5e84c54c00824bb9ddacfd439db694906328fc61 Merge parents 5e5b469 f42dec5 kate Tue Nov 24 09:55:57 2015 -0800 Fix merge conflict diff --cc src/hg/hgTracks/gtexTracks.c index 5ed3184,19197c0..2d12b65 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@@ -240,75 -238,39 +240,77 @@@ } } } 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; + extras->doLogTransform = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, GTEX_LOG_TRANSFORM, + GTEX_LOG_TRANSFORM_DEFAULT); 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; extras->maxMedian = gtexMaxMedianScore(NULL); /* Get geneModels in range */ //TODO: version the table name, move to lib char *modelTable = "gtexGeneModel"; struct hash *modelHash = loadGeneModels(modelTable); @@@ -463,185 -424,178 +465,183 @@@ 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) + static int gtexGeneGraphHeight(struct track *tg, struct gtexGeneInfo *geneInfo, 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; + struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; int i; double maxExp = 0.0; int expCount = geneBed->expCount; double expScore; for (i=0; i<expCount; i++) { if (doTop) expScore = (geneInfo->medians1 ? geneInfo->medians1[i] : geneBed->expScores[i]); else expScore = geneInfo->medians2[i]; maxExp = max(maxExp, expScore); } double viewMax = (double)cartUsualIntClosestToHome(cart, tg->tdb, FALSE, GTEX_MAX_LIMIT, GTEX_MAX_LIMIT_DEFAULT); double maxMedian = ((struct gtexGeneExtras *)tg->extraUiData)->maxMedian; - return valToClippedHeight(maxExp, maxMedian, viewMax, gtexMaxGraphHeight(), doLogTransform); + return valToClippedHeight(maxExp, maxMedian, viewMax, gtexMaxGraphHeight(), extras->doLogTransform); } static void gtexGeneDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, 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; } int heightPer = tg->heightPer; int graphX = gtexGraphX(geneBed); if (graphX < 0) return; - int topGraphHeight = gtexGeneGraphHeight(tg, geneInfo, doLogTransform, TRUE); + int topGraphHeight = gtexGeneGraphHeight(tg, geneInfo, 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); + 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 (!doLogTransform && expScore > viewMax) + if (!extras->doLogTransform && expScore > viewMax) hvGfxBox(hvg, x1, yZero-height+1, barWidth, 1, clipColor); x1 = x1 + barWidth + graphPadding; } #endif // 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); + extras->doLogTransform); if (graphPadding == 0 || sameString(colorScheme, GTEX_COLORS_GTEX)) hvGfxBox(hvg, x1, yZero, barWidth, height, fillColorIx); else hvGfxOutlinedBox(hvg, x1, yZero, barWidth, height, fillColorIx, lineColorIx); - if (!doLogTransform && expScore > viewMax) + if (!extras->doLogTransform && expScore > viewMax) hvGfxBox(hvg, x1, yZero + height, barWidth, 1, clipColor); x1 = x1 + barWidth + graphPadding; } #endif } #ifdef MULTI_REGION 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(geneInfo); return graphWidth; } #endif @@@ -829,90 -781,105 +827,107 @@@ 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 for each tissue (bar in the graph) or a single map for squish/dense modes */ + /* 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; + 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 struct gtexTissue *tissues = getTissues(); struct gtexTissue *tissue = NULL; - struct gtexGeneInfo *geneInfo = item; - struct gtexGeneBed *geneBed = geneInfo->geneBed; int barWidth = gtexBarWidth(); int padding = gtexGraphPadding(); double maxMedian = ((struct gtexGeneExtras *)tg->extraUiData)->maxMedian; int graphX = gtexGraphX(geneBed); if (graphX < 0) return; + // x1 is at left of graph - int x1 = insideX + graphX; + 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); - 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); + gtexMaxGraphHeight(), extras->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)); + tissueExpressionText(tissue, expScore, extras->doLogTransform, qualifier)); // add map box to comparison graph if (geneInfo->medians2) { double expScore = geneInfo->medians2[i]; int height = valToClippedHeight(expScore, maxMedian, viewMax, - gtexMaxGraphHeight(), doLogTransform); + gtexMaxGraphHeight(), extras->doLogTransform); int y = yZero + gtexGeneModelHeight() + gtexGeneMargin(); // y is top of bottom graph if (extras->isComparison && extras->isDifference) qualifier = "M-F"; mapBoxHc(hvg, start, end, x1, y, barWidth, height, tg->track, mapItemName, - tissueExpressionText(tissue, expScore, doLogTransform, qualifier)); + tissueExpressionText(tissue, expScore, extras->doLogTransform, qualifier)); } 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) { @@@ -955,32 -922,31 +970,31 @@@ 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;