUE;
     else
         isChecked = (hashLookup(checkHash, tis->name) != NULL);
     printf("<td><input type=checkbox name=\"%s\" value=\"%s\" %s %s></td>",
            name, tis->name, isChecked ? "checked" : "", isPopup ? "disabled" : "");
     // color patch
     printf("\n%s", makeTissueColorPatch(tis));
     // tissue name
     printf("\n<td>&nbsp;%s</td>", tis->description);
     // sample count
     int samples = hashIntValDefault(tscHash, tis->name, 0);
     printf("\n<td abbr='%05d' style='text-align: right; padding-right: 8px'>&nbsp;%d</td>", samples, samples);
     // organ
     printf("\n<td style='padding-right: 8px'>&nbsp;%s</td>", tis->organ);
     // system
     printf("\n<td>&nbsp;%s</td>", getSystem(tis));
 
     puts("\n</tr>");
     }
 puts("</tbody>");
 puts("</table>");
 char buf[512];
 safef(buf, sizeof(buf), "%s%s", cgiMultListShadowPrefix(), name);
 cgiMakeHiddenVar(buf, "0");
 }
 
 static void makeGroupedTissueCheckboxes(char *name, struct gtexTissue *tissues, struct slName *checked)
 {
 struct hash *checkHash = hashNew(0);
 struct slName *sel;
 for (sel = checked; sel != NULL; sel = sel->next)
     hashAdd(checkHash, sel->name, sel->name);
 puts("<table borderwidth=0><tr>");
 struct tissueSelect *brainTissues = NULL;
 struct tissueSelect *digestiveTissues = NULL;
 struct tissueSelect *reproductiveTissues = NULL;
 struct tissueSelect *otherTissues = NULL;
 struct tissueSelect *tsel;
 struct gtexTissue *tis;
 for (tis = tissues; tis != NULL; tis = tis->next)
     {
     AllocVar(tsel);
     tsel->name = tis->name;
     tsel->label = makeTissueLabel(tis);
     if (hashNumEntries(checkHash) == 0)
         tsel->checked = TRUE;
     else
         tsel->checked = (hashLookup(checkHash, tis->name) != NULL);
     char *system = getSystem(tis);
     if (sameString(SYSTEM_BRAIN, system))
         slAddHead(&brainTissues, tsel);
     else if (sameString(SYSTEM_REPRODUCTIVE, system))
         slAddHead(&reproductiveTissues, tsel);
     else if (sameString(SYSTEM_GASTRO, system))
         slAddHead(&digestiveTissues, tsel);
     else
         slAddHead(&otherTissues, tsel);
     }
 slReverse(&brainTissues);
 slReverse(&digestiveTissues);
 slReverse(&reproductiveTissues);
 slReverse(&otherTissues);
 makeGroupCheckboxes(name, "Brain", brainTissues);
 makeGroupCheckboxes(name, "Gastrointestinal", digestiveTissues);
 makeGroupCheckboxes(name, "Reproductive", reproductiveTissues);
 makeGroupCheckboxes(name, "Other", otherTissues);
 puts("</tr></table>");
 char buf[512];
 safef(buf, sizeof(buf), "%s%s", cgiMultListShadowPrefix(), name);
 cgiMakeHiddenVar(buf, "0");
 }
 
 static void makeAllTissueCheckboxes(char *name, struct gtexTissue *tissues, 
                                         struct slName *checked)
 {
 struct hash *checkHash = hashNew(0);
 struct slName *sel;
 for (sel = checked; sel != NULL; sel = sel->next)
     hashAdd(checkHash, sel->name, sel->name);
 puts("<table borderwidth=0><tr>");
 struct tissueSelect *tsel;
 struct gtexTissue *tis;
 struct tissueSelect *allTissues = NULL;
 for (tis = tissues; tis != NULL; tis = tis->next)
     {
     AllocVar(tsel);
     tsel->name = tis->name;
     tsel->label = makeTissueLabel(tis);
     if (hashNumEntries(checkHash) == 0)
         tsel->checked = TRUE;
     else
         tsel->checked = (hashLookup(checkHash, tis->name) != NULL);
     slAddHead(&allTissues, tsel);
     }
 slReverse(&allTissues);
 makeGroupCheckboxes(name, NULL, allTissues);
 puts("</tr></table>");
 char buf[512];
 safef(buf, sizeof(buf), "%s%s", cgiMultListShadowPrefix(), name);
 cgiMakeHiddenVar(buf, "0");
 }
 
 void gtexPortalLink(char *geneId)
 /* print URL to GTEX portal gene expression page using Ensembl Gene Id*/
 {
 printf("<a target='_blank' href='http://www.gtexportal.org/home/gene/%s'>"
         "View at GTEx portal</a>\n", geneId);
 }
 
 /* Convenience functions shared by hgTrackUi and hgGtexTrackSettings. hgTrackUi is for now still
  * available from right-click */
 
 void gtexGeneUiGeneLabel(struct cart *cart, char *track, struct trackDb *tdb)
 /* Radio buttons to select format of gene label */
 {
 char cartVar[1024];
 char *geneLabel = cartUsualStringClosestToHome(cart, tdb, isNameAtParentLevel(tdb, track), 
                         GTEX_LABEL, GTEX_LABEL_DEFAULT);
 printf("<b>Label:</b> ");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_LABEL);
 cgiMakeRadioButton(cartVar, GTEX_LABEL_SYMBOL , sameString(GTEX_LABEL_SYMBOL, geneLabel));
 printf("&nbsp;%s&nbsp;", "gene symbol");
 cgiMakeRadioButton(cartVar, GTEX_LABEL_ACCESSION, sameString(GTEX_LABEL_ACCESSION, geneLabel));
 printf("&nbsp;%s&nbsp;", "accession");
 cgiMakeRadioButton(cartVar, GTEX_LABEL_BOTH, sameString(GTEX_LABEL_BOTH, geneLabel));
 printf("&nbsp;%s&nbsp;", "both");
 }
 
 void gtexGeneUiCodingFilter(struct cart *cart, char *track, struct trackDb *tdb)
 /* Checkbox to restrict display to protein coding genes */
 {
 char cartVar[1024];
 puts("<b>Limit to protein coding genes:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_CODING_GENE_FILTER);
 boolean isCodingOnly = cartCgiUsualBoolean(cart, cartVar, GTEX_CODING_GENE_FILTER_DEFAULT);
 cgiMakeCheckBox(cartVar, isCodingOnly);
 }
 
 void gtexGeneUiGeneModel(struct cart *cart, char *track, struct trackDb *tdb)
 /* Checkbox to enable display of GTEx gene model */
 {
 char cartVar[1024];
 puts("<b>Show GTEx gene model:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_SHOW_EXONS);
 boolean showExons = cartCgiUsualBoolean(cart, cartVar, GTEX_SHOW_EXONS_DEFAULT);
 cgiMakeCheckBox(cartVar, showExons);
 }
 
 void gtexGeneUiLogTransform(struct cart *cart, char *track, struct trackDb *tdb)
 /* Checkbox to select log-transformed RPKM values */
 {
 char cartVar[1024];
 puts("<b>Log10 transform:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_LOG_TRANSFORM);
 boolean isLogTransform = cartCgiUsualBoolean(cart, cartVar, GTEX_LOG_TRANSFORM_DEFAULT);
 cgiMakeCheckBoxWithId(cartVar, isLogTransform, cartVar);
 jsOnEventByIdF("change", cartVar, "gtexTransformChanged('%s');", track);
 }
 
 void gtexGeneUiViewLimits(struct cart *cart, char *track, struct trackDb *tdb)
 /* Set viewing limits if log transform not checked */
 {
 char cartVar[1024];
 char buf[512];
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_LOG_TRANSFORM);
 boolean isLogTransform = cartCgiUsualBoolean(cart, cartVar, GTEX_LOG_TRANSFORM_DEFAULT);
 safef(buf, sizeof buf, "%sViewLimitsMaxLabel %s", track, isLogTransform ? "disabled" : "");
 printf("<span class='%s'><b>View limits maximum:</b></span>\n", buf);
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_MAX_VIEW_LIMIT);
 int viewMax = cartCgiUsualInt(cart, cartVar, GTEX_MAX_VIEW_LIMIT_DEFAULT);
 cgiMakeIntVarWithExtra(cartVar, viewMax, 4, isLogTransform ? "disabled" : "");
 char *version = gtexVersion(tdb->table);
 printf("<span class='%s'>  RPKM (range 0-%d)</span>\n", buf, round(gtexMaxMedianScore(version)));
 }
 
 void gtexGeneUi(struct cart *cart, struct trackDb *tdb, char *track, char *title, boolean boxed)
 /* GTEx (Genotype Tissue Expression) per gene data */
 {
 if (cartVarExists(cart, "ajax"))
     isPopup = TRUE;
 
 boxed = cfgBeginBoxAndTitle(tdb, boxed, title);
 printf("\n<table id=gtexGeneControls style='font-size:%d%%' %s>\n<tr><td>", 
         isPopup ? 75 : 100, boxed ?" width='100%'":"");
 
 char cartVar[1024];
 
 /* Gene labels  */
 puts("<div>");
 gtexGeneUiGeneLabel(cart, track, tdb);
 puts("</div>\n");
 
 /* Filter on coding genes */
 puts("<div>");
 gtexGeneUiCodingFilter(cart, track, tdb);
 
 /* Show exons in gene model */
 puts("&nbsp;&nbsp;");
 gtexGeneUiGeneModel(cart, track, tdb);
 puts("</div>");
 
 /* Data transform. When selected, the next control (view limits max) is disabled */
 
 puts("<div>");
 gtexGeneUiLogTransform(cart, track, tdb);
 
 /* Viewing limits max.  This control is disabled if log transform is selected */
 // construct class so JS can toggle
 puts("&nbsp;&nbsp;");
 gtexGeneUiViewLimits(cart, track, tdb);
 puts("</div>");
 
 #ifdef COMPARISON
 /* Sample selection */
 printf("<div><b>Samples:</b>&nbsp;");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_SAMPLES);
 char *selected = cartCgiUsualString(cart, cartVar, GTEX_SAMPLES_DEFAULT); 
 boolean isAllSamples = sameString(selected, GTEX_SAMPLES_ALL);
 safef(buf, sizeof buf, "gtexSamplesChanged(\"%s\");", track);
 char *command = buf;
 cgiMakeOnEventRadioButtonWithClass(cartVar, GTEX_SAMPLES_ALL, isAllSamples, NULL, "change", command);
 printf("All\n");
 cgiMakeOnEventRadioButtonWithClass(cartVar, GTEX_SAMPLES_COMPARE_SEX, !isAllSamples, NULL, "change", command);
 printf("Compare by gender\n");
 printf("</div>");
 
 /* Comparison type. Disabled if All samples selected. */
 safef(buf, sizeof buf, "%sComparisonLabel %s", track, isAllSamples ? "disabled" : "");
 printf("<div><b><span class='%s'>Comparison display:</b></span>", buf);
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_COMPARISON_DISPLAY);
 selected = cartCgiUsualString(cart, cartVar, GTEX_COMPARISON_DEFAULT); 
 boolean isMirror = sameString(selected, GTEX_COMPARISON_MIRROR);
 
 cgiMakeRadioButton(cartVar, GTEX_COMPARISON_DIFF, !isMirror);
 printf("<span class='%s'>Difference graph</span>", buf);
 cgiMakeRadioButton(cartVar, GTEX_COMPARISON_MIRROR, isMirror);
 printf("<span class='%s'>Two graphs</span>\n", buf);
 printf("</div>");
 #endif
 
 /* Color scheme */
 // We don't need the rainbow color scheme, but may want another (e.g. different
 // colors for brain tissues), so leaving code in for now.
 #ifdef COLOR_SCHEME
 printf("<p><b>Tissue colors:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_COLORS);
 selected = cartCgiUsualString(cart, cartVar, GTEX_COLORS_DEFAULT); 
 boolean isGtexColors = sameString(selected, GTEX_COLORS_GTEX);
 cgiMakeRadioButton(cartVar, GTEX_COLORS_GTEX, isGtexColors);
 printf("GTEx\n");
 cgiMakeRadioButton(cartVar, GTEX_COLORS_RAINBOW, !isGtexColors);
 printf("Rainbow\n");
 printf("</p>");
 #endif
 
 /* Tissue filter */
 printf("<br>");
 printf("<div><b>Tissues:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_TISSUE_SELECT);
 if (isPopup)
     {
     printf("<a href='%s?g=%s'><button type='button'>Change</button><a>", 
                 hTrackUiForTrack(track), track);
     }
 else
     {
     jsMakeCheckboxGroupSetClearButton(cartVar, TRUE);
     puts("&nbsp;");
     jsMakeCheckboxGroupSetClearButton(cartVar, FALSE);
     }
 printf("</div>");
 char *version = gtexVersion(tdb->table);
 struct gtexTissue *tissues = gtexGetTissues(version);
 struct slName *selectedValues = NULL;
 if (cartListVarExistsAnyLevel(cart, tdb, FALSE, GTEX_TISSUE_SELECT))
     selectedValues = cartOptionalSlNameListClosestToHome(cart, tdb, FALSE, GTEX_TISSUE_SELECT);
 char *selectType = cgiUsualString("tis", "table");
 if (sameString(selectType, "group"))
     makeGroupedTissueCheckboxes(cartVar, tissues, selectedValues);
 else if (sameString(selectType, "table"))
     makeTableTissueCheckboxes(cartVar, tissues, selectedValues, cart, track, version);
 else
     makeAllTissueCheckboxes(cartVar, tissues, selectedValues);
 
 puts("\n</table>\n");
 cfgEndBox(boxed);
 }
 
 /* GTEx eQTL track configuration */
 
 void gtexEqtlUiGene(struct cart *cart, char *track, struct trackDb *tdb)
 /* Limit to selected gene */
 // TODO: autocomplete
 {
 char cartVar[1024];
 puts("<b>Limit to eQTLs for gene: </b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_EQTL_GENE);
 char *gene = cartCgiUsualString(cart, cartVar, "");
 cgiMakeTextVar(cartVar, gene, 20);
 }
 
 #define GTEX_EQTL_EFFECT_MAX       15362.9
 // Maximum V6p effect size for CAVIAR 95% eQTLs
 // TODO: add to gtexInfo table
 
 void gtexEqtlUiEffectSize(struct cart *cart, char *track, struct trackDb *tdb)
 /* Limit to items with absolute value of effect size >= threshold.  Use largest
  * effect size in tissue list */
 {
 char cartVar[1024];
 puts("<b>Effect size minimum: </b>+-\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_EQTL_EFFECT);
 double effectMin = cartCgiUsualDouble(cart, cartVar, 0.0);
 cgiMakeDoubleVar(cartVar, effectMin, 7);
 printf(" FPKM (range 0-%0.1f)\n", GTEX_EQTL_EFFECT_MAX);
 }
 
 void gtexEqtlUiProbability(struct cart *cart, char *track, struct trackDb *tdb)
 /* Limit to items with specified probability.  Use largest probability in tissue list,
  * which is score/1000, so use that */
 {
 char cartVar[1024];
 puts("<b>Probability minimum:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_EQTL_PROBABILITY);
 double probMin = cartCgiUsualDouble(cart, cartVar, GTEX_EQTL_PROBABILITY_DEFAULT);
 cgiMakeDoubleVar(cartVar, probMin, 3);
 printf(" (range 0-1.0)\n");
 }
 
 void gtexEqtlUiTissueColor(struct cart *cart, char *track, struct trackDb *tdb)
 /* Control visibility color patch to indicate tissue (can be distracting in large regions) */
 {
 char cartVar[1024];
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_EQTL_TISSUE_COLOR);
 boolean showTissueColor = cartCgiUsualBoolean(cart, cartVar, GTEX_EQTL_TISSUE_COLOR_DEFAULT);
 cgiMakeCheckBox(cartVar, showTissueColor);
-puts("<b>Display tissue color (if single tissue eQTL)</b>\n");
+puts("<b>Display tissue color (single tissue eQTL)</b>\n");
 }
 
 void gtexEqtlClusterUi(struct cart *cart, struct trackDb *tdb, char *track, char *title, 
                         boolean boxed)
 /* GTEx (Genotype Tissue Expression) eQTL clusters. Use this on right-click,
  * (when hgGtexTrackSettings can't be) */
 {
 if (cartVarExists(cart, "ajax"))
     isPopup = TRUE;
 
 boxed = cfgBeginBoxAndTitle(tdb, boxed, title);
 printf("\n<table id=gtexEqtlClusterControls style='font-size:%d%%' %s>\n<tr><td>", 
         isPopup ? 75 : 100, boxed ?" width='100%'":"");
 
 char cartVar[1024];
 
 /* Gene filter  */
 puts("<div>");
 gtexEqtlUiGene(cart, track, tdb);
 puts("</div>\n");
 
 /* Absolute value of effect size */
 puts("<div>");
 gtexEqtlUiEffectSize(cart, track, tdb);
 puts("</div>\n");
 
 /* Probability eQTL is in CAVIAR 95% causal set */
 puts("<div>");
 puts("&nbsp;&nbsp;");
 gtexEqtlUiProbability(cart, track, tdb);
 puts("&nbsp;&nbsp;&nbsp;&nbsp;");
 
 /* Display or hide tissue color patch for single-tissue eQTL's */
 gtexEqtlUiTissueColor(cart, track, tdb);
 puts("</div>\n");
 
 /* Tissue filter */
 printf("<br>");
 printf("<div><b>Tissues:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_TISSUE_SELECT);
 if (isPopup)
     {
     printf("<a href='%s?g=%s'><button type='button'>Change</button><a>", 
                 hTrackUiForTrack(track), track);
     }
 else
     {
     jsMakeCheckboxGroupSetClearButton(cartVar, TRUE);
     puts("&nbsp;");
     jsMakeCheckboxGroupSetClearButton(cartVar, FALSE);
     }
 printf("</div>");
 if (!isPopup)
     {
     char *version = gtexVersion(tdb->table);
     struct gtexTissue *tissues = gtexGetTissues(version);
     struct slName *selectedValues = NULL;
     if (cartListVarExistsAnyLevel(cart, tdb, FALSE, GTEX_TISSUE_SELECT))
         selectedValues = cartOptionalSlNameListClosestToHome(cart, tdb, FALSE, GTEX_TISSUE_SELECT);
     char *selectType = cgiUsualString("tis", "table");
     if (sameString(selectType, "group"))
         makeGroupedTissueCheckboxes(cartVar, tissues, selectedValues);
     else if (sameString(selectType, "table"))
         makeTableTissueCheckboxes(cartVar, tissues, selectedValues, cart, track, version);
     else
         makeAllTissueCheckboxes(cartVar, tissues, selectedValues);
     }
 puts("\n</table>\n");
 cfgEndBox(boxed);
 }