aa3e13e1b4f4dd15e8ecb108d7369a586a75e7c9 kate Thu Oct 22 13:23:26 2015 -0700 Code cleanup, in preparation for branch merge. refs #15645 diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c index ea9436b..bbc9f92 100644 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@ -1,886 +1,849 @@ -/* GTEX tracks */ +/* 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" -#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}; +// NOTE: Sections to change for multi-region (vertical slice) display +// are marked with #ifdef MULTI_REGION struct gtexGeneExtras /* Track info */ { - double maxMedian; - char *graphType; - boolean isComparison; - struct rgbColor *colors; + double maxMedian; /* Maximum median rpkm for all tissues */ + boolean isComparison; /* Comparison of two sample sets (e.g. male/female). + 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 */ }; 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) +/***********************************************/ +/* Color gene models using GENCODE conventions */ + +// TODO: reuse GENCODE code for some/all of this ?? +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 */ { -unsigned char red, green, blue; -parseColor(rgb, &red, &green, &blue); -return (hvGfxFindColorIx(hvg, red, green, blue)); -//return MAKECOLOR_32(red, green, blue); -} + 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 = 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); +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; + 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 */ +/***********************************************/ +/* 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; } -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; -} +/*****************************************************************/ +/* Load sample data, gene info, and anything else needed to draw */ -static int gtexGeneHeight() +static struct hash *loadGeneModels(char *table) +/* Load gene models from table */ { - return 8; -} +struct sqlConnection *conn = hAllocConn(database); +struct sqlResult *sr; +char **row; +int rowOffset; +sr = hRangeQuery(conn, table, chromName, winStart, winEnd, NULL, &rowOffset); -static int gtexGeneMargin() +struct hash *modelHash = newHash(0); +struct genePred *model = NULL; +while ((row = sqlNextRow(sr)) != NULL) { - return 1; + model = genePredLoad(row+rowOffset); + hashAdd(modelHash, model->name, model); + } +sqlFreeResult(&sr); +hFreeConn(&conn); +return modelHash; } - -/* 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]; + // 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 + //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) +else { - model = genePredLoad(row+rowOffset); - hashAdd(modelHash, model->name, model); + // TODO: compute median for single graph based on filtering of sample set } -sqlFreeResult(&sr); -hFreeConn(&conn); -return modelHash; } static void gtexGeneLoadItems(struct track *tg) +/* Load method for track items */ { -// Get track UI info +/* Get track UI info */ struct gtexGeneExtras *extras; AllocVar(extras); tg->extraUiData = extras; - -// TODO: move test to lib -char *samples = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_SAMPLES, - GTEX_SAMPLES_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; - extras->maxMedian = gtexMaxMedianScore(NULL); -// Construct track items - -// Get geneModels in range -//TODO: version the table name ? +/* 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 +/* 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 +/* 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)) { - // 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; } +/***********************************************/ +/* 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 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 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; +} + +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; +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; +} + 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; } 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 }