529fd44f904b874ea9b1a5bc80fe5dec3a5970a8 kate Wed Mar 23 15:16:33 2016 -0700 Add checkbox to limit to protein coding genes (I keep wanting this option during testing.). refs #15645 diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c index 56c5e3a..caa71a4 100644 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@ -6,30 +6,31 @@ #include "common.h" #include "hgTracks.h" #include "hvGfx.h" #include "rainbow.h" #include "gtexInfo.h" #include "gtexGeneBed.h" #include "gtexTissue.h" #include "gtexTissueData.h" #include "gtexUi.h" #include "spaceSaver.h" struct gtexGeneExtras /* Track info */ { char *version; /* Suffix to table name, e.g. 'V6' */ + boolean codingOnly; /* User filter to limit display to coding genes */ double maxMedian; /* Maximum median rpkm for all tissues */ boolean isComparison; /* Comparison of two sample sets (e.g. male/female). */ boolean isDifference; /* True if comparison is shown as a single difference graph. False if displayed as two graphs, one oriented downward */ char *graphType; /* Additional info about graph (e.g. type of comparison graph */ struct rgbColor *colors; /* Color palette for tissues */ boolean doLogTransform; /* Log10(x+1) */ struct gtexTissue *tissues; /* Cache tissue names, descriptions */ struct hash *tissueFilter; /* For filter. NULL out excluded tissues */ }; struct gtexGeneInfo /* GTEx gene model, names, and expression medians */ { struct gtexGeneInfo *next; /* Next in singly linked list */ @@ -83,73 +84,73 @@ char *geneClass = gtexGeneClass(geneBed); if (geneClass == NULL) return statusColors.unknown; if (sameString(geneClass, "coding")) return statusColors.coding; if (sameString(geneClass, "nonCoding")) return statusColors.nonCoding; if (sameString(geneClass, "pseudo")) return statusColors.pseudo; return statusColors.unknown; } /***********************************************/ /* Cache tissue info */ -struct gtexTissue *getTissues() +struct gtexTissue *getTissues(char *version) /* Get and cache tissue metadata from database */ { static struct gtexTissue *gtexTissues = NULL; if (!gtexTissues) - gtexTissues = gtexGetTissues(); + gtexTissues = gtexGetTissues(version); return gtexTissues; } -int getTissueCount() +int getTissueCount(char *version) /* Get and cache the number of tissues in GTEx tissue table */ { static int tissueCount = 0; if (!tissueCount) - tissueCount = slCount(getTissues()); + tissueCount = slCount(getTissues(version)); return tissueCount; } -char *getTissueName(int id) +char *getTissueName(int id, char *version) /* Get tissue name from id, cacheing */ { static char **tissueNames = NULL; struct gtexTissue *tissue; -int count = getTissueCount(); +int count = getTissueCount(version); if (!tissueNames) { - struct gtexTissue *tissues = getTissues(); + struct gtexTissue *tissues = getTissues(version); AllocArray(tissueNames, count); for (tissue = tissues; tissue != NULL; tissue = tissue->next) tissueNames[tissue->id] = cloneString(tissue->name); } if (id >= count) errAbort("GTEx tissue table problem: can't find id %d\n", id); return tissueNames[id]; } -struct rgbColor *getGtexTissueColors() +struct rgbColor *getGtexTissueColors(char *version) /* Get RGB colors from tissue table */ { -struct gtexTissue *tissues = getTissues(); +struct gtexTissue *tissues = getTissues(version); struct gtexTissue *tissue = NULL; int count = slCount(tissues); struct rgbColor *colors; AllocArray(colors, count); int i = 0; for (tissue = tissues; tissue != NULL; tissue = tissue->next) { // TODO: reconcile colors[i] = (struct rgbColor){.r=COLOR_32_BLUE(tissue->color), .g=COLOR_32_GREEN(tissue->color), .b=COLOR_32_RED(tissue->color)}; //colors[i] = mgColorIxToRgb(NULL, tissue->color); i++; } return colors; } @@ -207,34 +208,34 @@ hashAdd(scoreHash, tissue, score); } sqlFreeResult(&sr); hFreeConn(&conn); // get tissue medians for each sample subset double *medians1; double *medians2; AllocArray(medians1, expCount); AllocArray(medians2, expCount); int i; for (i=0; i<geneBed->expCount; i++) { //medians1[i] = -1, medians2[i] = -1; // mark missing tissues ? struct slDouble *scores; - scores = hashFindVal(scoreHash1, getTissueName(i)); + scores = hashFindVal(scoreHash1, getTissueName(i, extras->version)); if (scores) medians1[i] = slDoubleMedian(scores); - scores = hashFindVal(scoreHash2, getTissueName(i)); + scores = hashFindVal(scoreHash2, getTissueName(i, extras->version)); if (scores) medians2[i] = slDoubleMedian(scores); } if (extras->isDifference) { for (i=0; i<geneBed->expCount; i++) { if (medians1[i] >= medians2[i]) { medians1[i] -= medians2[i]; medians2[i] = 0; } else { medians2[i] -= medians1[i]; @@ -242,31 +243,31 @@ } } } geneInfo->medians1 = medians1; geneInfo->medians2 = medians2; } } static int gtexGeneItemHeight(struct track *tg, void *item); static void filterTissues(struct track *tg) /* Check cart for tissue selection. NULL out unselected tissues in tissue list */ { struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; struct gtexTissue *tis = NULL; -extras->tissues = getTissues(); +extras->tissues = getTissues(extras->version); extras->tissueFilter = hashNew(0); if (cartListVarExistsAnyLevel(cart, tg->tdb, FALSE, GTEX_TISSUE_SELECT)) { struct slName *selectedValues = cartOptionalSlNameListClosestToHome(cart, tg->tdb, FALSE, GTEX_TISSUE_SELECT); if (selectedValues != NULL) { struct slName *name; for (name = selectedValues; name != NULL; name = name->next) hashAdd(extras->tissueFilter, name->name, name->name); return; } } /* no filter */ for (tis = extras->tissues; tis != NULL; tis = tis->next) @@ -296,67 +297,74 @@ tg->extraUiData = extras; /* Get version info from track table name */ extras->version = gtexVersionSuffix(tg->table); extras->doLogTransform = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, GTEX_LOG_TRANSFORM, GTEX_LOG_TRANSFORM_DEFAULT); char *samples = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_SAMPLES, GTEX_SAMPLES_DEFAULT); extras->graphType = cloneString(samples); if (sameString(samples, GTEX_SAMPLES_COMPARE_SEX)) extras->isComparison = TRUE; char *comparison = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COMPARISON_DISPLAY, GTEX_COMPARISON_DEFAULT); extras->isDifference = sameString(comparison, GTEX_COMPARISON_DIFF) ? TRUE : FALSE; extras->maxMedian = gtexMaxMedianScore(extras->version); - +extras->codingOnly = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, GTEX_CODING_GENE_FILTER, + GTEX_CODING_GENE_FILTER_DEFAULT); /* Get geneModels in range */ char buf[256]; char *modelTable = "gtexGeneModel"; safef(buf, sizeof(buf), "%s%s", modelTable, extras->version ? extras->version: ""); struct hash *modelHash = loadGeneModels(buf); /* Get geneBeds (names and all-sample tissue median scores) in range */ bedLoadItem(tg, tg->table, (ItemLoader)gtexGeneBedLoad); /* Create geneInfo items with BED and geneModels */ struct gtexGeneInfo *geneInfo = NULL, *list = NULL; struct gtexGeneBed *geneBed = (struct gtexGeneBed *)tg->items; /* Load tissue colors: GTEx or rainbow */ #ifdef COLOR_SCHEME char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS, GTEX_COLORS_DEFAULT); #else char *colorScheme = GTEX_COLORS_DEFAULT; #endif if (sameString(colorScheme, GTEX_COLORS_GTEX)) { - extras->colors = getGtexTissueColors(); + extras->colors = getGtexTissueColors(extras->version); } else { if (geneBed) { int expCount = geneBed->expCount; extras->colors = getRainbow(&saturatedRainbowAtPos, expCount); } } filterTissues(tg); while (geneBed != NULL) { + if (extras->codingOnly && !gtexGeneIsCoding(geneBed)) + { + // apologies for messy short-circuit + geneBed = geneBed->next; + continue; + } AllocVar(geneInfo); geneInfo->geneBed = geneBed; geneInfo->geneModel = hashFindVal(modelHash, geneBed->geneId); // sometimes this is missing, hash returns NULL. do we check? // NOTE: Consider loading all gene descriptions to save queries char query[256]; sqlSafef(query, sizeof(query), "select kgXref.description from kgXref where geneSymbol='%s'", geneBed->name); struct sqlConnection *conn = hAllocConn(database); char *desc = sqlQuickString(conn, query); hFreeConn(&conn); if (desc) { // hg38 known genes has extra detail about source; strip it char *fromDetail = strstrNoCase(desc, "(from"); if (fromDetail) @@ -510,31 +518,31 @@ hvGfxBox(hvg, x, y, graphWidth, 1, lightGray); } static int gtexGeneGraphHeight(struct track *tg, struct gtexGeneInfo *geneInfo, boolean doTop) /* Determine height in pixels of graph. This will be the box for tissue with highest expression If doTop is false, compute height of bottom graph of comparison */ { struct gtexGeneBed *geneBed = geneInfo->geneBed; struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; int i; double maxExp = 0.0; int expCount = geneBed->expCount; double expScore; for (i=0; i<expCount; i++) { - if (!filterTissue(tg, getTissueName(i))) + if (!filterTissue(tg, getTissueName(i, extras->version))) continue; if (doTop) expScore = (geneInfo->medians1 ? geneInfo->medians1[i] : geneBed->expScores[i]); else expScore = geneInfo->medians2[i]; maxExp = max(maxExp, expScore); } double viewMax = (double)cartUsualIntClosestToHome(cart, tg->tdb, FALSE, GTEX_MAX_LIMIT, GTEX_MAX_LIMIT_DEFAULT); double maxMedian = ((struct gtexGeneExtras *)tg->extraUiData)->maxMedian; return valToClippedHeight(maxExp, maxMedian, viewMax, gtexMaxGraphHeight(), extras->doLogTransform); } static void gtexGeneDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis) @@ -750,31 +758,31 @@ { genericMapItem(tg, hvg, item, itemName, itemName, start, end, x, y, width, height); return; } struct gtexGeneInfo *geneInfo = item; struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; struct gtexGeneBed *geneBed = geneInfo->geneBed; int topGraphHeight = gtexGeneGraphHeight(tg, geneInfo, TRUE); topGraphHeight = max(topGraphHeight, tl.fontHeight); // label int yZero = topGraphHeight + y - 1; // yZero is bottom of graph //int yGene = yZero + gtexGeneMargin() - 1; int x1 = insideX; // add maps to tissue bars in expresion graph -struct gtexTissue *tissues = getTissues(); +struct gtexTissue *tissues = getTissues(extras->version); struct gtexTissue *tissue = NULL; int barWidth = gtexBarWidth(); int padding = gtexGraphPadding(); double maxMedian = ((struct gtexGeneExtras *)tg->extraUiData)->maxMedian; int graphX = gtexGraphX(geneBed); if (graphX < 0) return; // x1 is at left of graph x1 = insideX + graphX; if (geneInfo->medians2) { // skip over labels in comparison graphs