5e5b469d59038d7717d302fd257dca1310b9d44a kate Tue Nov 24 08:52:47 2015 -0800 Add tissue filter to GTEX gene track. refs #15645 diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c index f6fbbbc..5ed3184 100644 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@ -16,30 +16,33 @@ #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 WARNING: These sections // are a bit out-of-date (refer to #ifndef MULTI code when integrating) struct gtexGeneExtras /* Track info */ { double maxMedian; /* Maximum median rpkm for all tissues */ boolean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). */ boolean isDifference; /* True if comparison is shown as a single difference graph. False if 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 */ + boolean doLogTransform; /* Log10(x+1) */ + struct gtexTissue *tissues; /* Cache tissue names, descriptions */ + struct hash *tissueFilter; /* For filter. NULL out excluded 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 */ }; /***********************************************/ @@ -237,30 +240,68 @@ } } } 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 filterTissues(struct track *tg) +/* Check cart for tissue selection. NULL out unselected tissues in tissue list */ +{ +struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; +struct gtexTissue *tis = NULL; +extras->tissues = getTissues(); +extras->tissueFilter = hashNew(0); +if (cartListVarExistsAnyLevel(cart, tg->tdb, FALSE, GTEX_TISSUE_SELECT)) + { + struct slName *selectedValues = cartOptionalSlNameListClosestToHome(cart, tg->tdb, + FALSE, GTEX_TISSUE_SELECT); + if (selectedValues != NULL) + { + struct slName *name; + for (name = selectedValues; name != NULL; name = name->next) + hashAdd(extras->tissueFilter, name->name, name->name); + return; + } + } +/* no filter */ +for (tis = extras->tissues; tis != NULL; tis = tis->next) + hashAdd(extras->tissueFilter, tis->name, tis->name); +} + +static int filteredTissueCount(struct track *tg) +/* Count of tissues to display */ +{ +struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; +return hashNumEntries(extras->tissueFilter); +} + +static boolean filterTissue(struct track *tg, char *name) +/* Does tissue pass filter */ +{ +struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; +return (hashLookup(extras->tissueFilter, name) != NULL); +} + 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; char *comparison = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COMPARISON_DISPLAY, GTEX_COMPARISON_DEFAULT); extras->isDifference = sameString(comparison, GTEX_COMPARISON_DIFF) ? TRUE : FALSE; @@ -278,30 +319,32 @@ 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 { 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); 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; @@ -361,37 +404,36 @@ static int gtexMaxGraphHeight() { #ifdef MULTI_REGION int winSize = virtWinBaseCount; // GALT CHANGED OLD winEnd - winStart; #else int winSize = winEnd - winStart; #endif 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 gtexGeneInfo *geneInfo) +static int gtexGraphWidth(struct track *tg, struct gtexGeneInfo *geneInfo) /* Width of GTEx graph in pixels */ { int barWidth = gtexBarWidth(); int padding = gtexGraphPadding(); -struct gtexGeneBed *geneBed = geneInfo->geneBed; -int count = geneBed->expCount; +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 */ { int start = max(gtex->chromStart, winStart); double scale = scaleForWindow(insideWidth, winStart, winEnd); int x1 = round((start - winStart) * scale); return x1; } static int gtexGeneModelHeight() { @@ -421,35 +463,35 @@ static int valToClippedHeight(double val, double maxVal, int maxView, int maxHeight, boolean doLogTransform) /* Convert a value from 0 to maxVal to 0 to maxHeight-1, with clipping, or log transform the value */ { double useVal = val; double useMax = maxVal; if (!doLogTransform) { useMax = maxView; if (val > maxView) useVal = maxView; } return valToHeight(useVal, useMax, gtexMaxGraphHeight(), doLogTransform); } -static void drawGraphBase(struct hvGfx *hvg, int x, int y, struct gtexGeneInfo *geneInfo) +static void drawGraphBase(struct track *tg, struct gtexGeneInfo *geneInfo, struct hvGfx *hvg, int x, int y) /* Draw faint line under graph to delineate extent when bars are missing (tissue w/ 0 expression) */ { Color lightGray = MAKECOLOR_32(0xD1, 0xD1, 0xD1); -int graphWidth = gtexGraphWidth(geneInfo); +int graphWidth = gtexGraphWidth(tg, geneInfo); hvGfxBox(hvg, x, y, graphWidth, 1, lightGray); } static int gtexGeneGraphHeight(struct track *tg, struct gtexGeneInfo *geneInfo, boolean doLogTransform, boolean doTop) /* Determine height in pixels of graph. This will be the box for tissue with highest expression If doTop is false, compute height of bottom graph of comparison */ { struct gtexGeneBed *geneBed = geneInfo->geneBed; int i; double maxExp = 0.0; int expCount = geneBed->expCount; double expScore; for (i=0; i<expCount; i++) { @@ -482,62 +524,65 @@ return; } int heightPer = tg->heightPer; int graphX = gtexGraphX(geneBed); if (graphX < 0) return; int topGraphHeight = gtexGeneGraphHeight(tg, geneInfo, doLogTransform, TRUE); 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); +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 // TODO: generalize if (geneInfo->medians2) { 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 gtexTissue *tis; +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)) { // 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 hvGfxOutlinedBox(hvg, x1, yZero-height+1, barWidth, height, fillColorIx, lineColorIx); // mark clipped bar with magenta tip @@ -550,34 +595,36 @@ // 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; #ifndef MULTI_REGION // draw comparison bar graph (upside down) x1 = startX; yZero = yGene + gtexGeneModelHeight() + 1; // yZero is at top of graph -drawGraphBase(hvg, keepX, yZero-1, geneInfo); +drawGraphBase(tg, geneInfo, hvg, keepX, yZero-1); -for (i=0; i<expCount; i++) +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)) { // 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 = geneInfo->medians2[i]; int height = valToClippedHeight(expScore, maxMedian, viewMax, gtexMaxGraphHeight(), doLogTransform); if (graphPadding == 0 || sameString(colorScheme, GTEX_COLORS_GTEX)) hvGfxBox(hvg, x1, yZero, barWidth, height, fillColorIx); else @@ -821,30 +868,32 @@ // 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); 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++) { + if (!filterTissue(tg, tissue->name)) + continue; double expScore = (geneInfo->medians1 ? geneInfo->medians1[i] : geneBed->expScores[i]); int height = valToClippedHeight(expScore, maxMedian, viewMax, gtexMaxGraphHeight(), doLogTransform); char *qualifier = NULL; if (extras->isComparison && extras->isDifference) qualifier = "F-M"; mapBoxHc(hvg, start, end, x1, yZero-height, barWidth, height, tg->track, mapItemName, tissueExpressionText(tissue, expScore, doLogTransform, qualifier)); // 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 + gtexGeneModelHeight() + gtexGeneMargin(); // y is top of bottom graph @@ -906,31 +955,32 @@ 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(geneInfo); +int graphWidth = gtexGraphWidth(tg, geneInfo); +int x; 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->freeItems = gtexGeneFreeItems; tg->mapItem = gtexGeneMapItem; tg->itemName = gtexGeneItemName; tg->mapItemName = gtexGeneItemName; tg->itemHeight = gtexGeneItemHeight; tg->itemStart = gtexGeneItemStart; tg->itemEnd = gtexGeneItemEnd;