0842d0243de1cbe7e9d579e3792b92e3b6a552ab kate Mon Aug 3 23:16:48 2015 -0700 Fix a few bugs - connection handling, bin field in genePred, more color handling - introduced while messing with schemas (to extend features and improve perf). refs #15645 diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c index c266343..a0c8552 100644 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@ -133,48 +133,43 @@ warn("scaled=%f\n", scaled); int y = scaled * (maxHeight); //uglyf("%.2f -> %.2f height %d", val, scaled, (int)scaled * (maxHeight-1)); return (maxHeight-1) - y; } struct gtexGeneExtras { double maxMedian; char *graphType; boolean isComparison; }; /* Cache tissue metadata */ -struct gtexTissue *getGtexTissues() +struct gtexTissue *getTissues() /* Get tissue metadata from database */ { static struct gtexTissue *gtexTissues = NULL; if (gtexTissues == NULL) - { - char query[1024]; - struct sqlConnection *conn = sqlConnect("hgFixed"); - sqlSafef(query, sizeof(query), "select * from gtexTissue order by id"); - gtexTissues = gtexTissueLoadByQuery(conn, query); - } + gtexTissues = gtexGetTissues(); return gtexTissues; } struct rgbColor *getGtexTissueColors() /* Get RGB colors from tissue table */ { -struct gtexTissue *tissues = getGtexTissues(); +struct gtexTissue *tissues = getTissues(); 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; } @@ -199,65 +194,71 @@ return 8; } static int gtexGeneMargin() { return 1; } static struct gtexGeneBed *loadComputedMedians(struct gtexGeneBed *geneBed, char *graphType) /* Compute medians based on graph type. Returns a list of 2 for comparison graph types */ /* TODO: add support for filter function */ { /* FIXME: dummy load of two for display implementation */ struct gtexGeneBed *medians = NULL, *medians2 = NULL; +AllocVar(medians); +medians->expCount = geneBed->expCount; +int i; + +#ifdef NEW struct sqlConnection *conn = hAllocConn("hgFixed"); if (conn == NULL) return NULL; char query[1024]; -AllocVar(medians); -medians->expCount = geneBed->expCount; // FIXME: experiment with query on sex + sqlSafef(query, sizeof(query), "select gtexTissue.id, gtexSampleData.score from gtexTissue, gtexSampleData, gtexSample, gtexDonor where gtexSampleData.tissue=gtexTissue.name and gtexSampleData.geneId='%s' and gtexSampleData.sample=gtexSample.name and gtexSample.donor=gtexDonor.name and gtexDonor.gender='F'", geneBed->geneId); struct slDouble **scores = NULL, *score = NULL; AllocArray(scores, geneBed->expCount); struct slPair *tissueScore = NULL, *tissueScores = sqlQuickPairList(conn, query); -int i; for (tissueScore = tissueScores; tissueScore != NULL; tissueScore = tissueScore->next) { AllocVar(score); i = sqlUnsigned(tissueScore->name); if (scores[i] == NULL) scores[i] = score; else slAddHead(&scores[i], score); } +hFreeConn(&conn); +#endif + AllocArray(medians->expScores, medians->expCount); for (i=0; i<geneBed->expCount; i++) - medians->expScores[i] = slDoubleMedian(scores[i]); + //medians->expScores[i] = slDoubleMedian(scores[i]); + medians->expScores[i] = geneBed->expScores[i]; AllocVar(medians2); medians2->expCount = geneBed->expCount; AllocArray(medians2->expScores, medians2->expCount); for (i = 0; i < medians2->expCount; ++i) medians2->expScores[i] = geneBed->expScores[i]; medians->next = medians2; -hFreeConn(&conn); return medians; } static void gtexGeneDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis) { struct gtexGeneBed *geneBed = item; initGeneColors(hvg); //warn("item: %s, xOff=%d\n", geneBed->name, xOff); // Color using transcriptClass Color statusColor; if (geneBed->transcriptClass == NULL) statusColor = statusColors.unknown; else if (sameString(geneBed->transcriptClass, "coding")) statusColor = statusColors.coding; @@ -321,75 +322,72 @@ colors = getGtexTissueColors(); } else { // currently the only other choice // TODO: cache this colors = getRainbow(&saturatedRainbowAtPos, expCount); //colors = getRainbow(&lightRainbowAtPos, expCount); } for (i=0; i<expCount; i++) { struct rgbColor fillColor = colors[i]; if (barWidth == 1 && sameString(colorScheme, GTEX_COLORS_GTEX)) { // brighten colors a bit so they'll be more visible at this scale - struct hslColor hsl = mgRgbToHsl(fillColor); - hsl.s = min(1000, hsl.s + 300); - fillColor = mgHslToRgb(hsl); + fillColor = gtexTissueBrightenColor(fillColor); } int fillColorIx = hvGfxFindColorIx(hvg, fillColor.r, fillColor.g, fillColor.b); double expScore = geneBed->expScores[i]; int height = valToHeight(expScore, maxMedian, gtexGraphHeight()); // TODO: adjust yGene to get gene track distance as desired //if (i ==0) uglyf("DRAW: expScore=%.2f, maxMedian=%.2f, graphHeight=%d, y=%d<br>", expScore, maxMedian, gtexGraphHeight(), y); //if (i ==0) uglyf("DRAW: yZero=%d, yMedian=%d, height=%d<br>", yZero, yMedian, height); if (graphPadding == 0 || sameString(colorScheme, GTEX_COLORS_GTEX)) hvGfxBox(hvg, x1, yZero-height, barWidth, height, fillColorIx); else hvGfxOutlinedBox(hvg, x1, yZero-height, barWidth, height, fillColorIx, lineColorIx); x1 = x1 + barWidth + graphPadding; } // mark gene extent int yGene = yZero + gtexGeneMargin() - 1; // load & draw gene model char query[1024]; char **row; -sqlSafef(query, sizeof query, "select * from gtexGeneModel where name='%s'", geneBed->geneId); +// FIXME: move to load items (load all in range) +char *modelTable = "gtexGeneModel"; +int hasBin = hOffsetPastBin(database, geneBed->chrom, modelTable); +sqlSafef(query, sizeof query, "select * from %s where name='%s'", modelTable, geneBed->geneId); struct sqlConnection *conn = hAllocConn(database); if (conn == NULL) return; -//uglyf("query: %s<br>", query); -struct sqlResult *sr = sqlGetResult(conn, query); struct genePred *geneModel = NULL; -if (sr != NULL) - { +struct sqlResult *sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) - geneModel = genePredLoad(row); + geneModel = genePredLoad(row + hasBin); sqlFreeResult(&sr); -} +hFreeConn(&conn); if (geneModel == NULL) return; struct linkedFeatures *lf = linkedFeaturesFromGenePred(tg, geneModel, FALSE); tg->heightPer = gtexGeneHeight()+1; lf->filterColor = statusColor; linkedFeaturesDrawAt(tg, lf, hvg, xOff, yGene, scale, font, color, tvSquish); tg->heightPer = heightPer; -hFreeConn(&conn); if (!extras->isComparison || slCount(computedMedians) != 2) return; // draw comparison graph (upside down) x1 = startX; // yZero is at top of graph yZero = yGene + gtexGeneHeight(); for (i=0; i<expCount; i++) { struct rgbColor fillColor = colors[i]; if (barWidth == 1 && sameString(colorScheme, GTEX_COLORS_GTEX)) { // brighten colors a bit so they'll be more visible at this scale @@ -411,31 +409,31 @@ } } static void gtexGeneMapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end, int x, int y, int width, int height) /* Create a map box for each tissue (bar in the graph) or a single map for squish/dense modes */ { //uglyf("map item: itemName=%s, mapItemName=%s, start=%d, end=%d, x=%d, y=%d, width=%d, height=%d, insideX=%d<br>", //itemName, mapItemName, start, end, x, y, width, height, insideX); if (tg->visibility == tvDense || tg->visibility == tvSquish) { genericMapItem(tg, hvg, item, itemName, itemName, start, end, x, y, width, height); } -struct gtexTissue *tissues = getGtexTissues(); +struct gtexTissue *tissues = getTissues(); struct gtexTissue *tissue = NULL; struct gtexGeneBed *gtex = item; int barWidth = gtexBarWidth(); int padding = gtexGraphPadding(); double maxMedian = ((struct gtexGeneExtras *)tg->extraUiData)->maxMedian; int graphX = gtexGraphX((struct gtexGeneBed *)item); if (graphX < 0) return; // x1 is at left of graph int x1 = insideX + graphX; int i = 0; int yZero = gtexGraphHeight() + y - 1; for (tissue = tissues; tissue != NULL; tissue = tissue->next, i++) @@ -449,31 +447,31 @@ mapBoxHc(hvg, start, end, x1, yMedian+1, barWidth, height, tg->track, mapItemName, tissue->description); //if (i==0) uglyf("MAP: expScore=%.2f, maxMedian=%.2f, graphHeight=%d, y=%d<br>", expScore, maxMedian, gtexGraphHeight(), y); //if (i==0) uglyf("MAP: x=%d, x1=%d, y=%d, yZero=%d<br>", x, x1, y, yZero); //if (i==0) uglyf("MAP: yZero=%d, yMedian=%d, height=%d<br>", yZero, yMedian, height); x1 = x1 + barWidth + padding; } } static struct gtexGeneBed *loadGtexGeneBed(char **row) { struct gtexGeneBed *geneBed = gtexGeneBedLoad(row); // TODO: rethink schemas // for now... replace expScores with medians from tissue data file #ifdef NEW -struct gtexTissue *tissue = NULL, *tissues = getGtexTissues(); +struct gtexTissue *tissue = NULL, *tissues = getTissues(); int i=0; char query[1024]; struct sqlConnection *conn = hAllocConn("hgFixed"); for (tissue = tissues; tissue != NULL; tissue = tissue->next, i++) { sqlSafef(query, sizeof(query), "select * from gtexTissueData where geneId='%s' and tissue='%s'", geneBed->geneId, tissue->name); struct gtexTissueData *tissueData = gtexTissueDataLoadByQuery(conn, query); geneBed->expScores[i] = tissueData->median; } hFreeConn(&conn); #endif return geneBed; } @@ -481,31 +479,30 @@ static void gtexGeneLoadItems(struct track *tg) { bedLoadItem(tg, tg->table, (ItemLoader)loadGtexGeneBed); struct gtexGeneExtras *extras; AllocVar(extras); tg->extraUiData = extras; // TODO: move test to lib char *graphType = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_GRAPH, GTEX_GRAPH_DEFAULT); extras->graphType = cloneString(graphType); if (sameString(graphType, GTEX_GRAPH_AGE) || sameString(graphType, GTEX_GRAPH_SEX)) extras->isComparison = TRUE; - extras->maxMedian = gtexMaxMedianScore(NULL); } static int gtexGeneItemHeight(struct track *tg, void *item) { if ((item == NULL) || (tg->visibility == tvSquish) || (tg->visibility == tvDense)) return 0; int extra = 0; if (((struct gtexGeneExtras *)tg->extraUiData)->isComparison) extra = gtexGraphHeight() + 2; //uglyf("GTEX itemHeight extra = %d<br>", extra); return gtexGraphHeight() + gtexGeneMargin() + gtexGeneHeight() + extra; } static int gtexTotalHeight(struct track *tg, enum trackVisibility vis)