8c908f948b09826c6cb4452ee5b282aca41be85e galt Tue Dec 8 21:52:59 2015 -0800 Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it. diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c index b99fe3d..667c78f 100644 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@ -307,40 +307,43 @@ 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 */ char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS, GTEX_COLORS_DEFAULT); if (sameString(colorScheme, GTEX_COLORS_GTEX)) { extras->colors = getGtexTissueColors(); } else { + if (geneBed) + { int expCount = geneBed->expCount; extras->colors = getRainbow(&saturatedRainbowAtPos, expCount); } + } filterTissues(tg); while (geneBed != NULL) { AllocVar(geneInfo); geneInfo->geneBed = geneBed; - geneInfo->geneModel = hashFindVal(modelHash, geneBed->geneId); + geneInfo->geneModel = hashFindVal(modelHash, geneBed->geneId); // sometimes this is missing, hash returns NULL. do we check? slAddHead(&list, geneInfo); geneBed = geneBed->next; geneInfo->geneBed->next = NULL; if (extras->isComparison && (tg->visibility == tvFull || tg->visibility == tvPack)) // compute medians based on configuration (comparisons, and later, filters) loadComputedMedians(geneInfo, extras); geneInfo->height = gtexGeneItemHeight(tg, geneInfo); } slReverse(&list); tg->items = list; } /***********************************************/ /* Draw */ @@ -351,73 +354,74 @@ #define MAX_GRAPH_PADDING 2 #define WIN_MED_GRAPH 500000 #define MED_GRAPH_HEIGHT 60 #define MED_BAR_WIDTH 3 #define MED_GRAPH_PADDING 1 #define MIN_GRAPH_HEIGHT 20 #define MIN_BAR_WIDTH 1 #define MIN_GRAPH_PADDING 0 #define MARGIN_WIDTH 1 static int gtexBarWidth() { -int winSize = winEnd - winStart; +long winSize = virtWinBaseCount; if (winSize < WIN_MAX_GRAPH) return MAX_BAR_WIDTH; else if (winSize < WIN_MED_GRAPH) return MED_BAR_WIDTH; else return MIN_BAR_WIDTH; } static int gtexGraphPadding() { -int winSize = winEnd - winStart; +long winSize = virtWinBaseCount; + if (winSize < WIN_MAX_GRAPH) return MAX_GRAPH_PADDING; else if (winSize < WIN_MED_GRAPH) return MED_GRAPH_PADDING; else return MIN_GRAPH_PADDING; } static int gtexMaxGraphHeight() { -int winSize = winEnd - winStart; +long winSize = virtWinBaseCount; if (winSize < WIN_MAX_GRAPH) return MAX_GRAPH_HEIGHT; else if (winSize < WIN_MED_GRAPH) return MED_GRAPH_HEIGHT; else return MIN_GRAPH_HEIGHT; } static int gtexGraphWidth(struct track *tg, struct gtexGeneInfo *geneInfo) /* Width of GTEx graph in pixels */ { int barWidth = gtexBarWidth(); int padding = gtexGraphPadding(); int count = filteredTissueCount(tg); int labelWidth = geneInfo->medians2 ? tl.mWidth : 0; return (barWidth * count) + (padding * (count-1)) + labelWidth + 2; } static int gtexGraphX(struct gtexGeneBed *gtex) -/* Locate graph on X, relative to viewport. Return -1 if it won't fit */ +/* Locate graph on X, relative to viewport. */ { int start = max(gtex->chromStart, winStart); double scale = scaleForWindow(insideWidth, winStart, winEnd); int x1 = round((start - winStart) * scale); return x1; } static int gtexGeneModelHeight() { return 8; } static int gtexGeneMargin() { return 1; @@ -493,34 +497,64 @@ struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; struct gtexGeneBed *geneBed = geneInfo->geneBed; // Color in dense mode using transcriptClass Color statusColor = getTranscriptStatusColor(hvg, geneBed); if (vis != tvFull && vis != tvPack) { bedDrawSimpleAt(tg, geneBed, hvg, xOff, y, scale, font, statusColor, vis); return; } int heightPer = tg->heightPer; int graphX = gtexGraphX(geneBed); if (graphX < 0) return; +// draw gene model +int topGraphHeight = gtexGeneGraphHeight(tg, geneInfo, TRUE); +topGraphHeight = max(topGraphHeight, tl.fontHeight); +int yZero = topGraphHeight + y - 1; // yZero is bottom of graph +int yGene = yZero + gtexGeneMargin() - 1; +tg->heightPer = gtexGeneModelHeight() + 1; +if (geneInfo->geneModel) // some BEDs do not have a corresponding geneModel record + { + struct linkedFeatures *lf = linkedFeaturesFromGenePred(tg, geneInfo->geneModel, FALSE); + lf->filterColor = statusColor; + linkedFeaturesDrawAt(tg, lf, hvg, xOff, yGene, scale, font, color, tvSquish); + } +tg->heightPer = heightPer; +} + +static int gtexGeneNonPropPixelWidth(struct track *tg, void *item) +/* Return end chromosome coordinate of item, including graph */ +{ +struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; +int graphWidth = gtexGraphWidth(tg, geneInfo); +return graphWidth; +} + +static void gtexGeneNonPropDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, + double scale, MgFont *font, Color color, enum trackVisibility vis) +{ +struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; +struct gtexGeneBed *geneBed = geneInfo->geneBed; int topGraphHeight = gtexGeneGraphHeight(tg, geneInfo, TRUE); topGraphHeight = max(topGraphHeight, tl.fontHeight); int yZero = topGraphHeight + y - 1; // yZero is bottom of graph +int yGene = yZero + gtexGeneMargin()-1; +int graphX = gtexGraphX(geneBed); int x1 = xOff + graphX; // x1 is at left of graph int keepX = x1; drawGraphBase(tg, geneInfo, hvg, keepX, yZero+1); int startX = x1; struct rgbColor lineColor = {.r=0}; int lineColorIx = hvGfxFindColorIx(hvg, lineColor.r, lineColor.g, lineColor.b); int barWidth = gtexBarWidth(); int graphPadding = gtexGraphPadding(); char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS, GTEX_COLORS_DEFAULT); Color labelColor = MG_GRAY; Color clipColor = MG_MAGENTA; // add labels to comparison graphs @@ -552,38 +586,30 @@ } int fillColorIx = hvGfxFindColorIx(hvg, fillColor.r, fillColor.g, fillColor.b); double expScore = (geneInfo->medians1 ? geneInfo->medians1[i] : geneBed->expScores[i]); int height = valToClippedHeight(expScore, maxMedian, viewMax, gtexMaxGraphHeight(), extras->doLogTransform); if (graphPadding == 0 || sameString(colorScheme, GTEX_COLORS_GTEX)) hvGfxBox(hvg, x1, yZero-height+1, barWidth, height, fillColorIx); else hvGfxOutlinedBox(hvg, x1, yZero-height+1, barWidth, height, fillColorIx, lineColorIx); // mark clipped bar with magenta tip if (!extras->doLogTransform && expScore > viewMax) hvGfxBox(hvg, x1, yZero-height+1, barWidth, 1, clipColor); x1 = x1 + barWidth + graphPadding; } -// draw gene model -int yGene = yZero + gtexGeneMargin() - 1; -tg->heightPer = gtexGeneModelHeight() + 1; -struct linkedFeatures *lf = linkedFeaturesFromGenePred(tg, geneInfo->geneModel, FALSE); -lf->filterColor = statusColor; -linkedFeaturesDrawAt(tg, lf, hvg, xOff, yGene, scale, font, color, tvSquish); -tg->heightPer = heightPer; - if (!geneInfo->medians2) return; // draw comparison bar graph (upside down) x1 = startX; yZero = yGene + gtexGeneModelHeight() + 1; // yZero is at top of graph drawGraphBase(tg, geneInfo, hvg, keepX, yZero-1); for (i=0, tis=extras->tissues; i<expCount; i++, tis=tis->next) { if (!filterTissue(tg, tis->name)) continue; struct rgbColor fillColor = extras->colors[i]; if (barWidth == 1 && sameString(colorScheme, GTEX_COLORS_GTEX)) { @@ -608,119 +634,90 @@ static int gtexGeneItemHeightOptionalMax(struct track *tg, void *item, boolean isMax) { if (tg->visibility == tvSquish || tg->visibility == tvDense) return 0; if (isMax) { int extra = 0; if (((struct gtexGeneExtras *)tg->extraUiData)->isComparison) extra = gtexMaxGraphHeight() + 2; return gtexMaxGraphHeight() + gtexGeneMargin() + gtexGeneModelHeight() + extra; } if (item == NULL) return 0; struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; + if (geneInfo->height != 0) return geneInfo->height; int topGraphHeight = gtexGeneGraphHeight(tg, geneInfo, TRUE); topGraphHeight = max(topGraphHeight, tl.fontHeight); int bottomGraphHeight = 0; boolean isComparison = ((struct gtexGeneExtras *)tg->extraUiData)->isComparison; if (isComparison) { bottomGraphHeight = max(gtexGeneGraphHeight(tg, geneInfo, FALSE), tl.fontHeight) + gtexGeneMargin(); } int height = topGraphHeight + bottomGraphHeight + gtexGeneMargin() + gtexGeneModelHeight(); return height; } static int gtexGeneMaxHeight(struct track *tg) /* Maximum height in pixels of a gene graph */ { return gtexGeneItemHeightOptionalMax(tg, NULL, TRUE); } static int gtexGeneItemHeight(struct track *tg, void *item) { return gtexGeneItemHeightOptionalMax(tg, item, FALSE); } -static void gtexGeneDrawItemsFull(struct track *tg, int seqStart, int seqEnd, - struct hvGfx *hvg, int xOff, int yOff, int width, - MgFont *font, Color color, enum trackVisibility vis) -/* Draw GTEx gene graphs in full mode. Special handling as they are variable height */ -{ -double scale = scaleForWindow(width, seqStart, seqEnd); -struct slList *item; -int y = yOff + 1; -for (item = tg->items; item != NULL; item = item->next) - { - tg->drawItemAt(tg, item, hvg, xOff, y, scale, font, color, vis); - genericDrawNextItem(tg, item, hvg, xOff, y, scale, color, vis); - int height = gtexGeneItemHeight(tg, item); - y += height; - } -} - -void gtexGeneDrawItems(struct track *tg, int seqStart, int seqEnd, - struct hvGfx *hvg, int xOff, int yOff, int width, - MgFont *font, Color color, enum trackVisibility vis) -/* Draw GTEx gene graphs, which are of variable height so require custom layout in full - * and pack modes */ -{ -if (vis == tvDense || vis == tvSquish) - genericDrawItems(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); -else if (vis == tvFull) - gtexGeneDrawItemsFull(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); -else if (vis == tvPack) - genericDrawItems(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); -} - static char *tissueExpressionText(struct gtexTissue *tissue, double expScore, boolean doLogTransform, char *qualifier) /* Construct mouseover text for tissue graph */ { static char buf[128]; safef(buf, sizeof(buf), "%s (%.1f %s%s%sRPKM)", tissue->description, doLogTransform ? log10(expScore+1.0) : expScore, qualifier != NULL ? qualifier : "", qualifier != NULL ? " " : "", doLogTransform ? "log " : ""); return buf; } 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 on gene model and label, and one for each tissue (bar in the graph) in * pack or ful modes. Just single map for squish/dense modes */ { if (tg->visibility == tvDense || tg->visibility == tvSquish) { genericMapItem(tg, hvg, item, itemName, itemName, start, end, x, y, width, height); return; } - // add map boxes to gene model and label 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; +if (!geneInfo->geneModel) + return; int geneStart = max(geneInfo->geneModel->txStart, winStart); int geneEnd = min(geneInfo->geneModel->txEnd, winEnd); double scale = scaleForWindow(insideWidth, winStart, winEnd); int x1 = round((double)((int)geneStart-winStart)*scale) + x; int x2 = round((double)((int)geneEnd-winStart)*scale) + x; int w = x2-x1; char query[256]; sqlSafef(query, sizeof(query), "select kgXref.description from kgXref, knownToEnsembl where knownToEnsembl.value='%s' and knownToEnsembl.name=kgXref.kgID", geneBed->transcriptId); struct sqlConnection *conn = hAllocConn(database); char *desc = sqlQuickString(conn, query); hFreeConn(&conn); mapBoxHc(hvg, start, end, x, yGene, w, gtexGeneModelHeight()-1, tg->track, mapItemName, desc); // add maps to tissue bars in expresion graph @@ -781,80 +778,94 @@ struct gtexGeneBed *geneBed = geneInfo->geneBed; return geneBed->name; } static int gtexGeneHeight(void *item) { struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; assert(geneInfo->height != 0); return geneInfo->height; } static int gtexGeneTotalHeight(struct track *tg, enum trackVisibility vis) /* Figure out total height of track. Set in track and also return it */ { int height = 0; -struct gtexGeneInfo *item; + if (tg->visibility == tvSquish || tg->visibility == tvDense) { height = tgFixedTotalHeightOptionalOverflow(tg, vis, tl.fontHeight+1, tl.fontHeight, FALSE); } -else if (tg->visibility == tvFull) - { - for (item = tg->items; item != NULL; item = item->next) - height += gtexGeneItemHeight(tg, item); - } -else if (tg->visibility == tvPack) +else if ((tg->visibility == tvPack) || (tg->visibility == tvFull)) { if (!tg->ss) { // layout -- initially as fixed height int height = gtexGeneMaxHeight(tg); tgFixedTotalHeightOptionalOverflow(tg, vis, height, height, FALSE); // TODO: allow oflow ? } // set variable height rows if (tg->ss->rowCount != 0) { if (!tg->ss->rowSizes) - height = spaceSaverSetRowHeights(tg->ss, gtexGeneHeight); - else + { + // collect the rowSizes data across all windows + assert(currentWindow==windows); // first window + assert(tg->ss->vis == vis); // viz matches, we have the right one + struct spaceSaver *ssHold; + AllocVar(ssHold); + struct track *tgSave = tg; + for(tg=tgSave; tg; tg=tg->nextWindow) + { + assert(tgSave->ss->vis == tg->ss->vis); // viz matches, we have the right one + spaceSaverSetRowHeights(tg->ss, ssHold, gtexGeneHeight); + } + // share the rowSizes data across all windows + for(tg=tgSave; tg; tg=tg->nextWindow) + { + tg->ss->rowSizes = ssHold->rowSizes; + } + tg = tgSave; + } height = spaceSaverGetRowHeightsTotal(tg->ss); } } tg->height = height; + return height; } static int gtexGeneItemStart(struct track *tg, void *item) /* Return end chromosome coordinate of item, including graph */ { struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; struct gtexGeneBed *geneBed = geneInfo->geneBed; return geneBed->chromStart; } static int gtexGeneItemEnd(struct track *tg, void *item) /* Return end chromosome coordinate of item, including graph */ { struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; struct gtexGeneBed *geneBed = geneInfo->geneBed; double scale = scaleForWindow(insideWidth, winStart, winEnd); int graphWidth = gtexGraphWidth(tg, geneInfo); return max(geneBed->chromEnd, max(winStart, geneBed->chromStart) + graphWidth/scale); } void gtexGeneMethods(struct track *tg) { -tg->drawItems = gtexGeneDrawItems; tg->drawItemAt = gtexGeneDrawAt; tg->loadItems = gtexGeneLoadItems; tg->mapItem = gtexGeneMapItem; tg->itemName = gtexGeneItemName; tg->mapItemName = gtexGeneItemName; tg->itemHeight = gtexGeneItemHeight; tg->itemStart = gtexGeneItemStart; tg->itemEnd = gtexGeneItemEnd; tg->totalHeight = gtexGeneTotalHeight; +tg->nonPropDrawItemAt = gtexGeneNonPropDrawAt; +tg->nonPropPixelWidth = gtexGeneNonPropPixelWidth; }