dff3f2a22bb375a6ec0eb38ab29b8bdc1e0de9d2 braney Thu May 9 11:47:45 2019 -0700 fix filters on bigBeds with over 32 fields. Fix justification of dense left label on gdcCancer track diff --git src/hg/hgTracks/lollyTrack.c src/hg/hgTracks/lollyTrack.c index 0328707..ca821b2 100644 --- src/hg/hgTracks/lollyTrack.c +++ src/hg/hgTracks/lollyTrack.c @@ -1,336 +1,332 @@ /* 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_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 */ unsigned radius; /* radius of the top of the lolly */ unsigned height; /* height of the lolly */ Color color; /* color of the lolly */ }; static void lollyDrawItems(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) /* Draw a list of lolly structures. */ { double scale = scaleForWindow(width, seqStart, seqEnd); struct lolly *popList = tg->items, *pop; int trackHeight = tg->lollyCart->height; if (popList == NULL) // nothing to draw return; if ( tg->visibility == tvDense) // in dense mode we just track lines { for (pop = popList; pop; pop = pop->next) { int sx = ((pop->start - seqStart) + .5) * scale + xOff; // x coord of center (lower region) hvGfxLine(hvg, sx, yOff, sx , yOff+ tl.fontHeight, pop->color); } return; } boolean noMapBoxes = FALSE; int numItems = slCount(popList); if ( numItems > 5000) { char buffer[4096]; safef(buffer, sizeof buffer, "Too many (%d) items in window. Zoom in or set viewing range to be more restrictive.", numItems); noMapBoxes = TRUE; mapBoxHgcOrHgGene(hvg, winStart, winEnd, xOff, yOff, width, trackHeight, tg->track, "", buffer, "hgTracks", FALSE, NULL); } // first draw the lines so they won't overlap any lollies for (pop = popList; pop; pop = pop->next) { int sx = ((pop->start - seqStart) + .5) * scale + xOff; // x coord of center (lower region) hvGfxLine(hvg, sx, yOff + trackHeight, sx , yOff+(trackHeight - pop->height), MG_GRAY); } // now draw the sucker part! for (pop = popList; pop; pop = pop->next) { 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); + hvGfxTextRight(hvg, xOff, yOff+fontHeight, width - 1, fontHeight, color, font, tg->shortLabel); return; } hvGfxText(hvg, xOff, yOff+centerLabel, color, font, tg->shortLabel); 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 -", lollyCart->upperLimit); hvGfxTextRight(hvg, xOff, yOff + LOLLY_DIAMETER, width - 1, fontHeight, color, font, upper); char lower[1024]; if (lollyCart->lowerLimit < lollyCart->upperLimit) { 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); + bigBedMethods(tg, tg->tdb, tg->lollyCart->wordCount, tg->lollyCart->words); 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) /* Calculate standard deviation. */ { 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 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)); // throw away items that don't pass the filters if (!bigBedFilterInterval(bedRow, filters)) continue; // clip out lollies that aren't in our display range double val = atof(bedRow[lollyField - 1]); if (!((lollyCart->autoScale == wiggleScaleAuto) || ((val >= lollyCart->minY) && (val <= lollyCart->maxY) ))) continue; // don't draw lollies off the screen if (atoi(bedRow[1]) < winStart) continue; AllocVar(pop); slAddHead(&popList, pop); pop->val = val; pop->start = atoi(bedRow[1]); pop->end = atoi(bedRow[2]); pop->name = cloneString(bedRow[3]); count++; // sumData += val; // sumSquares += val * val; if (val > maxVal) maxVal = val; if (val < minVal) 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 = 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 double average = sumData/count; double stdDev = calcStdFromSums(sumData, sumSquares, count); for(pop = popList; pop; pop = pop->next) { if (pop->val > average + stdDev / 5) { pop->color = MG_RED; pop->radius = 8; pop->height = 3 * tl.fontHeight; } else if (pop->val < average - stdDev / 5) { pop->color = MG_GREEN; pop->radius = 3; pop->height = 1 * tl.fontHeight; } else { pop->color = MG_GRAY; pop->radius = 5; pop->height = 2 * tl.fontHeight; } } #endif // NOTUSED slSort(&popList, cmpHeight); tg->items = popList; } static struct lollyCartOptions *lollyCartOptionsNew(struct cart *cart, struct trackDb *tdb, int wordCount, char *words[]) // the structure that is attached to the track structure { struct lollyCartOptions *lollyCart; AllocVar(lollyCart); int maxHeightPixels; int minHeightPixels; int defaultHeight; /* pixels per item */ int settingsDefault; cartTdbFetchMinMaxPixels(cart, tdb, MIN_HEIGHT_PER, atoi(DEFAULT_HEIGHT_PER), atoi(DEFAULT_HEIGHT_PER), &minHeightPixels, &maxHeightPixels, &settingsDefault, &defaultHeight); lollyCart->height = defaultHeight; lollyCart->autoScale = wigFetchAutoScaleWithCart(cart,tdb, tdb->track, NULL); 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 */ { -char *ourWords[2]; -ourWords[0] = "bigBed"; -ourWords[1] = "4"; -bigBedMethods(track, tdb,2,ourWords); +bigBedMethods(track, tdb, wordCount, words); struct lollyCartOptions *lollyCart = lollyCartOptionsNew(cart, tdb, wordCount, words); lollyCart->radius = 5; +lollyCart->words = words; +lollyCart->wordCount = wordCount; track->loadItems = lollyLoadItems; track->drawItems = lollyDrawItems; track->totalHeight = lollyHeight; track->drawLeftLabels = lollyLeftLabels; track->lollyCart = lollyCart; }