2eb99e0866866ceddb4a2cce801a37bb0df7997e kate Wed Oct 21 17:59:25 2015 -0700 Cleanup trackUi in prep for merging into main. refs #15645 diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c index 390c029..ea9436b 100644 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@ -1,886 +1,886 @@ /* GTEX 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" #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 //#define GENCODE_CODING_COLOR 0x0c0c78 // rgb(12,12,120) //#define GENCODE_NONCODING_COLOR 0x006400 // rgb(0,100,0) //#define GENCODE_PROBLEM_COLOR 0xfe000 //rgb(254,0,0) #define GENCODE_CODING_COLOR "12,12,120" #define GENCODE_NONCODING_COLOR "0,100,0" #define GENCODE_PROBLEM_COLOR "254,0,0" #define UNKNOWN_COLOR "1,1,1" static struct statusColors { Color coding; Color nonCoding; Color problem; Color unknown; } statusColors = {0,0,0}; struct gtexGeneExtras /* Track info */ { double maxMedian; char *graphType; boolean isComparison; struct rgbColor *colors; }; 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 */ }; static int findColorIx(struct hvGfx *hvg, char *rgb) { unsigned char red, green, blue; parseColor(rgb, &red, &green, &blue); return (hvGfxFindColorIx(hvg, red, green, blue)); //return MAKECOLOR_32(red, green, blue); } static void initGeneColors(struct hvGfx *hvg) { if (statusColors.coding != 0) return; statusColors.coding = findColorIx(hvg, GENCODE_CODING_COLOR); statusColors.nonCoding = findColorIx(hvg, GENCODE_NONCODING_COLOR); statusColors.problem = findColorIx(hvg, GENCODE_PROBLEM_COLOR); statusColors.unknown = findColorIx(hvg, UNKNOWN_COLOR); } 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; } 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 gtexGraphHeight() { #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; // TODO: save labels in extras int labelWidth = geneInfo->medians2 ? 5 : 0; return (barWidth * count) + (padding * (count-1)) + labelWidth + 2; ; } 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 */ // TODO: support linear or log scale { if (val == 0.0) return 0; // smallest counts are 1x10e-3, translate to counter negativity //double scaled = (log10(val) + 3.001)/(log10(maxVal) + 3.001); 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); //uglyf("%.2f -> %.2f height %d", val, scaled, (int)scaled * (maxHeight-1)); return (scaled * (maxHeight-1)); } // TODO: whack this static int valToY(double val, double maxVal, int maxHeight) /* Convert a value from 0 to maxVal to 0 to height-1 */ { if (val == 0.0) return 0; //double scaled = (log10(val)+3.001)/(log10(maxVal)+3.001); double scaled = log10(val+1.0) / log10(maxVal+1.0); if (scaled < 0) warn("scaled=%f\n", scaled); int y = scaled * (maxHeight); //uglyf("%.2f -> %.2f height %d", val, scaled, (int)scaled * (maxHeight-1)); return (maxHeight-1) - y; } /* Cache tissue metadata */ 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; } 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); //int end = min(gtex->chromEnd, winEnd); //if (start > end) //return -1; double scale = scaleForWindow(insideWidth, winStart, winEnd); int x1 = round((start - winStart) * scale); //int x2 = round((end - winStart) * scale); //int width = gtexGraphWidth(gtex); //if (x1 + width > x2) //return -1; return x1; } static int gtexGeneHeight() { return 8; } static int gtexGeneMargin() { return 1; } /* Track info generated during load, used by draw */ static void loadComputedMedians(struct gtexGeneInfo *geneInfo, struct gtexGeneExtras *extras) /* Compute medians based on graph type. Returns a list of 2 for comparison graph types */ /* TODO: add support for filter function */ { struct gtexGeneBed *geneBed = geneInfo->geneBed; int expCount = geneBed->expCount; //char *graphType = extras->graphType; 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]; 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); } geneInfo->medians1 = medians1; geneInfo->medians2 = medians2; } } 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 gtexGeneLoadItems(struct track *tg) { // Get track UI info struct gtexGeneExtras *extras; AllocVar(extras); tg->extraUiData = extras; // TODO: move test to lib -char *graphType = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_GRAPH, - GTEX_GRAPH_DEFAULT); -extras->graphType = cloneString(graphType); -if (sameString(graphType, GTEX_GRAPH_AGE) || sameString(graphType, GTEX_GRAPH_SEX)) +char *samples = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_SAMPLES, + GTEX_SAMPLES_DEFAULT); +extras->graphType = cloneString(samples); +if (sameString(samples, GTEX_SAMPLES_COMPARE_SEX)) extras->isComparison = TRUE; extras->maxMedian = gtexMaxMedianScore(NULL); // Construct track items // Get geneModels in range //TODO: version the table name ? 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); uglyf("Loaded %d gtexGene items<BR>\n", slCount(tg->items)); // Create geneInfo items with BED and geneModels attached struct gtexGeneInfo *geneInfo = NULL, *list = NULL; struct gtexGeneBed *geneBed = (struct gtexGeneBed *)tg->items; char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS, GTEX_COLORS_DEFAULT); if (sameString(colorScheme, GTEX_COLORS_GTEX)) { // retrieve from table extras->colors = getGtexTissueColors(); } else { // currently the only other choice int expCount = geneBed->expCount; extras->colors = getRainbow(&saturatedRainbowAtPos, expCount); //colors = getRainbow(&lightRainbowAtPos, 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; } slReverse(&list); tg->items = list; } static void gtexGeneDrawAt(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; 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; } struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; if (extras->isComparison && (tg->visibility == tvFull || tg->visibility == tvPack)) //&& gtexGraphHeight() != MIN_GRAPH_HEIGHT) // compute medians based on configuration (comparisons, and later, filters) loadComputedMedians(geneInfo, extras); int heightPer = tg->heightPer; int graphX = gtexGraphX(geneBed); if (graphX < 0) return; // yZero is at bottom of graph int yZero = gtexGraphHeight() + y - 1; // draw faint line under graph to delineate extent when bars are missing (tissue w/ 0 expression) // TODO: skip missing bars -- then we can lose the gray line (at least for non-comparison mode) //uglyf("DRAW: xOff=%d, x1=%d, y=%d, yZero=%d<br>", xOff, x1, y, yZero); #ifndef MULTI_REGION // x1 is at left of graph int x1 = xOff + graphX; int startX = x1; Color lightGray = MAKECOLOR_32(0xD1, 0xD1, 0xD1); int graphWidth = gtexGraphWidth(geneInfo); hvGfxBox(hvg, x1, yZero+1, graphWidth, 1, lightGray); 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); int barWidth = gtexBarWidth(); int graphPadding = gtexGraphPadding(); char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS, GTEX_COLORS_DEFAULT); Color labelColor = MG_GRAY; // TODO: generalize if (geneInfo->medians2) { // add labels to comparison graphs //FIXME: compute these int charHeight = 5; int labelWidth = 5; hvGfxText(hvg, x1, yZero-charHeight, labelColor, font, "F"); hvGfxText(hvg, x1, yZero + gtexGeneHeight() + gtexGeneMargin(), labelColor, font, "M"); startX = startX + labelWidth + 2; x1 = startX; } /* TODO: Remove DEBUG code here */ struct gtexTissue *tissues = getTissues(); struct gtexTissue *tissue = tissues; /* DEBUG */ 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]); //double expScore = geneBed->expScores[i]; /* if (expScore < 1) expScore = 0.0; */ // DEBUG code here //uglyf("%s: score=%.2f<br>", tissue->description, expScore); tissue = tissue->next; // END DEBUG int height = valToHeight(expScore, maxMedian, gtexGraphHeight(), doLogTransform); // TODO: adjust yGene to get gene track distance as desired //if (i ==0) uglyf("DRAW: expScore=%.2f, maxMedian=%.2f, graphHeight=%d, y=%d<br>", expScore, maxMedian, gtexGraphHeight(), y); //if (i ==0) uglyf("DRAW: yZero=%d, yMedian=%d, height=%d<br>", yZero, yMedian, height); 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; } #endif // mark gene extent int yGene = yZero + gtexGeneMargin() - 1; // draw gene model tg->heightPer = gtexGeneHeight()+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 graph (upside down) x1 = startX; // yZero is at top of graph yZero = yGene + gtexGeneHeight(); 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 = geneBed->expScores[i]; double expScore = geneInfo->medians2[i]; //if (expScore < 1) //expScore = 0.0; int height = valToHeight(expScore, maxMedian, gtexGraphHeight(), doLogTransform); // TODO: adjust yGene instead of yMedian+1 to get gene track distance as desired //if (i ==0) uglyf("DRAW2: expScore=%.2f, maxMedian=%.2f, graphHeight=%d, y=%d<br>", expScore, maxMedian, gtexGraphHeight(), y); //if (i ==0) uglyf("DRAW2: yZero=%d, height=%d<br>", yZero, height); 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 } #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; } struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; if (extras->isComparison && (tg->visibility == tvFull || tg->visibility == tvPack)) //&& gtexGraphHeight() != MIN_GRAPH_HEIGHT) // compute medians based on configuration (comparisons, and later, filters) loadComputedMedians(geneInfo, extras); 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; // x1 is at left of graph int x1 = xOff + graphX; int startX = x1; // yZero is at bottom of graph int yZero = gtexGraphHeight() + y - 1; // draw faint line under graph to delineate extent when bars are missing (tissue w/ 0 expression) // TODO: skip missing bars -- then we can lose the gray line (at least for non-comparison mode) Color lightGray = MAKECOLOR_32(0xD1, 0xD1, 0xD1); int graphWidth = gtexGraphWidth(geneInfo); hvGfxBox(hvg, x1, yZero+1, graphWidth, 1, lightGray); //uglyf("DRAW: xOff=%d, x1=%d, y=%d, yZero=%d<br>", xOff, x1, y, yZero); int barWidth = gtexBarWidth(); int graphPadding = gtexGraphPadding(); char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS, GTEX_COLORS_DEFAULT); Color labelColor = MG_GRAY; // TODO: generalize if (geneInfo->medians2) { // add labels to comparison graphs //FIXME: compute these int charHeight = 5; int labelWidth = 5; hvGfxText(hvg, x1, yZero-charHeight, labelColor, font, "F"); hvGfxText(hvg, x1, yZero + gtexGeneHeight() + gtexGeneMargin(), labelColor, font, "M"); startX = startX + labelWidth + 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]); //double expScore = geneBed->expScores[i]; /* if (expScore < 1) expScore = 0.0; */ int height = valToHeight(expScore, maxMedian, gtexGraphHeight(), doLogTransform); // TODO: adjust yGene to get gene track distance as desired //if (i ==0) uglyf("DRAW: expScore=%.2f, maxMedian=%.2f, graphHeight=%d, y=%d<br>", expScore, maxMedian, gtexGraphHeight(), y); //if (i ==0) uglyf("DRAW: yZero=%d, yMedian=%d, height=%d<br>", yZero, yMedian, height); 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 = gtexGeneHeight()+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 is at top of graph yZero = yGene + gtexGeneHeight(); 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 = geneBed->expScores[i]; double expScore = geneInfo->medians2[i]; //if (expScore < 1) //expScore = 0.0; int height = valToHeight(expScore, maxMedian, gtexGraphHeight(), doLogTransform); // TODO: adjust yGene instead of yMedian+1 to get gene track distance as desired //if (i ==0) uglyf("DRAW2: expScore=%.2f, maxMedian=%.2f, graphHeight=%d, y=%d<br>", expScore, maxMedian, gtexGraphHeight(), y); //if (i ==0) uglyf("DRAW2: yZero=%d, height=%d<br>", yZero, height); 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 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 */ { //uglyf("map item: itemName=%s, mapItemName=%s, start=%d, end=%d, x=%d, y=%d, width=%d, height=%d, insideX=%d<br>", //itemName, mapItemName, start, end, x, y, width, height, insideX); if (tg->visibility == tvDense || tg->visibility == tvSquish) { genericMapItem(tg, hvg, item, itemName, itemName, start, end, x, y, width, height); return; } 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; if (geneInfo->medians2) { // add labels to comparison graphs //FIXME: compute these int labelWidth = 5; x1 = x1 + labelWidth + 2; } int i = 0; int yZero = gtexGraphHeight() + y - 1; for (tissue = tissues; tissue != NULL; tissue = tissue->next, i++) { double expScore = geneBed->expScores[i]; //TODO: use valToHeight int yMedian = valToY(expScore, maxMedian, gtexGraphHeight()) + y; int height = yZero - yMedian; // TODO: call genericMapItem //genericMapItem(tg, hvg, item, itemName, tissue->description, start, end, x1, y, barWidth, height); mapBoxHc(hvg, start, end, x1, yMedian+1, barWidth, height, tg->track, mapItemName, tissue->description); //if (i==0) uglyf("MAP: expScore=%.2f, maxMedian=%.2f, graphHeight=%d, y=%d<br>", expScore, maxMedian, gtexGraphHeight(), y); //if (i==0) uglyf("MAP: x=%d, x1=%d, y=%d, yZero=%d<br>", x, x1, y, yZero); //if (i==0) uglyf("MAP: yZero=%d, yMedian=%d, height=%d<br>", yZero, yMedian, height); x1 = x1 + barWidth + padding; } } #ifdef OLD static struct gtexGeneBed *loadGtexGeneBed(char **row) { struct gtexGeneBed *geneBed = gtexGeneBedLoad(row); // TODO: rethink schemas // for now... replace expScores with medians from tissue data file struct gtexTissue *tissue = NULL, *tissues = getTissues(); int i=0; char query[1024]; struct sqlConnection *conn = hAllocConn("hgFixed"); for (tissue = tissues; tissue != NULL; tissue = tissue->next, i++) { sqlSafef(query, sizeof(query), "select * from gtexTissueData where geneId='%s' and tissue='%s'", geneBed->geneId, tissue->name); struct gtexTissueData *tissueData = gtexTissueDataLoadByQuery(conn, query); geneBed->expScores[i] = tissueData->median; } hFreeConn(&conn); return geneBed; } #endif 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 gtexGeneItemHeight(struct track *tg, void *item) { if ((item == NULL) || (tg->visibility == tvSquish) || (tg->visibility == tvDense)) return 0; int extra = 0; if (((struct gtexGeneExtras *)tg->extraUiData)->isComparison) extra = gtexGraphHeight() + 2; //uglyf("GTEX itemHeight extra = %d<br>", extra); return gtexGraphHeight() + gtexGeneMargin() + gtexGeneHeight() + extra; } static int gtexTotalHeight(struct track *tg, enum trackVisibility vis) /* Figure out total height of track */ { int height; int extra = 0; if (((struct gtexGeneExtras *)tg->extraUiData)->isComparison) extra = gtexGraphHeight() + 2; if (tg->visibility == tvSquish || tg->visibility == tvDense) height = 10; else height = gtexGraphHeight() + gtexGeneMargin() + gtexGeneHeight() + extra; //uglyf("GTEX totalHeight = %d<br>", height); return tgFixedTotalHeightOptionalOverflow(tg, vis, height, height, FALSE); } 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->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 = gtexTotalHeight; #ifdef MULTI_REGION tg->nonPropDrawItemAt = gtexGeneNonPropDrawAt; tg->nonPropPixelWidth = gtexGeneNonPropPixelWidth; #endif }