9f48c12faa3df72b9ab3e6455095ee897c646532 kate Tue Oct 20 21:56:56 2015 -0700 Scale graph limits and place X axis labels appropriately for variously ranged graphs, and log transformed data. refs #15645 diff --git src/hg/hgc/gtexClick.c src/hg/hgc/gtexClick.c index 5734f12..5195750 100644 --- src/hg/hgc/gtexClick.c +++ src/hg/hgc/gtexClick.c @@ -1,465 +1,467 @@ /* Details pages for 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 "hash.h" #include "hdb.h" #include "trashDir.h" #include "hgc.h" #include "jsHelper.h" #include "rainbow.h" #include "hvGfx.h" #include "gtexUi.h" #include "gtexGeneBed.h" #include "gtexTissue.h" #include "gtexSampleData.h" boolean doLogTransform = FALSE; struct gtexGeneBed *gtexGene = NULL; struct tissueSampleVals /* RPKM expression values for multiple samples */ { struct tissueSampleVals *next; char *name; /* GTEx tissue name */ char *description; /* GTEx tissue description */ int color; /* GTEx tissue color */ int count; /* number of samples */ double *vals; /* RPKM values */ double min, max; /* minimum, maximum value */ double q1, median, q3; /* quartiles */ struct slDouble *valList; /* used to create val array */ }; int cmpTissueSampleValsMedianScore(const void *va, const void *vb) /* Compare RPKM scores */ { const struct tissueSampleVals *a = *((struct tissueSampleVals **)va); const struct tissueSampleVals *b = *((struct tissueSampleVals **)vb); if (a->median == b->median) return 0; return (a->median > b->median ? 1: -1); } void RGtexBoxplot(struct tissueSampleVals *tsvList) { // Tissue list is now sorted by GTEx tissue ordering. // Sort by score descending. slSort(&tsvList, cmpTissueSampleValsMedianScore); slReverse(&tsvList); // Create R data frame struct tempName dfTn; trashDirFile(&dfTn, "hgc", "gtexGene", ".df.txt"); FILE *f = fopen(dfTn.forCgi, "w"); if (f == NULL) errAbort("can't create temp file %s", dfTn.forCgi); fprintf(f, "sample\ttissue\trpkm\n"); struct tissueSampleVals *tsv; int i; int sampleId=1; for (tsv = tsvList; tsv != NULL; tsv = tsv->next) { int count = tsv->count; for (i=0; i<count; i++) fprintf(f, "%d\t%s\t%0.3f\n", sampleId++, tsv->name, tsv->vals[i]); } fclose(f); // Plot to PNG file struct tempName pngTn; trashDirFile(&pngTn, "hgc", "gtexGene", ".png"); char cmd[256]; // Exec R in quiet mode, without reading/saving environment or workspace -safef(cmd, sizeof(cmd), "Rscript --gui=X11 --vanilla --slave gtex/geneBoxplot.R %s %s %s", - gtexGene->name, dfTn.forCgi, pngTn.forHtml); +//safef(cmd, sizeof(cmd), "Rscript --gui=X11 --vanilla --slave gtex/geneBoxplot.R %s %s %s", +safef(cmd, sizeof(cmd), "Rscript --vanilla --slave gtex/geneBoxplot.R %s %s %s %s", + gtexGene->name, dfTn.forCgi, pngTn.forHtml, + doLogTransform ? "log=TRUE" : "log=FALSE"); int ret = system(cmd); if (ret == 0) { - //printf("<IMG SRC = \"%s\" BORDER=1><BR>\n", pngTn.forHtml); - printf("<IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d><BR>\n", + printf("<IMG SRC = \"%s\" BORDER=1><BR>\n", pngTn.forHtml); + //printf("<IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d><BR>\n", //pngTn.forHtml, imageWidth, imageHeight); - pngTn.forHtml, 900, 500); + //pngTn.forHtml, 900, 500); } } void d3GtexBoxplot(struct tissueSampleVals *tsvList) { //puts("<script src='http://www.d3plus.org/js/d3.js'></script>\n"); //puts("<script src='http://www.d3plus.org/js/d3plus.js'></script>\n"); printf("<div id='expGraph'></div>\n"); jsIncludeFile("d3.min.js", NULL); jsIncludeFile("d3plus.gtex.js", NULL); jsTrackingVar("geneName", gtexGene->name); jsTrackingVar("geneId", gtexGene->geneId); jsIncludeFile("gtex.js", NULL); } /* Dimensions of image parts */ int pad = 2; int margin = 1; //int graphHeight = 400; int graphHeight = 325; //int barWidth = 3; int barWidth = 12; int titleHeight = 30; int xAxisHeight = 100; int yAxisWidth = 50; int axisMargin = 5; /* Dimensions of image overall and our portion within it. */ int imageWidth, imageHeight, innerWidth, innerHeight, innerXoff, innerYoff; int plotWidth, plotHeight; /* just the plot */ void setImageDims(int expCount) /* Set up image according to count */ { innerHeight = graphHeight + 2*pad; innerWidth = pad + expCount*(pad + barWidth); plotWidth = innerWidth + 2*margin; plotHeight = innerHeight + 2*margin; imageWidth = plotWidth + yAxisWidth; imageHeight = plotHeight + xAxisHeight + titleHeight; innerXoff = yAxisWidth + margin; innerYoff = titleHeight + margin; } struct rgbColor rgbFromIntColor(int color) { return (struct rgbColor){.r=COLOR_32_BLUE(color), .g=COLOR_32_GREEN(color), .b=COLOR_32_RED(color)}; } int valToY(double val, double maxVal, int height) /* Convert a value from 0 to maxVal to 0 to height-1 */ { double scaled = val/maxVal; int y = scaled * (height-1); return height - 1 - y; } void drawPointSmear(struct hvGfx *hvg, int xOff, int yOff, int height, struct tissueSampleVals *tsv, double maxExp, int colorIx, double midClipMin, double midClipMax) /* Draw a point for each sample value. */ { int i, size = tsv->count; double *vals = tsv->vals; // Min becomes max after valToY because graph flipped int yMin = valToY(midClipMax, maxExp, height); int yMax = valToY(midClipMin, maxExp, height); for (i=0; i<size; ++i) { double exp = vals[i]; int y = valToY(exp, maxExp, height); if (y < yMin || y > yMax) { y += yOff; hvGfxDot(hvg, xOff-1, y, colorIx); hvGfxDot(hvg, xOff+1, y, colorIx); hvGfxDot(hvg, xOff, y-1, colorIx); hvGfxDot(hvg, xOff, y+1, colorIx); } } } void drawBoxAndWhiskers(struct hvGfx *hvg, int fillColorIx, int x, int y, struct tissueSampleVals *tsv, double maxExp) /* Draw a Tukey-type box plot. JK */ { struct rgbColor lineColor = {.r=128, .g=128, .b=128}; int lineColorIx = hvGfxFindColorIx(hvg, lineColor.r, lineColor.g, lineColor.b); int medianColorIx = hvGfxFindColorIx(hvg,0,0,0); int whiskColorIx = hvGfxFindColorIx(hvg,192,192,192); double xCen = x + barWidth/2; if (tsv->count > 1) { /* Cache a few fields from tsv in local variables */ double q1 = tsv->q1, q3 = tsv->q3, median = tsv->median; /* Figure out position of first quarter, median, and third quarter in screen Y coordinates */ int yQ1 = valToY(q1, maxExp, graphHeight) + y; int yQ3 = valToY(q3, maxExp, graphHeight) + y; int yMedian = valToY(median, maxExp, graphHeight); /* Draw a filled box that covers the middle two quarters */ int qHeight = yQ1 - yQ3 + 1; hvGfxOutlinedBox(hvg, x, yQ3, barWidth, qHeight, fillColorIx, lineColorIx); /* Figure out whiskers as 1.5x distance from median to nearest quarter */ double iq3 = q3 - median; double iq1 = median - q1; double whisk1 = q1 - 1.5 * iq1; double whisk2 = q3 + 1.5 * iq3; /* If whiskers extend past min or max point, clip them */ if (whisk1 < tsv->min) whisk1 = tsv->min; if (whisk2 > tsv->max) whisk2 = tsv->max; /* Convert whiskers to screen coordinates and do some sanity checks */ int yWhisk1 = valToY(whisk1, maxExp, graphHeight) + y; int yWhisk2 = valToY(whisk2, maxExp, graphHeight) + y; assert(yQ1 <= yWhisk1); assert(yQ3 >= yWhisk2); /* Draw horizontal lines of whiskers and median */ hvGfxBox(hvg, x, yWhisk1, barWidth, 1, whiskColorIx); hvGfxBox(hvg, x, yWhisk2, barWidth, 1, whiskColorIx); /* Draw median, 2 thick */ hvGfxBox(hvg, x, y + yMedian-1, barWidth, 2, medianColorIx); /* Draw lines from mid quarters to whiskers */ hvGfxBox(hvg, xCen, yWhisk2, 1, yQ3 - yWhisk2, whiskColorIx); hvGfxBox(hvg, xCen, yQ1, 1, yWhisk1 - yQ1, whiskColorIx); /* Draw any outliers outside of whiskers */ drawPointSmear(hvg, xCen, y, graphHeight, tsv, maxExp, lineColorIx, whisk1, whisk2); } } void drawGtexBoxplot(struct tissueSampleVals *tsList, double maxVal) { // Tissue list is now sorted by GTEx tissue ordering. // Sort by score descending. slSort(&tsList, cmpTissueSampleValsMedianScore); slReverse(&tsList); // Initialize graphics for Box-and-whiskers plot setImageDims(slCount(tsList)); struct tempName pngTn; trashDirFile(&pngTn, "hgc", "gtexGene", ".png"); //uglyf("Trash file: %s\n", pngTn.forCgi); struct hvGfx *hvg = hvGfxOpenPng(imageWidth, imageHeight, pngTn.forCgi, FALSE); //hvGfxSetClip(hvg, 0, 0, imageWidth, imageHeight); // needed ? int x=innerXoff + pad, y = innerYoff + pad; struct tissueSampleVals *tsv; for (tsv = tsList; tsv != NULL; tsv = tsv->next) { struct rgbColor fillColor = rgbFromIntColor(tsv->color); int fillColorIx = hvGfxFindColorIx(hvg, fillColor.r, fillColor.g, fillColor.b); drawBoxAndWhiskers(hvg, fillColorIx, x, y, tsv, maxVal); x += barWidth + pad; } //hvGfxUnclip(hvg); /* Draw title */ int blackColorIx = hvGfxFindColorIx(hvg, 0,0,0); char title[256]; // TODO: get tissue count and release from tables safef(title, sizeof(title), "%s Gene Expression in 53 Tissues from GTEx (V4 release, 2014) - %s", gtexGene->name, doLogTransform ? "log10(RPKM+1)" : "(RPKM)"); hvGfxTextCentered(hvg, 0, innerYoff, imageWidth, titleHeight, blackColorIx, mgMediumFont(), title); /* Draw axes */ x = innerXoff - margin; // Y axis, tick marks, and labels hvGfxLine(hvg, x, innerYoff, x, plotHeight, blackColorIx); // for now, just mark the max value char buf[16]; safef(buf, sizeof(buf), "%d -", round(maxVal)); hvGfxText(hvg, x-24, innerYoff-8, blackColorIx, mgMediumFont(), buf); // X axis y = innerYoff + plotHeight; hvGfxLine(hvg, innerXoff, y, plotWidth, y, blackColorIx); // Draw vertical labels on separate graphics object, rotate, then merge /* struct memGvx *mg = mgNew(imageHeight, imageWidth); MgFont *font = mgMediumFont(); int lineHeight = mgFontLineHeight(font)-1; y += lineHeight; mgTextRight(mg, 0+1, y+1, width-1, lineHeight, MG_BLACK, font, labels[i]); hvGfxMergeWithPng(hvg, mgRotate90(mg)); // or try using mg lib entirely, via mgSavePng. */ #ifdef TICKS /* Figure tick intervals. GTEx portal uses .5 for log, 2, 5, 10, 20, 50, 100 for linear. * With 7-12 ticks. 5-10 seems nicer to me. Here's how it's done for browser ruler */ static long figureTickSpan(long totalLength, int maxNumTicks) /* Figure out whether ticks on ruler should be 1, 5, 10, 50, 100, 500, * 1000, etc. units apart. */ { int roughTickLen = totalLength/maxNumTicks; int i; int tickLen = 1; for (i=0; i<9; ++i) { if (roughTickLen < tickLen) return tickLen; tickLen *= 5; if (roughTickLen < tickLen) return tickLen; tickLen *= 2; } return 1000000000; } #endif hvGfxClose(&hvg); printf("<IMG SRC = \"%s\" BORDER=1><BR>\n", pngTn.forHtml); /*printf("<IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d><BR>\n", pngTn.forHtml, imageWidth, imageHeight); */ //cloneString(gifTn.forHtml); } void doGtexGeneExpr(struct trackDb *tdb, char *item) /* Details of GTEX gene expression item */ { // Load item from table */ // TODO: Get full details from Data table //char sampleTable[128]; //safef(sampleTable, sizeof(able), "%sSampleData", tdb->table); struct sqlConnection *conn = hAllocConn(database); char **row; char query[512]; struct sqlResult *sr; int expCount = 0; if (sqlTableExists(conn, tdb->table)) { sqlSafef(query, sizeof(query), "select * from %s where name = '%s'", tdb->table, item); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { gtexGene = gtexGeneBedLoad(row); expCount = gtexGene->expCount; } sqlFreeResult(&sr); } hFreeConn(&conn); genericHeader(tdb, item); if (gtexGene != NULL) { // TODO: link to UCSC gene printf("<b>Gene:</b> %s<br>", gtexGene->name); printf("<b>Ensembl ID:</b> %s<br>\n", gtexGene->geneId); printf("<a target='_blank' href='http://www.gtexportal.org/home/gene/%s'>View at GTEx portal</a><br>\n", gtexGene->geneId); puts("<p>"); } // Get full sample data for this gene char *sampleDataTable = "gtexSampleData"; conn = hAllocConn("hgFixed"); assert(sqlTableExists(conn, sampleDataTable)); sqlSafef(query, sizeof(query), "select * from %s where geneId='%s'", sampleDataTable, gtexGene->geneId); sr = sqlGetResult(conn, query); struct hash *tsHash = hashNew(0); struct tissueSampleVals *tsv; struct hashEl *hel; struct slDouble *val; double maxVal = 0; struct gtexSampleData *sd = NULL; while ((row = sqlNextRow(sr)) != NULL) { sd = gtexSampleDataLoad(row); if ((hel = hashLookup(tsHash, sd->tissue)) == NULL) { AllocVar(tsv); hashAdd(tsHash, sd->tissue, tsv); } else tsv = (struct tissueSampleVals *)hel->val; maxVal = max(maxVal, sd->score); val = slDoubleNew(sd->score); slAddHead(&tsv->valList, val); } // Fill in tissue descriptions, fill values array and calculate stats for plotting // Then make a list, suitable for sorting by tissue or score struct gtexTissue *tis = NULL, *tissues = gtexGetTissues(); struct tissueSampleVals *tsList = NULL; int i; doLogTransform = cartUsualBooleanClosestToHome(cart, tdb, FALSE, GTEX_LOG_TRANSFORM, GTEX_LOG_TRANSFORM_DEFAULT); if (doLogTransform) maxVal = log10(maxVal+1.0); for (tis = tissues; tis != NULL; tis = tis->next) { tsv = hashMustFindVal(tsHash, tis->name); tsv->name = tis->name; tsv->description = tis->description; tsv->color = tis->color; int count = tsv->count = slCount(tsv->valList); double *vals = AllocArray(tsv->vals, count); for (i=0; i<count; i++) { val = slPopHead(&tsv->valList); if (doLogTransform) vals[i] = log10(val->val+1.0); else vals[i] = val->val; } doubleBoxWhiskerCalc(tsv->count, tsv->vals, &tsv->min, &tsv->q1, &tsv->median, &tsv->q3, &tsv->max); slAddHead(&tsList, tsv); } // TODO: Remove one char *viz = cgiUsualString("viz", "c"); if (sameString(viz, "d3")) d3GtexBoxplot(tsList); else if (sameString(viz, "R")) RGtexBoxplot(tsList); else drawGtexBoxplot(tsList, maxVal); // Track description printTrackHtml(tdb); // Print out tissue table with color assignments #ifdef DEBUG conn = hAllocConn("hgFixed"); char *tissueTable = "gtexTissue"; if (sqlTableExists(conn, tissueTable)) { dyStringPrintf(dy, "<table>"); dyStringPrintf(dy, "<tr><td><b>Color<b></td><td><b>Tissue<b></td></tr>\n"); int i; double invExpCount = 1.0/expCount; char query[512]; sqlSafef(query, sizeof(query), "select * from %s", tissueTable); struct sqlResult *sr = sqlGetResult(conn, query); for (i=0; i<expCount; i++) { row = sqlNextRow(sr); if (row == NULL) break; struct gtexTissue *tissue = gtexTissueLoad(row); double colPos = invExpCount * i; struct rgbColor color = saturatedRainbowAtPos(colPos); dyStringPrintf(dy, "<tr><td bgcolor='#%02X%02X%02X'></td><td>%s</td></tr>\n", color.r, color.g, color.b, tissue->description); } sqlFreeResult(&sr); } hFreeConn(&conn); dyStringPrintf(dy, "</table>"); puts(dy->string); //cartWebStart(cart, database, "List of items assayed in %s", clusterTdb->shortLabel); //genericClickHandlerPlus(tdb, item, item, dy->string); dyStringFree(&dy); #endif }