4000e8aea0030674a50b1b4a1cb3bb5dafcbeea2 kate Tue Jan 26 16:11:25 2016 -0800 Remove rainbow color scheme option. It would require noticeable work to implement fully (e.g. for tissue filter on trackUi and boxplot on hgc) and doesn't have an immediate use case. Leaving in the code as I can see there could be a need for alternate color schemes (e.g. distinct colors for brain). refs #15645 diff --git src/hg/lib/gtexUi.c src/hg/lib/gtexUi.c index 93f954d..34d7d52 100644 --- src/hg/lib/gtexUi.c +++ src/hg/lib/gtexUi.c @@ -1,344 +1,346 @@ /* 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 "gtexTissue.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" static void initTissueTableStyle() { puts("<style>\n" "#tissueTable th, #tissueTable td {\n" "font-size: 75%;\n" "}\n" "</style>\n"); } static char *makeTissueColorPatch(struct gtexTissue *tis) { char buf[256]; safef(buf, sizeof(buf), "<td style='width:10px;' bgcolor=%X></td>", tis->color); return(cloneString(buf)); } static char *makeTissueLabel(struct gtexTissue *tis) { char buf[256]; safef(buf, sizeof(buf), "<td style='width:10px;' bgcolor=%X></td>" "<td> %s</td>", tis->color, tis->description); return(cloneString(buf)); } static char *getSystem(struct gtexTissue *tis) { 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); 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 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"); } static void makeTableTissueCheckboxes(char *name, struct gtexTissue *tissues, struct slName *checked, struct cart *cart) { initTissueTableStyle(); char *onClick = ""; // Sortable table can't be displayed when UI is activated from right-click (popup mode) if (!cartVarExists(cart, "ajax")) { 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='2' 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'>"); printf("\n<th> <input type=hidden name='%s' class='sortOrder' value='%s'></th>\n", orderVar, sortOrder); puts("<th> </th>"); printf("<th id='tissue' class='sortable sort1' %s " "align='left' title='Sort on tissue'> Tissue</th>", onClick); printf("<th id='samples' abbr='use' class='sortable sort2' %s " "align='left' title='Sort on sample count'> Samples</th>", onClick); printf("<th id='organ' class='sortable sort3' %s " "align='left' title='Sort on organ'> Organ</th>", onClick); printf("<th id='system' class='sortable sort4' %s " "align='left' title='Sort on system'> System</th>", onClick); puts("\n</tr>"); puts("</thead>"); /* table body */ printf("<tbody class='sortable noAltColors initBySortOrder'>"); struct hash *tscHash = gtexGetTissueSampleCount(); 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></td>", name, tis->name, isChecked ? "checked" : ""); // 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: 10px'> %d</td>", samples, samples); // organ printf("\n<td style='padding-right: 10px'> %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"); } void gtexGeneUi(struct cart *cart, struct trackDb *tdb, char *track, char *title, boolean boxed) /* GTEx (Genotype Tissue Expression) per gene data */ { boxed = cfgBeginBoxAndTitle(tdb, boxed, title); printf("<table%s><tr><td>",boxed?" width='100%'":""); char cartVar[1024]; char *selected = NULL; /* Sample selection */ printf("<b>Samples:</b> "); safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_SAMPLES); selected = cartCgiUsualString(cart, cartVar, GTEX_SAMPLES_DEFAULT); boolean isAllSamples = sameString(selected, GTEX_SAMPLES_ALL); cgiMakeRadioButton(cartVar, GTEX_SAMPLES_ALL, isAllSamples); printf("All\n"); cgiMakeRadioButton(cartVar, GTEX_SAMPLES_COMPARE_SEX, !isAllSamples); printf("Compare by gender\n"); printf("</p>"); /* Comparison type */ printf("<p><b>Comparison display:</b>\n"); 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("Difference graph\n"); cgiMakeRadioButton(cartVar, GTEX_COMPARISON_MIRROR, isMirror); printf("Two graphs\n"); printf("</p>"); /* Data transform */ printf("<p><b>Log10 transform:</b>\n"); safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_LOG_TRANSFORM); boolean isLogTransform = cartCgiUsualBoolean(cart, cartVar, GTEX_LOG_TRANSFORM_DEFAULT); cgiMakeCheckBox(cartVar, isLogTransform); /* Viewing limits max */ printf(" <b>View limits maximum:</b>\n"); safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_MAX_LIMIT); // TODO: set max and initial limits from gtexInfo table int viewMax = cartCgiUsualInt(cart, cartVar, GTEX_MAX_LIMIT_DEFAULT); cgiMakeIntVar(cartVar, viewMax, 4); printf(" RPKM (range 10-180000)<br>\n"); printf("</p>"); /* Color scheme */ // Not sure if we still want this option +#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("<p><b>Tissue selection:</b>\n"); safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_TISSUE_SELECT); jsMakeCheckboxGroupSetClearButton(cartVar, TRUE); puts(" "); jsMakeCheckboxGroupSetClearButton(cartVar, FALSE); struct gtexTissue *tissues = gtexGetTissues(); 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); else makeAllTissueCheckboxes(cartVar, tissues, selectedValues); cfgEndBox(boxed); }