f0add51e132dbab425e76cabc6626a31a74f47e9 kate Tue Apr 28 12:29:40 2020 -0700 Support TPM in GTEx V8 gene expression. refs #25130 diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c index 6a0ac36..0162d2b 100644 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@ -1,1185 +1,1188 @@ /* 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" #include "spaceSaver.h" enum geneLabelStyle { LABEL_GENE_SYMBOL = 0, LABEL_GENE_ACCESSION = 1, LABEL_BOTH = 2 }; static enum geneLabelStyle getLabelStyle(char *cartVar) /* Get enum corresponding to cart var */ { if (sameString(GTEX_LABEL_SYMBOL, cartVar)) return LABEL_GENE_SYMBOL; if (sameString(GTEX_LABEL_ACCESSION, cartVar)) return LABEL_GENE_ACCESSION; if (sameString(GTEX_LABEL_BOTH, cartVar)) return LABEL_BOTH; return LABEL_GENE_SYMBOL; } struct gtexGeneExtras /* Track info */ { char *version; /* Suffix to table name, e.g. 'V6' */ boolean codingOnly; /* User filter to limit display to coding genes */ boolean showExons; /* Show gene model exons */ boolean noWhiteout; /* Suppress whiteout of graph background (allow highlight, blue lines) */ enum geneLabelStyle labelStyle; /* Show gene symbol, accession, or both */ 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; /* Tissue names, descriptions */ int tissueCount; /* Tissue count - derived from above */ char **tissueNames; /* Tissue names by id - derived from above */ char **tissueLabels; /* Tissue labels by id - derived from above */ char **tissueDescriptions; /* Tissue descriptions by id - derived from above */ 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, type, exp count and medians from BED table */ struct genePred *geneModel; /* Gene structure from model table */ char *label; /* Name, accession, or both */ char *description; /* Gene description */ double *medians1; /* Computed medians */ double *medians2; /* Computed medians for comparison (inverse) graph */ int height; /* Item height in pixels */ }; #define MAX_DESC 200 /***********************************************/ /* Color gene models using GENCODE conventions */ static struct rgbColor codingColor = {12, 12, 120}; // #0C0C78 static struct rgbColor nonCodingColor = {0, 100, 0}; // #006400 static struct rgbColor pseudoColor = {255,51,255}; // #FF33FF static struct rgbColor problemColor = {254, 0, 0}; // #FE0000 static struct rgbColor unknownColor = {1, 1, 1}; static struct statusColors /* Color values for gene models */ { Color coding; Color nonCoding; Color pseudo; Color problem; Color unknown; } statusColors = {0,0,0,0}; static void initGeneColors(struct hvGfx *hvg) /* Get and cache indexes for color values */ { if (statusColors.coding != 0) return; statusColors.coding = hvGfxFindColorIx(hvg, codingColor.r, codingColor.g, codingColor.b); statusColors.nonCoding = hvGfxFindColorIx(hvg, nonCodingColor.r, nonCodingColor.g, nonCodingColor.b); statusColors.pseudo = hvGfxFindColorIx(hvg, pseudoColor.r, pseudoColor.g, pseudoColor.b); statusColors.problem = hvGfxFindColorIx(hvg, problemColor.r, problemColor.g, problemColor.b); statusColors.unknown = hvGfxFindColorIx(hvg, unknownColor.r, unknownColor.g, unknownColor.b); } static Color getGeneClassColor(struct hvGfx *hvg, struct gtexGeneBed *geneBed) /* Find GENCODE color for gene type. */ { initGeneColors(hvg); char *geneClass = gtexGeneClass(geneBed); if (geneClass == NULL) return statusColors.unknown; if (sameString(geneClass, "coding")) return statusColors.coding; if (sameString(geneClass, "nonCoding")) return statusColors.nonCoding; if (sameString(geneClass, "pseudo")) return statusColors.pseudo; return statusColors.unknown; } /***********************************************/ /* Cache tissue info */ struct gtexTissue *getTissues(struct track *tg, char *version) /* Get and cache tissue metadata from database */ { struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; if (!extras->tissues) extras->tissues = gtexGetTissues(version); return extras->tissues; } int getTissueCount(struct track *tg, char *version) /* Get and cache the number of tissues in GTEx tissue table */ { struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; if (!extras->tissueCount) extras->tissueCount = slCount(getTissues(tg, version)); return extras->tissueCount; } char *getTissueName(struct track *tg, int id, char *version) /* Get tissue name from id, cacheing */ { struct gtexTissue *tissue; int count = getTissueCount(tg, version); struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; if (!extras->tissueNames) { struct gtexTissue *tissues = getTissues(tg, version); AllocArray(extras->tissueNames, count); for (tissue = tissues; tissue != NULL; tissue = tissue->next) extras->tissueNames[tissue->id] = cloneString(tissue->name); } if (id >= count) errAbort("GTEx tissue table problem: can't find id %d\n", id); return extras->tissueNames[id]; } char *getTissueDescription(struct track *tg, int id, char *version) /* Get tissue description from id, cacheing */ { struct gtexTissue *tissue; int count = getTissueCount(tg, version); struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; if (!extras->tissueDescriptions) { struct gtexTissue *tissues = getTissues(tg, version); AllocArray(extras->tissueDescriptions, count); for (tissue = tissues; tissue != NULL; tissue = tissue->next) extras->tissueDescriptions[tissue->id] = cloneString(tissue->description); } if (id >= count) errAbort("GTEx tissue table problem: can't find id %d\n", id); return extras->tissueDescriptions[id]; } struct rgbColor *getGtexTissueColors(struct track *tg, char *version) /* Get RGB colors from tissue table */ { struct gtexTissue *tissues = getTissues(tg, version); struct gtexTissue *tissue = NULL; int count = getTissueCount(tg, version); struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; if (!extras->colors) { AllocArray(extras->colors, count); int i = 0; for (tissue = tissues; tissue != NULL; tissue = tissue->next) { // TODO: reconcile extras->colors[i] = (struct rgbColor){.r=COLOR_32_BLUE(tissue->color), .g=COLOR_32_GREEN(tissue->color), .b=COLOR_32_RED(tissue->color)}; //colors[i] = mgColorIxToRgb(NULL, tissue->color); i++; } } return extras->colors; } /*****************************************************************/ /* Load sample data, gene info, and anything else needed to draw */ static struct hash *loadGeneModels(char *table) /* Load gene models from table */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; sr = hRangeQuery(conn, table, chromName, winStart, winEnd, NULL, &rowOffset); struct hash *modelHash = newHash(0); struct genePred *model = NULL; while ((row = sqlNextRow(sr)) != NULL) { model = genePredLoad(row+rowOffset); hashAdd(modelHash, model->name, model); } sqlFreeResult(&sr); hFreeConn(&conn); return modelHash; } static void loadComputedMedians(struct track *tg, struct gtexGeneInfo *geneInfo) /* Compute medians based on graph type. Returns a list of 2 for comparison graph types */ { struct gtexGeneBed *geneBed = geneInfo->geneBed; int expCount = geneBed->expCount; struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; if (extras->isComparison) { // create two score hashes, one for each sample subset struct hash *scoreHash1 = hashNew(0), *scoreHash2 = hashNew(0); struct sqlConnection *conn = hAllocConn("hgFixed"); char query[1024]; char **row; sqlSafef(query, sizeof(query), "select gtexSampleData.sample, gtexDonor.gender, gtexSampleData.tissue, gtexSampleData.score from gtexSampleData, gtexSample, gtexDonor where gtexSampleData.geneId='%s' and gtexSampleData.sample=gtexSample.sampleId and gtexSample.donor=gtexDonor.name", geneBed->geneId); struct sqlResult *sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char gender = *row[1]; // TODO: generalize for other comparison graphs (this code just for M/F comparison) struct hash *scoreHash = ((gender == 'F') ? scoreHash1 : scoreHash2); char *tissue = cloneString(row[2]); struct slDouble *score = slDoubleNew(sqlDouble(row[3])); // create hash of lists of scores, keyed by tissue name double *tissueScores = hashFindVal(scoreHash, tissue); if (tissueScores) slAddHead(tissueScores, score); else hashAdd(scoreHash, tissue, score); } sqlFreeResult(&sr); hFreeConn(&conn); // get tissue medians for each sample subset double *medians1; double *medians2; AllocArray(medians1, expCount); AllocArray(medians2, expCount); int i; for (i=0; i<geneBed->expCount; i++) { //medians1[i] = -1, medians2[i] = -1; // mark missing tissues ? struct slDouble *scores; scores = hashFindVal(scoreHash1, getTissueName(tg, i, extras->version)); if (scores) medians1[i] = slDoubleMedian(scores); scores = hashFindVal(scoreHash2, getTissueName(tg, i, extras->version)); if (scores) medians2[i] = slDoubleMedian(scores); } if (extras->isDifference) { for (i=0; i<geneBed->expCount; i++) { if (medians1[i] >= medians2[i]) { medians1[i] -= medians2[i]; medians2[i] = 0; } else { medians2[i] -= medians1[i]; medians1[i] = 0; } } } geneInfo->medians1 = medians1; geneInfo->medians2 = medians2; } } static int gtexSquishItemHeight() /* Height of squished item (request to have it larger than usual) */ { return tl.fontHeight - tl.fontHeight/2; } static int gtexGeneBoxModelHeight() /* Height of indicator box drawn under graph to show gene extent */ { long winSize = virtWinBaseCount; //FIXME: dupes!! #define WIN_MAX_GRAPH 50000 #define WIN_MED_GRAPH 500000 #define MAX_GENE_BOX_HEIGHT 2 #define MED_GENE_BOX_HEIGHT 2 #define MIN_GENE_BOX_HEIGHT 1 if (winSize < WIN_MAX_GRAPH) return MAX_GENE_BOX_HEIGHT; else if (winSize < WIN_MED_GRAPH) return MED_GENE_BOX_HEIGHT; else return MIN_GENE_BOX_HEIGHT; } 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(tg, extras->version); 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 int maxTissueForGene(struct gtexGeneBed *geneBed) /* Return id of highest expressed tissue for gene, if significantly higher than median. * If none are over threshold, return -1 */ { double maxScore = 0.0, expScore; double totalScore = 0.0; int maxNum = 0, i; int expCount = geneBed->expCount; for (i=0; i<expCount; i++) { expScore = geneBed->expScores[i]; if (expScore > maxScore) { maxScore = max(maxScore, expScore); maxNum = i; } totalScore += expScore; } // threshold to consider this gene tissue specific -- a tissue contributes > 10% to // total expression level if (totalScore < 1 || maxScore <= totalScore * .1) return -1; return maxNum; } static Color gtexGeneItemColor(struct track *tg, void *item, struct hvGfx *hvg) /* A bit of tissue-specific coloring in squish mode only, on geneBed item */ { struct gtexGeneBed *geneBed = (struct gtexGeneBed *)item; int id = maxTissueForGene(geneBed); if (id < 0) return MG_BLACK; struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; struct rgbColor color = extras->colors[id]; return hvGfxFindColorIx(hvg, color.r, color.g, color.b); } static void gtexGeneLoadItems(struct track *tg) /* Load method for track items */ { /* Initialize colors for visibilities that don't display actual barchart */ if (tg->visibility == tvSquish || tg->limitedVis == tvSquish) tg->itemColor = gtexGeneItemColor; tg->colorShades = shadesOfGray; /* Get track UI info */ struct gtexGeneExtras *extras; AllocVar(extras); tg->extraUiData = extras; /* Get version info from track table name */ extras->version = gtexVersionSuffix(tg->table); 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(extras->version); extras->codingOnly = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, GTEX_CODING_GENE_FILTER, GTEX_CODING_GENE_FILTER_DEFAULT); extras->showExons = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, GTEX_SHOW_EXONS, GTEX_SHOW_EXONS_DEFAULT); extras->noWhiteout = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, GTEX_NO_WHITEOUT, GTEX_NO_WHITEOUT_DEFAULT); extras->labelStyle = getLabelStyle(cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_LABEL, GTEX_LABEL_DEFAULT)); /* Get geneModels in range */ char buf[256]; char *modelTable = "gtexGeneModel"; safef(buf, sizeof(buf), "%s%s", modelTable, extras->version ? extras->version: ""); struct hash *modelHash = loadGeneModels(buf); /* Get geneBeds (names and all-sample tissue median scores) in range */ char *filter = getScoreFilterClause(cart, tg->tdb, NULL); bedLoadItemWhere(tg, tg->table, filter, (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 */ #ifdef COLOR_SCHEME char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS, GTEX_COLORS_DEFAULT); #else char *colorScheme = GTEX_COLORS_DEFAULT; #endif if (sameString(colorScheme, GTEX_COLORS_GTEX)) { extras->colors = getGtexTissueColors(tg, extras->version); } else { if (geneBed) { int expCount = geneBed->expCount; extras->colors = getRainbow(&saturatedRainbowAtPos, expCount); } } filterTissues(tg); while (geneBed != NULL) { if (extras->codingOnly && !gtexGeneIsCoding(geneBed)) { // apologies for messy short-circuit geneBed = geneBed->next; continue; } AllocVar(geneInfo); geneInfo->geneBed = geneBed; // set label if (extras->labelStyle == LABEL_GENE_SYMBOL) geneInfo->label = geneBed->name; else if (extras->labelStyle == LABEL_GENE_ACCESSION) geneInfo->label = geneBed->geneId; else if (extras->labelStyle == LABEL_BOTH) { char buf[256]; safef(buf, sizeof(buf), "%s/%s", geneBed->name, geneBed->geneId); geneInfo->label = cloneString(buf); } else geneInfo->label = ""; // get description geneInfo->geneModel = hashFindVal(modelHash, geneBed->geneId); // sometimes this is missing, hash returns NULL. do we check? // NOTE: Consider loading all gene descriptions to save queries char query[256]; sqlSafef(query, sizeof(query), "select kgXref.description from kgXref where geneSymbol='%s'", geneBed->name); struct sqlConnection *conn = hAllocConn(database); char *desc = sqlQuickString(conn, query); hFreeConn(&conn); if (desc) { // hg38 known genes has extra detail about source; strip it char *fromDetail = strstrNoCase(desc, "(from"); if (fromDetail) *fromDetail = 0; if (strlen(desc) > MAX_DESC) strcpy(desc+MAX_DESC, "..."); // also strip 'homo sapiens' prefix #define SPECIES_PREFIX "Homo sapiens " if (startsWith(SPECIES_PREFIX, desc)) desc += strlen(SPECIES_PREFIX); geneInfo->description = desc; } else geneInfo->description = geneInfo->geneBed->name; 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(tg, geneInfo); geneInfo->height = gtexGeneItemHeight(tg, geneInfo); } slReverse(&list); tg->items = list; } /***********************************************/ /* Draw */ /* Bargraph layouts for three window sizes */ #define WIN_MAX_GRAPH 50000 #define MAX_GRAPH_HEIGHT 175 #define MAX_BAR_WIDTH 5 #define MAX_GRAPH_PADDING 2 #define WIN_MED_GRAPH 500000 #define MED_GRAPH_HEIGHT 100 #define MED_BAR_WIDTH 3 #define MED_GRAPH_PADDING 1 #define MIN_BAR_WIDTH 1 #define MIN_GRAPH_PADDING 0 #define MARGIN_WIDTH 1 static int gtexBarWidth() { 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 enum trackVisibility gtexGeneModelVis(struct gtexGeneExtras *extras) { if (!extras->showExons) return tvSquish; long winSize = virtWinBaseCount; if (winSize < WIN_MED_GRAPH && !extras->isComparison) return tvPack; return tvSquish; } static int gtexGeneModelHeight(struct gtexGeneExtras *extras) { if (!extras->showExons) return gtexGeneBoxModelHeight()+3; enum trackVisibility vis = gtexGeneModelVis(extras); if (vis == tvSquish) return trunc(tl.fontHeight/2) + 1; return tl.fontHeight; } static int gtexGraphPadding() { 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() { long winSize = virtWinBaseCount; if (winSize < WIN_MAX_GRAPH) return MAX_GRAPH_HEIGHT; else if (winSize < WIN_MED_GRAPH) return MED_GRAPH_HEIGHT; else return tl.fontHeight * 4; } 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. */ { int start = max(gtex->chromStart, winStart); double scale = scaleForWindow(insideWidth, winStart, winEnd); int x1 = round((start - winStart) * scale); return x1; } static int gtexGeneMargin() { return 1; } static int valToHeight(double val, double maxVal, int maxHeight, boolean doLogTransform) /* Log-scale and convert a value from 0 to maxVal to 0 to maxHeight-1 */ { if (val == 0.0) return 0; double scaled = 0.0; if (doLogTransform) scaled = log10(val+1.0) / log10(maxVal+1.0); else scaled = val/maxVal; if (scaled < 0) warn("scaled=%f\n", scaled); return (scaled * (maxHeight-1)); } 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 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 (!filterTissue(tg, getTissueName(tg, i, extras->version))) continue; 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_VIEW_LIMIT, GTEX_MAX_VIEW_LIMIT_DEFAULT); double maxMedian = ((struct gtexGeneExtras *)tg->extraUiData)->maxMedian; return valToClippedHeight(maxExp, maxMedian, viewMax, gtexMaxGraphHeight(), extras->doLogTransform); } static void drawGraphBox(struct track *tg, struct gtexGeneInfo *geneInfo, struct hvGfx *hvg, int x, int y) /* Draw white background for graph */ { Color lighterGray = MAKECOLOR_32(0xF3, 0xF3, 0xF3); int width = gtexGraphWidth(tg, geneInfo); int height = gtexGeneGraphHeight(tg, geneInfo, TRUE); hvGfxOutlinedBox(hvg, x, y-height, width, height, MG_WHITE, lighterGray); } 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(tg, geneInfo); hvGfxBox(hvg, x, y, graphWidth, 1, lightGray); } 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 gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; struct gtexGeneBed *geneBed = geneInfo->geneBed; if (vis == tvDense) { bedDrawSimpleAt(tg, geneBed, hvg, xOff, y, scale, font, MG_WHITE, vis); // color ignored (using grayscale) return; } if (vis == tvSquish) { Color color = gtexGeneItemColor(tg, geneBed, hvg); int height = gtexSquishItemHeight(); drawScaledBox(hvg, geneBed->chromStart, geneBed->chromEnd, scale, xOff, y, height, color); return; } 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(); int heightPer = tg->heightPer; tg->heightPer = gtexGeneModelHeight(extras); Color statusColor = getGeneClassColor(hvg, geneBed); if (geneInfo->geneModel && extras->showExons) { struct linkedFeatures *lf = linkedFeaturesFromGenePred(tg, geneInfo->geneModel, FALSE); lf->filterColor = statusColor; linkedFeaturesDrawAt(tg, lf, hvg, xOff, yGene-1, scale, font, color, gtexGeneModelVis(extras)); } else { int height = gtexGeneBoxModelHeight(); drawScaledBox(hvg, geneBed->chromStart, geneBed->chromEnd, scale, xOff, yGene+1, height, statusColor); } 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) { if (vis != tvFull && vis != tvPack) return; struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; 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); if (!extras->noWhiteout) drawGraphBox(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 if (geneInfo->medians2) { hvGfxText(hvg, x1, yZero - tl.fontHeight + 2, labelColor, font, "F"); hvGfxText(hvg, x1, yZero + gtexGeneModelHeight(extras) + gtexGeneMargin() + 1, labelColor, font, "M"); startX = startX + tl.mWidth+2; x1 = startX; } // draw bar graph double viewMax = (double)cartUsualIntClosestToHome(cart, tg->tdb, FALSE, GTEX_MAX_VIEW_LIMIT, GTEX_MAX_VIEW_LIMIT_DEFAULT); double maxMedian = ((struct gtexGeneExtras *)tg->extraUiData)->maxMedian; int i; int expCount = geneBed->expCount; 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(), 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, 2, clipColor); x1 = x1 + barWidth + graphPadding; } if (!geneInfo->medians2) return; // draw comparison bar graph (upside down) x1 = startX; yZero = yGene + gtexGeneModelHeight(extras) + 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)) { // brighten colors a bit so they'll be more visible at this scale struct hslColor hsl = mgRgbToHsl(fillColor); hsl.s = min(1000, hsl.s + 200); 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(), 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); // mark clipped bar with magenta tip if (!extras->doLogTransform && expScore > viewMax) hvGfxBox(hvg, x1, yZero + height-1, barWidth, 2, clipColor); x1 = x1 + barWidth + graphPadding; } } static int gtexGeneItemHeightOptionalMax(struct track *tg, void *item, boolean isMax) { // It seems that this can be called early or late enum trackVisibility vis = tg->visibility; if (tg->limitedVisSet) vis = tg->limitedVis; int height; if (vis == tvSquish || vis == tvDense) { if (vis == tvSquish) { tg->lineHeight = gtexSquishItemHeight(); tg->heightPer = tg->lineHeight; } height = tgFixedItemHeight(tg, item); return height; } struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; if (isMax) { int extra = 0; if (((struct gtexGeneExtras *)tg->extraUiData)->isComparison) extra = gtexMaxGraphHeight() + 2; height= gtexMaxGraphHeight() + gtexGeneMargin() + gtexGeneModelHeight(extras) + extra; return height; } 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(); } height = topGraphHeight + bottomGraphHeight + gtexGeneMargin() + gtexGeneModelHeight(extras); return height; } static int gtexGeneItemHeight(struct track *tg, void *item) { int height = gtexGeneItemHeightOptionalMax(tg, item, FALSE); return height; } static char *tissueExpressionText(struct gtexTissue *tissue, double expScore, - boolean doLogTransform, char *qualifier) + boolean doLogTransform, char *qualifier, char *version) /* Construct mouseover text for tissue graph */ { static char buf[128]; -doLogTransform = FALSE; // for now, always display expression level on graph as raw RPKM -safef(buf, sizeof(buf), "%s (%.1f %s%s%sRPKM)", tissue->description, +doLogTransform = FALSE; // for now, always display expression level on graph as raw RPKM/TPM +safef(buf, sizeof(buf), "%s (%.1f %s%s%s%s)", tissue->description, doLogTransform ? log10(expScore+1.0) : expScore, qualifier != NULL ? qualifier : "", qualifier != NULL ? " " : "", - doLogTransform ? "log " : ""); + doLogTransform ? "log " : "", + sameString(version, "V8") ? "TPM" : "RPKM"); return buf; } static void getItemX(int start, int end, int *x1, int *x2) /* Return startX, endX based on item coordinates and current window */ // Residual (largely replaced by drawScaledBox -- still used by gene model bmap box { int s = max(start, winStart); int e = min(end, winEnd); double scale = scaleForWindow(insideWidth, winStart, winEnd); assert(x1); *x1 = round((double)((int)s-winStart)*scale + insideX); assert(x2); *x2 = round((double)((int)e-winStart)*scale + insideX); } 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); } 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 full mode. Just single map for squish/dense modes */ { if (tg->limitedVis == tvDense) { genericMapItem(tg, hvg, item, itemName, itemName, start, end, x, y, width, height); return; } struct gtexGeneInfo *geneInfo = item; struct gtexGeneBed *geneBed = geneInfo->geneBed; struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; int geneStart = geneBed->chromStart; int geneEnd = geneBed->chromEnd; if (tg->limitedVis == tvSquish) { int tisId = maxTissueForGene(geneBed); char *maxTissue = ""; if (tisId > 1) maxTissue = getTissueDescription(tg, tisId, extras->version); char buf[128]; safef(buf, sizeof buf, "%s %s", geneBed->name, maxTissue); int x1, x2; getItemX(geneStart, geneEnd, &x1, &x2); int width = max(1, x2-x1); mapBoxHc(hvg, geneStart, geneEnd, x1, y, width, height, tg->track, mapItemName, buf); return; } int topGraphHeight = gtexGeneGraphHeight(tg, geneInfo, TRUE); topGraphHeight = max(topGraphHeight, tl.fontHeight); // label int yZero = topGraphHeight + y - 1; // yZero is bottom of graph int x1 = insideX; // add maps to tissue bars in expresion graph struct gtexTissue *tissues = getTissues(tg, extras->version); struct gtexTissue *tissue = NULL; 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 x1 = insideX + graphX; if (geneInfo->medians2) { // skip over labels in comparison graphs x1 = x1 + tl.mWidth+ 2; } int i = 0; double viewMax = (double)cartUsualIntClosestToHome(cart, tg->tdb, FALSE, GTEX_MAX_VIEW_LIMIT, GTEX_MAX_VIEW_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(), extras->doLogTransform); char *qualifier = NULL; if (extras->isComparison && extras->isDifference) qualifier = "F-M"; mapBoxHc(hvg, geneStart, geneEnd, x1, yZero-height, barWidth, height, tg->track, mapItemName, - tissueExpressionText(tissue, expScore, extras->doLogTransform, qualifier)); + tissueExpressionText(tissue, expScore, extras->doLogTransform, qualifier, + extras->version)); // add map box to comparison graph if (geneInfo->medians2) { double expScore = geneInfo->medians2[i]; int height = valToClippedHeight(expScore, maxMedian, viewMax, gtexMaxGraphHeight(), extras->doLogTransform); int y = yZero + gtexGeneModelHeight(extras) + gtexGeneMargin(); // y is top of bottom graph if (extras->isComparison && extras->isDifference) qualifier = "M-F"; mapBoxHc(hvg, geneStart, geneEnd, x1, y, barWidth, height, tg->track, mapItemName, - tissueExpressionText(tissue, expScore, extras->doLogTransform, qualifier)); + tissueExpressionText(tissue, expScore, extras->doLogTransform, qualifier, + extras->version)); } x1 = x1 + barWidth + padding; } // add map boxes with description to gene model if (geneInfo->geneModel && geneInfo->description) { // perhaps these are just start, end ? int itemStart = geneInfo->geneModel->txStart; int itemEnd = gtexGeneItemEnd(tg, item); int x1, x2; getItemX(itemStart, itemEnd, &x1, &x2); int w = x2-x1; int labelWidth = mgFontStringWidth(tl.font, itemName); if (x1-labelWidth <= insideX) labelWidth = 0; // map over label int itemHeight = geneInfo->height; mapBoxHc(hvg, geneStart, geneEnd, x1-labelWidth, y, labelWidth, itemHeight-3, tg->track, mapItemName, geneInfo->description); // map over gene model (extending to end of item) int geneModelHeight = gtexGeneModelHeight(extras); mapBoxHc(hvg, geneStart, geneEnd, x1, y+itemHeight-geneModelHeight-3, w, geneModelHeight, tg->track, mapItemName, geneInfo->description); } } static char *gtexGeneItemName(struct track *tg, void *item) /* Return gene name */ { struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; return geneInfo->label; } 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; int lineHeight = 0; int heightPer = 0; if (vis == tvDense) { heightPer = tl.fontHeight; lineHeight=heightPer+1; } else if (vis == tvSquish) { // for visibility, set larger than the usual squish, which is half font height heightPer = gtexSquishItemHeight() * 2; // the squish packer halves this lineHeight=heightPer+1; } else if ((vis == tvPack) || (vis == tvFull)) { // layout -- initially as fixed height heightPer = tl.fontHeight; lineHeight=heightPer; } height = tgFixedTotalHeightOptionalOverflow(tg, vis, lineHeight, heightPer, FALSE); if ((vis == tvPack) || (vis == tvFull)) { // set variable height rows if (tg->ss && tg->ss->rowCount != 0) { if (!tg->ss->rowSizes) { // 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; } struct spaceSaver *ss = findSpaceSaver(tg, vis); // ss is a list now assert(ss); // viz matches, we have the right one height = spaceSaverGetRowHeightsTotal(ss); } } tg->height = height; return height; } static void gtexGenePreDrawItems(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) { if (vis == tvSquish || vis == tvDense) { // NonProp routines not relevant to these modes, and they interfere // NOTE: they must be installed by gtexGeneMethods() for pack mode tg->nonPropDrawItemAt = NULL; tg->nonPropPixelWidth = NULL; } } void gtexGeneMethods(struct track *tg) /* Install handlers for GTEx Gene track */ { tg->drawItemAt = gtexGeneDrawAt; tg->preDrawItems = gtexGenePreDrawItems; 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; } void gtexEqtlTissueMethods(struct track *tg) /* Install handler for GTEx eQTL Tissues track */ { tg->itemNameColor = blackItemNameColor; }