d1d559e9bee7fcaec3a50ae43688ca436656ad7b kate Wed Nov 18 08:25:58 2015 -0800 Finish variable height item packing. Adds an optional rowSizes field to spaceSaver. refs #15645 diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c index e8f65dc..03439e5 100644 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@ -1,53 +1,56 @@ /* GTEx (Genotype Tissue Expression) tracks */ /* Copyright (C) 2015 The Regents of the University of California * See README in this or parent directory for licensing information. */ #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" +// TODO: move spaceSaver code to simpleTracks +#include "spaceSaver.h" // NOTE: Sections to change for multi-region (vertical slice) display // are marked with #ifdef MULTI_REGION. WARNING: These sections // are a bit out-of-date (refer to #ifndef MULTI code when integrating) struct gtexGeneExtras /* Track info */ { double maxMedian; /* Maximum median rpkm for all tissues */ boolean isComparison; /* Comparison of two sample sets (e.g. male/female). 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 */ }; struct gtexGeneInfo /* GTEx gene model, names, and expression medians */ { struct gtexGeneInfo *next; /* Next in singly linked list */ struct gtexGeneBed *geneBed;/* Gene name, id, canonical transcript, exp count and medians from BED table */ struct genePred *geneModel; /* Gene structure from model table */ double *medians1; /* Computed medians */ double *medians2; /* Computed medians for comparison (inverse) graph */ + int height; /* Item height in pixels */ }; /***********************************************/ /* Color gene models using GENCODE conventions */ // TODO: reuse GENCODE code for some/all of this ?? // MAKE_COLOR_32 ? struct rgbColor codingColor = {12, 12, 120}; // #0C0C78 struct rgbColor noncodingColor = {0, 100, 0}; // #006400 struct rgbColor problemColor = {254, 0, 0}; // #FE0000 struct rgbColor unknownColor = {1, 1, 1}; static struct statusColors /* Color values for gene models */ { @@ -214,30 +217,32 @@ if (scores) medians1[i] = slDoubleMedian(scores); scores = hashFindVal(scoreHash2, getTissueName(i)); if (scores) medians2[i] = slDoubleMedian(scores); } geneInfo->medians1 = medians1; geneInfo->medians2 = medians2; } else { // TODO: compute median for single graph based on filtering of sample set } } +static int gtexGeneItemHeight(struct track *tg, void *item); + static void gtexGeneLoadItems(struct track *tg) /* Load method for track items */ { /* Get track UI info */ struct gtexGeneExtras *extras; AllocVar(extras); tg->extraUiData = extras; 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; extras->maxMedian = gtexMaxMedianScore(NULL); /* Get geneModels in range */ @@ -263,30 +268,31 @@ { 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); + geneInfo->height = gtexGeneItemHeight(tg, geneInfo); } 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 @@ -449,57 +455,54 @@ 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; } 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); -if (vis == tvPack) - topGraphHeight = gtexMaxGraphHeight(); 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; Color clipColor = MG_MAGENTA; // add labels to comparison graphs // TODO: generalize if (geneInfo->medians2) { - hvGfxText(hvg, x1, yZero - tl.fontHeight, labelColor, font, "F"); - hvGfxText(hvg, x1, yZero + gtexGeneModelHeight() + gtexGeneMargin(), labelColor, font, "M"); + hvGfxText(hvg, x1, yZero - tl.fontHeight + 1, labelColor, font, "F"); + hvGfxText(hvg, x1, yZero + gtexGeneModelHeight() + gtexGeneMargin() + 1, 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]; @@ -684,38 +687,40 @@ 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; boolean doLogTransform = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, GTEX_LOG_TRANSFORM, GTEX_LOG_TRANSFORM_DEFAULT); int topGraphHeight = gtexGeneGraphHeight(tg, geneInfo, doLogTransform, TRUE); +topGraphHeight = max(topGraphHeight, tl.fontHeight); int bottomGraphHeight = 0; boolean isComparison = ((struct gtexGeneExtras *)tg->extraUiData)->isComparison; if (isComparison) { - topGraphHeight = max(topGraphHeight, tl.fontHeight); bottomGraphHeight = max(gtexGeneGraphHeight(tg, geneInfo, doLogTransform, 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) { @@ -774,34 +779,31 @@ 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); -if (geneInfo->medians2) topGraphHeight = max(topGraphHeight, tl.fontHeight); // label -if (tg->visibility == tvPack) - topGraphHeight = gtexGeneMaxHeight(tg); 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++) { 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); // add map box to comparison graph if (geneInfo->medians2) { double expScore = geneInfo->medians2[i]; @@ -811,49 +813,64 @@ 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 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) { - // layout as fixed height - int maxHeight = gtexGeneMaxHeight(tg); - height = tgFixedTotalHeightOptionalOverflow(tg, vis, maxHeight, maxHeight, FALSE); // TODO: allow oflow ? + 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->rowSizes) + height = spaceSaverSetRowHeights(tg->ss, gtexGeneHeight); + else + 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 */