1bd7f92d8aab55d8344619031c510ba8ad6b92fd kate Fri Nov 20 04:41:21 2015 -0800 Add map boxes with mouseover showing gene description to labe and gene model. Still needs some work on extent. refs #15645 diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c index f6fbbbc..19197c0 100644 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@ -1,945 +1,961 @@ /* 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 WARNING: These sections // are a bit out-of-date (refer to #ifndef MULTI code when integrating) struct gtexGeneExtras /* Track info */ { double maxMedian; /* Maximum median rpkm for all tissues */ boolean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). */ 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 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 */ { Color coding; Color noncoding; 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.problem = hvGfxFindColorIx(hvg, problemColor.r, problemColor.g, problemColor.b); statusColors.unknown = hvGfxFindColorIx(hvg, unknownColor.r, unknownColor.g, unknownColor.b); } static Color getTranscriptStatusColor(struct hvGfx *hvg, struct gtexGeneBed *geneBed) /* Find GENCODE color for transcriptClass of canonical transcript */ { initGeneColors(hvg); if (geneBed->transcriptClass == NULL) return statusColors.unknown; if (sameString(geneBed->transcriptClass, "coding")) return statusColors.coding; if (sameString(geneBed->transcriptClass, "nonCoding")) return statusColors.noncoding; if (sameString(geneBed->transcriptClass, "problem")) return statusColors.problem; return statusColors.unknown; } /***********************************************/ /* Cache tissue info */ struct gtexTissue *getTissues() /* Get and cache tissue metadata from database */ { static struct gtexTissue *gtexTissues = NULL; if (!gtexTissues) gtexTissues = gtexGetTissues(); return gtexTissues; } int getTissueCount() /* Get and cache the number of tissues in GTEx tissue table */ { static int tissueCount = 0; if (!tissueCount) tissueCount = slCount(getTissues()); return tissueCount; } char *getTissueName(int id) /* Get tissue name from id, cacheing */ { static char **tissueNames = NULL; struct gtexTissue *tissue; int count = getTissueCount(); if (!tissueNames) { struct gtexTissue *tissues = getTissues(); AllocArray(tissueNames, count); for (tissue = tissues; tissue != NULL; tissue = tissue->next) tissueNames[tissue->id] = cloneString(tissue->name); } if (id >= count) errAbort("GTEx tissue table problem: can't find id %d\n", id); return tissueNames[id]; } struct rgbColor *getGtexTissueColors() /* Get RGB colors from tissue table */ { struct gtexTissue *tissues = getTissues(); struct gtexTissue *tissue = NULL; int count = slCount(tissues); struct rgbColor *colors; AllocArray(colors, count); int i = 0; for (tissue = tissues; tissue != NULL; tissue = tissue->next) { // TODO: reconcile 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 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 gtexGeneInfo *geneInfo, struct gtexGeneExtras *extras) /* Compute medians based on graph type. Returns a list of 2 for comparison graph types */ { struct gtexGeneBed *geneBed = geneInfo->geneBed; int expCount = geneBed->expCount; 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(i)); if (scores) medians1[i] = slDoubleMedian(scores); scores = hashFindVal(scoreHash2, getTissueName(i)); 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; } 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; +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); /* Get geneBeds (names and all-sample tissue median scores) in range */ bedLoadItem(tg, tg->table, (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 */ 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); } 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 #define MED_GRAPH_HEIGHT 60 #define MED_BAR_WIDTH 3 #define MED_GRAPH_PADDING 1 #define MIN_GRAPH_HEIGHT 20 #define MIN_BAR_WIDTH 1 #define MIN_GRAPH_PADDING 0 #define MARGIN_WIDTH 1 static int gtexBarWidth() { #ifdef MULTI_REGION int winSize = virtWinBaseCount; // GALT CHANGED OLD winEnd - winStart; #else int winSize = winEnd - winStart; #endif 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 int gtexGraphPadding() { #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_PADDING; else if (winSize < WIN_MED_GRAPH) return MED_GRAPH_PADDING; else return MIN_GRAPH_PADDING; } 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) /* Width of GTEx graph in pixels */ { int barWidth = gtexBarWidth(); int padding = gtexGraphPadding(); struct gtexGeneBed *geneBed = geneInfo->geneBed; int count = geneBed->expCount; 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() { return 8; } 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 void drawGraphBase(struct hvGfx *hvg, int x, int y, struct gtexGeneInfo *geneInfo) /* 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); 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); 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 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); 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 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 #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; } 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) // TODO: skip missing bars Color lightGray = MAKECOLOR_32(0xD1, 0xD1, 0xD1); int graphWidth = gtexGraphWidth(geneInfo); hvGfxBox(hvg, x1, yZero+1, graphWidth, 1, lightGray); int barWidth = gtexBarWidth(); int graphPadding = gtexGraphPadding(); char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS, GTEX_COLORS_DEFAULT); Color labelColor = MG_GRAY; if (geneInfo->medians2) { // add labels to comparison graphs // TODO: generalize hvGfxText(hvg, x1, yZero-tl.fontHeight, labelColor, font, "F"); hvGfxText(hvg, x1, yZero + gtexGeneModelHeight() + gtexGeneMargin(), labelColor, font, "M"); startX = startX + tl.mWidth + 2; x1 = startX; } 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 = valToHeight(expScore, maxMedian, gtexMaxGraphHeight(), doLogTransform); + int height = valToHeight(expScore, maxMedian, gtexMaxGraphHeight(), extras->doLogTransform); if (graphPadding == 0 || sameString(colorScheme, GTEX_COLORS_GTEX)) hvGfxBox(hvg, x1, yZero-height, barWidth, height, fillColorIx); else hvGfxOutlinedBox(hvg, x1, yZero-height, barWidth, height, fillColorIx, lineColorIx); x1 = x1 + barWidth + graphPadding; } // mark gene extent int yGene = yZero + gtexGeneMargin() - 1; /* GALT NOT DONE HERE NOW // draw gene model tg->heightPer = gtexGeneModelHeight()+1; struct linkedFeatures *lf = linkedFeaturesFromGenePred(tg, geneInfo->geneModel, FALSE); lf->filterColor = statusColor; // GALT linkedFeaturesDrawAt(tg, lf, hvg, xOff, yGene, scale, font, color, tvSquish); tg->heightPer = heightPer; */ if (!geneInfo->medians2) return; // draw comparison graph (upside down) x1 = startX; yZero = yGene + gtexGeneModelHeight(); // yZero is at top of graph 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 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 = valToHeight(expScore, maxMedian, gtexMaxGraphHeight(), doLogTransform); + int height = valToHeight(expScore, maxMedian, 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); x1 = x1 + barWidth + graphPadding; } } #endif 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); +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, doLogTransform, FALSE), + bottomGraphHeight = max(gtexGeneGraphHeight(tg, geneInfo, 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) { return gtexGeneItemHeightOptionalMax(tg, item, FALSE); } 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); genericDrawNextItem(tg, item, hvg, xOff, y, scale, color, vis); int height = gtexGeneItemHeight(tg, item); y += height; } } void gtexGeneDrawItems(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, which are of variable height so require custom layout in full * and pack modes */ { if (vis == tvDense || vis == tvSquish) genericDrawItems(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); else if (vis == tvFull) gtexGeneDrawItemsFull(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); else if (vis == tvPack) genericDrawItems(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); } 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++) { 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) { 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) { 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 */ { struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; struct gtexGeneBed *geneBed = geneInfo->geneBed; double scale = scaleForWindow(insideWidth, winStart, winEnd); int graphWidth = gtexGraphWidth(geneInfo); 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; tg->totalHeight = gtexGeneTotalHeight; #ifdef MULTI_REGION tg->nonPropDrawItemAt = gtexGeneNonPropDrawAt; tg->nonPropPixelWidth = gtexGeneNonPropPixelWidth; #endif }