c28867b853a769949049ae459cee687bcad25aca kate Fri Jul 24 13:07:01 2015 -0700 Add support for comparison graphs (2 graphs, one top and one below inverted, based on splitting samples by sex or age). First cut of display only. refs #15645 diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c index ba91a5a..c4d9df3 100644 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@ -93,46 +93,56 @@ else if (winSize < WIN_MED_GRAPH) return MED_GRAPH_HEIGHT; else return MIN_GRAPH_HEIGHT; } static int gtexGraphWidth(struct gtexGeneBed *gtex) /* Width of GTEx graph in pixels */ { int barWidth = gtexBarWidth(); int padding = gtexGraphPadding(); int count = gtex->expCount; return (barWidth * count) + (padding * (count-1)); } -static int valToY(double val, double maxVal, int height) + +static int valToHeight(double val, double maxVal, int maxHeight) +/* Convert a value from 0 to maxVal to 0 to maxHeight-1 */ +{ +double scaled = val/maxVal; +return (scaled * (maxHeight-1)); +} + +static int valToY(double val, double maxVal, int maxHeight) /* Convert a value from 0 to maxVal to 0 to height-1 */ { double scaled = val/maxVal; -int y = scaled * (height); -return (height-1) - y; +int y = scaled * (maxHeight); +return (maxHeight-1) - y; + //int y = scaled * (height-1); //return (height - 1) - y; } struct gtexGeneExtras { - double maxExp; + double maxExp; // TODO: remove this local normalization factor + char *graphType; + boolean isComparison; }; - /* Cache tissue metadata */ struct gtexTissue *getGtexTissues() /* 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); } return gtexTissues; } @@ -170,71 +180,108 @@ //if (x1 + width > x2) //return -1; return x1; } static int gtexGeneHeight() { 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); +/* TODO: move to lib */ +medians->expCount = geneBed->expCount; +AllocArray(medians->expScores, medians->expCount); +int i; +for (i = 0; i < medians->expCount; ++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; +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; else if (sameString(geneBed->transcriptClass, "nonCoding")) statusColor = statusColors.nonCoding; else if (sameString(geneBed->transcriptClass, "problem")) statusColor = statusColors.problem; else statusColor = statusColors.unknown; if (vis != tvFull && vis != tvPack) { bedDrawSimpleAt(tg, item, hvg, xOff, y, scale, font, statusColor, vis); return; } +struct gtexGeneBed *computedMedians = NULL; // 1 or 2 (if comparison) + // with medians computed for sample subsets + +struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; +if ((extras->isComparison) && + (tg->visibility == tvFull || tg->visibility == tvPack) && + gtexGraphHeight() != MIN_GRAPH_HEIGHT) + { + // compute medians based on configuration (comparisons, and later, filters) + computedMedians = loadComputedMedians(geneBed, extras->graphType); + } int i; int expCount = geneBed->expCount; double maxExp = ((struct gtexGeneExtras *)tg->extraUiData)->maxExp; struct rgbColor lineColor = {.r=0}; int lineColorIx = hvGfxFindColorIx(hvg, lineColor.r, lineColor.g, lineColor.b); int heightPer = tg->heightPer; int graphX = gtexGraphX(geneBed); if (graphX < 0) return; // x1 is at left of graph int x1 = xOff + graphX; +int startX = x1; // yZero is at bottom of graph int yZero = gtexGraphHeight() + y - 1; // draw faint line under graph to delineate extent when bars are missing (tissue w/ 0 expression) +// TODO: skip missing bars -- then we can lose the gray line (at least for non-comparison mode) Color lightGray = MAKECOLOR_32(0xD1, 0xD1, 0xD1); int graphWidth = gtexGraphWidth(geneBed); hvGfxBox(hvg, x1, yZero+1, graphWidth, 1, lightGray); //uglyf("DRAW: xOff=%d, x1=%d, y=%d, yZero=%d<br>", xOff, x1, y, yZero); int barWidth = gtexBarWidth(); int graphPadding = gtexGraphPadding(); char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS, GTEX_COLORS_DEFAULT); struct rgbColor *colors; if (sameString(colorScheme, GTEX_COLORS_GTEX)) { // retrieve from table // TODO: cache this @@ -248,31 +295,32 @@ //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); } int fillColorIx = hvGfxFindColorIx(hvg, fillColor.r, fillColor.g, fillColor.b); double expScore = geneBed->expScores[i]; int yMedian = valToY(expScore, maxExp, gtexGraphHeight()) + y; - //int height = yZero - yMedian + 1; + //int foo = valToY(expScore, maxExp, gtexGraphHeight()); + //int yMedian = yZero - height; int height = yZero - yMedian; // TODO: adjust yGene instead of yMedian+1 to get gene track distance as desired //if (i ==0) uglyf("DRAW: expScore=%.2f, maxExp=%.2f, graphHeight=%d, y=%d<br>", expScore, maxExp, 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, yMedian+1, barWidth, height, fillColorIx); else hvGfxOutlinedBox(hvg, x1, yMedian+1, barWidth, height, fillColorIx, lineColorIx); x1 = x1 + barWidth + graphPadding; } // mark gene extent int yGene = yZero + gtexGeneMargin() - 1; // load & draw gene model @@ -288,30 +336,61 @@ struct genePred *geneModel = NULL; if (sr != NULL) { if ((row = sqlNextRow(sr)) != NULL) geneModel = genePredLoad(row); sqlFreeResult(&sr); } 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 + struct hslColor hsl = mgRgbToHsl(fillColor); + hsl.s = min(1000, hsl.s + 300); + fillColor = mgHslToRgb(hsl); + } + int fillColorIx = hvGfxFindColorIx(hvg, fillColor.r, fillColor.g, fillColor.b); + double expScore = geneBed->expScores[i]; + int height = valToHeight(expScore, maxExp, gtexGraphHeight()); + // TODO: adjust yGene instead of yMedian+1 to get gene track distance as desired + //if (i ==0) uglyf("DRAW2: expScore=%.2f, maxExp=%.2f, graphHeight=%d, y=%d<br>", expScore, maxExp, gtexGraphHeight(), y); + //if (i ==0) uglyf("DRAW2: yZero=%d, height=%d<br>", yZero, height); + if (graphPadding == 0 || sameString(colorScheme, GTEX_COLORS_GTEX)) + hvGfxBox(hvg, x1, yZero, barWidth, height, fillColorIx); + else + hvGfxOutlinedBox(hvg, x1, yZero, barWidth, height, fillColorIx, lineColorIx); + x1 = x1 + barWidth + graphPadding; + } } 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(); @@ -337,71 +416,88 @@ // TODO: call genericMapItem //genericMapItem(tg, hvg, item, itemName, tissue->description, start, end, x1, y, barWidth, height); mapBoxHc(hvg, start, end, x1, yMedian+1, barWidth, height, tg->track, mapItemName, tissue->description); //if (i==0) uglyf("MAP: expScore=%.2f, maxExp=%.2f, graphHeight=%d, y=%d<br>", expScore, maxExp, 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) { return gtexGeneBedLoad(row); } -static void gtexGeneLoadItems(struct track *track) +static void gtexGeneLoadItems(struct track *tg) { -bedLoadItem(track, track->table, (ItemLoader)loadGtexGeneBed); +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; + double maxExp = 0.0; int i; struct gtexGeneBed *geneBed; -for (geneBed = track->items; geneBed != NULL; geneBed = geneBed->next) +// TODO: Remove this fake (window-based) normalization +for (geneBed = tg->items; geneBed != NULL; geneBed = geneBed->next) for (i=0; i<geneBed->expCount; i++) maxExp = (geneBed->expScores[i] > maxExp ? geneBed->expScores[i] : maxExp); -struct gtexGeneExtras *extras; -AllocVar(extras); extras->maxExp = maxExp; -track->extraUiData = extras; - } -static int gtexGeneItemHeight(struct track *track, void *item) +static int gtexGeneItemHeight(struct track *tg, void *item) { -if ((item == NULL) || (track->visibility == tvSquish) || (track->visibility == tvDense)) +if ((item == NULL) || (tg->visibility == tvSquish) || (tg->visibility == tvDense)) return 0; -return gtexGraphHeight() + + gtexGeneMargin() + gtexGeneHeight(); +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 *track, enum trackVisibility vis) +static int gtexTotalHeight(struct track *tg, enum trackVisibility vis) /* Figure out total height of track */ { int height; -if (track->visibility == tvSquish || track->visibility == tvDense) +int extra = 0; +if (((struct gtexGeneExtras *)tg->extraUiData)->isComparison) + extra = gtexGraphHeight() + 2; +if (tg->visibility == tvSquish || tg->visibility == tvDense) height = 10; else - height = gtexGraphHeight() + gtexGeneMargin() + gtexGeneHeight(); -return tgFixedTotalHeightOptionalOverflow(track, vis, height, height, FALSE); + height = gtexGraphHeight() + gtexGeneMargin() + gtexGeneHeight() + extra; +//uglyf("GTEX totalHeight = %d<br>", height); +return tgFixedTotalHeightOptionalOverflow(tg, vis, height, height, FALSE); } -static int gtexGeneItemEnd(struct track *track, void *item) +static int gtexGeneItemEnd(struct track *tg, void *item) /* Return end chromosome coordinate of item, including graph */ { struct gtexGeneBed *geneBed = (struct gtexGeneBed *)item; double scale = scaleForWindow(insideWidth, winStart, winEnd); int graphWidth = gtexGraphWidth(geneBed); return max(geneBed->chromEnd, max(winStart, geneBed->chromStart) + graphWidth/scale); } -void gtexGeneMethods(struct track *track) +void gtexGeneMethods(struct track *tg) { -track->drawItemAt = gtexGeneDrawAt; -track->loadItems = gtexGeneLoadItems; -track->mapItem = gtexGeneMapItem; -track->itemHeight = gtexGeneItemHeight; -track->itemEnd = gtexGeneItemEnd; -track->totalHeight = gtexTotalHeight; +tg->drawItemAt = gtexGeneDrawAt; +tg->loadItems = gtexGeneLoadItems; +tg->mapItem = gtexGeneMapItem; +tg->itemHeight = gtexGeneItemHeight; +tg->itemEnd = gtexGeneItemEnd; +tg->totalHeight = gtexTotalHeight; }