127b6b678948569c41e56db76db116e2a3836beb braney Wed May 8 14:14:39 2019 -0700 Add a pack mode to bigLolly that shows the data as bigBed diff --git src/hg/hgTracks/lollyTrack.c src/hg/hgTracks/lollyTrack.c index 0127ed4..0328707 100644 --- src/hg/hgTracks/lollyTrack.c +++ src/hg/hgTracks/lollyTrack.c @@ -1,32 +1,31 @@ /* lollyTrack -- load and draw lollys */ /* Copyright (C) 2019 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "obscure.h" #include "hgTracks.h" #include "bedCart.h" #include "bigWarn.h" #include "lolly.h" #include "limits.h" #include "float.h" #include "bigBedFilter.h" -#define LOLLY_RADIUS 5 -#define LOLLY_DIAMETER 2 * LOLLY_RADIUS +#define LOLLY_DIAMETER 2 * lollyCart->radius /* the lolly colors */ static int lollyPalette[] = { 0x1f77b4, 0xff7f0e, 0x2ca02c, 0xd62728, 0x9467bd, 0x8c564b, 0xe377c2, 0x7f7f7f, 0xbcbd22, 0x17becf }; struct lolly { struct lolly *next; char *name; /* the mouseover name */ double val; /* value in the data file */ unsigned start; /* genomic start address */ unsigned end; /* genomic end address */ @@ -79,67 +78,80 @@ { int sx = ((pop->start - seqStart) + .5) * scale + xOff; // x coord of center (lower region) hvGfxCircle(hvg, sx, yOff + trackHeight - pop->radius - pop->height, pop->radius, pop->color, TRUE); if (!noMapBoxes) mapBoxHgcOrHgGene(hvg, pop->start, pop->end, sx - pop->radius, yOff + trackHeight - pop->radius - pop->height - pop->radius, 2 * pop->radius,2 * pop->radius, tg->track, pop->name, pop->name, NULL, TRUE, NULL); } } void lollyLeftLabels(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, int height, boolean withCenterLabels, MgFont *font, Color color, enum trackVisibility vis) // draw the labels on the left margin { +struct lollyCartOptions *lollyCart = tg->lollyCart; int fontHeight = tl.fontHeight+1; int centerLabel = (height/2)-(fontHeight/2); if ( tg->visibility == tvDense) { hvGfxText(hvg, xOff, yOff+fontHeight, color, font, tg->shortLabel); return; } hvGfxText(hvg, xOff, yOff+centerLabel, color, font, tg->shortLabel); -if (isnan(tg->lollyCart->upperLimit)) +if (isnan(lollyCart->upperLimit)) { hvGfxTextRight(hvg, xOff, yOff + LOLLY_DIAMETER, width - 1, fontHeight, color, font, "NO DATA"); return; } char upper[1024]; -safef(upper, sizeof(upper), "%g -", tg->lollyCart->upperLimit); +safef(upper, sizeof(upper), "%g -", lollyCart->upperLimit); hvGfxTextRight(hvg, xOff, yOff + LOLLY_DIAMETER, width - 1, fontHeight, color, font, upper); char lower[1024]; -if (tg->lollyCart->lowerLimit < tg->lollyCart->upperLimit) +if (lollyCart->lowerLimit < lollyCart->upperLimit) { - safef(lower, sizeof(lower), "%g _", tg->lollyCart->lowerLimit); + safef(lower, sizeof(lower), "%g _", lollyCart->lowerLimit); hvGfxTextRight(hvg, xOff, yOff+height-fontHeight - LOLLY_DIAMETER, width - 1, fontHeight, color, font, lower); } } static int lollyHeight(struct track *tg, enum trackVisibility vis) /* calculate height of all the lollys being displayed */ { if ( tg->visibility == tvDense) return tl.fontHeight; +// if we're pack, then use bigBed drawing +if (tg->visibility == tvPack) + { + char *ourWords[2]; + ourWords[0] = "bigBed"; + ourWords[1] = "4"; + bigBedMethods(tg, tg->tdb,2,ourWords); + tg->mapsSelf = FALSE; + tg->drawLeftLabels = NULL; + return tg->totalHeight(tg, vis); + } + // return the height we calculated at load time return tg->lollyCart->height; } #ifdef NOTUSED double calcVarianceFromSums(double sum, double sumSquares, bits64 n) /* Calculate variance. */ { double var = sumSquares - sum*sum/n; if (n > 1) var /= n-1; return var; } double calcStdFromSums(double sum, double sumSquares, bits64 n) @@ -148,39 +160,44 @@ return sqrt(calcVarianceFromSums(sum, sumSquares, n)); } #endif // NOTUSED int cmpHeight(const void *va, const void *vb) // sort the lollies by height { const struct lolly *a = *((struct lolly **)va); const struct lolly *b = *((struct lolly **)vb); return a->height - b->height; } void lollyLoadItems(struct track *tg) // load lollies from the data file { +struct lollyCartOptions *lollyCart = tg->lollyCart; +if (tg->visibility == tvSquish) + { + lollyCart->radius = 2; + lollyCart->height /= 3; + } struct lm *lm = lmInit(0); struct bbiFile *bbi = fetchBbiForTrack(tg); struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chromName, winStart, winEnd, 0, lm); char *bedRow[bbi->fieldCount]; char startBuf[16], endBuf[16]; struct lolly *popList = NULL, *pop; unsigned lollyField = 5; // we use the score field by default -struct lollyCartOptions *lollyCart = tg->lollyCart; char *setting = trackDbSetting(tg->tdb, "lollyField"); if (setting != NULL) lollyField = atoi(setting); double minVal = DBL_MAX, maxVal = -DBL_MAX; //double sumData = 0.0, sumSquares = 0.0; unsigned count = 0; int trackHeight = tg->lollyCart->height; struct bigBedFilter *filters = bigBedBuildFilters(cart, bbi, tg->tdb); for (bb = bbList; bb != NULL; bb = bb->next) { bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow)); @@ -212,31 +229,31 @@ minVal = val; } if (count == 0) lollyCart->upperLimit = lollyCart->lowerLimit = NAN; // no lollies in range else if (lollyCart->autoScale == wiggleScaleAuto) { lollyCart->upperLimit = maxVal; lollyCart->lowerLimit = minVal; } double range = lollyCart->upperLimit - lollyCart->lowerLimit; int usableHeight = trackHeight - 2 * LOLLY_DIAMETER; for(pop = popList; pop; pop = pop->next) { - pop->radius = LOLLY_RADIUS; + pop->radius = lollyCart->radius; pop->color = MG_RED; if (range == 0.0) { pop->height = usableHeight ; pop->color = lollyPalette[0] | 0xff000000; } else { pop->height = usableHeight * (pop->val - lollyCart->lowerLimit) / range + LOLLY_DIAMETER; int colorIndex = 8 * (pop->val - lollyCart->lowerLimit) / range; pop->color = lollyPalette[colorIndex] | 0xff000000; } } #ifdef NOTUSED // a method of scaling assuming a sort of normal distribution @@ -292,28 +309,28 @@ double tDbMinY; /* data range limits from trackDb type line */ double tDbMaxY; /* data range limits from trackDb type line */ char *trackWords[8]; /* to parse the trackDb type line */ int trackWordCount = 0; /* to parse the trackDb type line */ wigFetchMinMaxYWithCart(cart, tdb, tdb->track, &lollyCart->minY, &lollyCart->maxY, &tDbMinY, &tDbMaxY, trackWordCount, trackWords); lollyCart->upperLimit = lollyCart->maxY; lollyCart->lowerLimit = lollyCart->minY; return lollyCart; } void lollyMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]) /* bigLolly track type methods */ { -struct lollyCartOptions *lollyCart = lollyCartOptionsNew(cart, tdb, wordCount, words); char *ourWords[2]; ourWords[0] = "bigBed"; ourWords[1] = "4"; bigBedMethods(track, tdb,2,ourWords); -if (tdb->visibility == tvDense) - return; + +struct lollyCartOptions *lollyCart = lollyCartOptionsNew(cart, tdb, wordCount, words); +lollyCart->radius = 5; track->loadItems = lollyLoadItems; track->drawItems = lollyDrawItems; track->totalHeight = lollyHeight; track->drawLeftLabels = lollyLeftLabels; track->lollyCart = lollyCart; }