bf18fbc459d663c8559dcfec513675ec165bcbc3 kate Mon May 1 12:23:14 2017 -0700 Fix problem with GTEx viewLimits input box noted by QA during review of this track (similar controls). Id name was changed for barchart in JS -- needed update in GTEx. refs #18736 diff --git src/hg/lib/gtexUi.c src/hg/lib/gtexUi.c index b3fdf83..986c326 100644 --- src/hg/lib/gtexUi.c +++ src/hg/lib/gtexUi.c @@ -1,485 +1,485 @@ /* 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); } char *gtexGeneTrackUiName() /* 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> %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> <input type=hidden name='%s' class='sortOrder' value='%s'></th>\n", orderVar, sortOrder); puts("<th> </th>"); printf("<th id='tissue' class='%s sort1' %s align='left'> Tissue</th>", sortableClass, onClick); printf("<th id='samples' abbr='use' class='%s sort2' %s align='left'> Samples</th>", sortableClass, onClick); printf("<th id='organ' class='%s sort3' %s align='left'> Organ</th>", sortableClass, onClick); printf("<th id='system' class='%s sort4' %s align='left'> 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> %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'> %d</td>", samples, samples); // organ printf("\n<td style='padding-right: 8px'> %s</td>", tis->organ); // system printf("\n<td> %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(" %s ", "gene symbol"); cgiMakeRadioButton(cartVar, GTEX_LABEL_ACCESSION, sameString(GTEX_LABEL_ACCESSION, geneLabel)); printf(" %s ", "accession"); cgiMakeRadioButton(cartVar, GTEX_LABEL_BOTH, sameString(GTEX_LABEL_BOTH, geneLabel)); printf(" %s ", "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_LIMIT); -int viewMax = cartCgiUsualInt(cart, cartVar, GTEX_MAX_LIMIT_DEFAULT); +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(" "); 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(" "); gtexGeneUiViewLimits(cart, track, tdb); puts("</div>"); #ifdef COMPARISON /* Sample selection */ printf("<div><b>Samples:</b> "); 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(" "); 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); }