2ad7640d9646a8968d002801cb68e102cb2f69a4 kate Sun Nov 15 12:55:10 2015 -0800 Mostly working with variable heigt item layout in full mode. diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c index e64e887..63b921b 100644 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@ -260,30 +260,33 @@ extras->colors = getGtexTissueColors(); } else { int expCount = geneBed->expCount; extras->colors = getRainbow(&saturatedRainbowAtPos, expCount); } while (geneBed != NULL) { AllocVar(geneInfo); geneInfo->geneBed = geneBed; geneInfo->geneModel = hashFindVal(modelHash, geneBed->geneId); 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); } slReverse(&list); tg->items = list; } /***********************************************/ /* Draw */ /* Bargraph layouts for three window sizes */ #define WIN_MAX_GRAPH 20000 #define MAX_GRAPH_HEIGHT 100 #define MAX_BAR_WIDTH 5 #define MAX_GRAPH_PADDING 2 #define WIN_MED_GRAPH 500000 @@ -439,42 +442,39 @@ double scale, MgFont *font, Color color, enum trackVisibility vis) /* Draw tissue expression bar graph over gene model. Optionally, draw a second graph under gene, to compare sample sets */ { struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; struct gtexGeneBed *geneBed = geneInfo->geneBed; boolean doLogTransform = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, GTEX_LOG_TRANSFORM, GTEX_LOG_TRANSFORM_DEFAULT); // 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; } -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) - loadComputedMedians(geneInfo, extras); int heightPer = tg->heightPer; int graphX = gtexGraphX(geneBed); if (graphX < 0) return; int topGraphHeight = gtexGeneGraphHeight(tg, geneInfo, doLogTransform, TRUE); +if (geneInfo->medians2) + topGraphHeight = max(topGraphHeight, tl.fontHeight); int yZero = topGraphHeight + y - 1; // yZero is bottom of graph #ifndef MULTI_REGION int x1 = xOff + graphX; // x1 is at left of graph int keepX = x1; // FIXME: Too many X's! drawGraphBase(hvg, keepX, yZero+1, geneInfo); 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; @@ -485,30 +485,31 @@ if (geneInfo->medians2) { hvGfxText(hvg, x1, yZero - tl.fontHeight, labelColor, font, "F"); hvGfxText(hvg, x1, yZero + gtexGeneHeight() + gtexGeneMargin(), labelColor, font, "M"); startX = startX + tl.mWidth+2; x1 = startX; } // draw bar graph // TODO: share this code with other graph double viewMax = (double)cartUsualIntClosestToHome(cart, tg->tdb, FALSE, GTEX_MAX_LIMIT, GTEX_MAX_LIMIT_DEFAULT); double maxMedian = ((struct gtexGeneExtras *)tg->extraUiData)->maxMedian; int i; int expCount = geneBed->expCount; +struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; for (i=0; i<expCount; i++) { struct rgbColor fillColor = extras->colors[i]; if (barWidth == 1 && sameString(colorScheme, GTEX_COLORS_GTEX)) { // brighten colors a bit so they'll be more visible at this scale fillColor = gtexTissueBrightenColor(fillColor); } 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(), doLogTransform); if (graphPadding == 0 || sameString(colorScheme, GTEX_COLORS_GTEX)) hvGfxBox(hvg, x1, yZero-height+1, barWidth, height, fillColorIx); else @@ -574,35 +575,30 @@ #ifdef MULTI_REGION 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; // Color in dense mode using transcriptClass // GALT REMOVE Color statusColor = getTranscriptStatusColor(hvg, geneBed); if (vis != tvFull && vis != tvPack) { //GALT bedDrawSimpleAt(tg, geneBed, hvg, xOff, y, scale, font, statusColor, vis); return; } -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) - loadComputedMedians(geneInfo, extras); int i; int expCount = geneBed->expCount; double maxMedian = ((struct gtexGeneExtras *)tg->extraUiData)->maxMedian; struct rgbColor lineColor = {.r=0}; int lineColorIx = hvGfxFindColorIx(hvg, lineColor.r, lineColor.g, lineColor.b); // GALT REMOVE int heightPer = tg->heightPer; int graphX = gtexGraphX(geneBed); if (graphX < 0) return; int x1 = xOff + graphX; // x1 is at left of graph int startX = x1; int yZero = gtexMaxGraphHeight() + y - 1; // yZero is at bottom of graph // draw faint line under graph to delineate extent when bars are missing (tissue w/ 0 expression) @@ -683,31 +679,35 @@ } } #endif static int gtexGeneItemHeight(struct track *tg, void *item) { if ((item == NULL) || (tg->visibility == tvSquish) || (tg->visibility == tvDense)) return 0; boolean doLogTransform = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, GTEX_LOG_TRANSFORM, GTEX_LOG_TRANSFORM_DEFAULT); struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; int topGraphHeight = gtexGeneGraphHeight(tg, geneInfo, doLogTransform, TRUE); int bottomGraphHeight = 0; boolean isComparison = ((struct gtexGeneExtras *)tg->extraUiData)->isComparison; if (isComparison) - bottomGraphHeight = gtexGeneGraphHeight(tg, geneInfo, doLogTransform, FALSE); + { + topGraphHeight = max(topGraphHeight, tl.fontHeight); + bottomGraphHeight = max(gtexGeneGraphHeight(tg, geneInfo, doLogTransform, FALSE), + tl.fontHeight) + gtexGeneMargin(); + } int height = topGraphHeight + bottomGraphHeight + gtexGeneMargin() + gtexGeneHeight(); return height; } 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); @@ -752,46 +752,52 @@ if (graphX < 0) return; // x1 is at left of graph int x1 = insideX + graphX; if (geneInfo->medians2) { // skip over labels in comparison graphs x1 = x1 + tl.mWidth+ 2; } int i = 0; boolean doLogTransform = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, GTEX_LOG_TRANSFORM, GTEX_LOG_TRANSFORM_DEFAULT); int topGraphHeight = gtexGeneGraphHeight(tg, geneInfo, doLogTransform, TRUE); -int yZero = topGraphHeight + y - 1; // yZero is bottom of graph +if (geneInfo->medians2) + topGraphHeight = max(topGraphHeight, tl.fontHeight); // label +int yZero = topGraphHeight + y - 1; // yZero is bottom of (top) graph double viewMax = (double)cartUsualIntClosestToHome(cart, tg->tdb, FALSE, GTEX_MAX_LIMIT, GTEX_MAX_LIMIT_DEFAULT); for (tissue = tissues; tissue != NULL; tissue = tissue->next, i++) { - int height = valToClippedHeight(geneBed->expScores[i], maxMedian, viewMax, + double expScore = (geneInfo->medians1 ? geneInfo->medians1[i] : geneBed->expScores[i]); + int height = valToClippedHeight(expScore, maxMedian, viewMax, gtexMaxGraphHeight(), doLogTransform); - mapBoxHc(hvg, start, end, x1, yZero-height, barWidth, height, tg->track, mapItemName, tissue->description); + mapBoxHc(hvg, start, end, x1, yZero-height, barWidth, height, tg->track, mapItemName, + tissue->description); // add map box to comparison graph if (geneInfo->medians2) { double expScore = geneInfo->medians2[i]; - int height = valToClippedHeight(expScore, maxMedian, viewMax, gtexMaxGraphHeight(), doLogTransform); - int y = yZero + gtexGeneHeight() + gtexGeneMargin(); - mapBoxHc(hvg, start, end, x1, y, barWidth, height, tg->track, mapItemName, tissue->description); + int height = valToClippedHeight(expScore, maxMedian, viewMax, + gtexMaxGraphHeight(), doLogTransform); + int y = yZero + gtexGeneHeight() + gtexGeneMargin(); // y is top of bottom graph + mapBoxHc(hvg, start, end, x1, y, barWidth, height, tg->track, mapItemName, + tissue->description); } x1 = x1 + barWidth + padding; } } static char *gtexGeneItemName(struct track *tg, void *item) /* Return gene name */ { struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; struct gtexGeneBed *geneBed = geneInfo->geneBed; return geneBed->name; } static int gtexGeneTotalHeight(struct track *tg, enum trackVisibility vis) /* Figure out total height of track. Set in track and also return it */