fc724a23c9a0ad34a6ff6e530eb93945fd94a5c5 kate Sun Mar 11 18:24:53 2018 -0700 Add score filtering. refs #17512 diff --git src/hg/hgTracks/interactTrack.c src/hg/hgTracks/interactTrack.c index 0e21a78..117a666 100644 --- src/hg/hgTracks/interactTrack.c +++ src/hg/hgTracks/interactTrack.c @@ -1,371 +1,385 @@ /* interactTrack -- draw interaction between two genomic regions */ /* Copyright (C) 2018 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 "interact.h" #include "interactUi.h" static int interactTotalHeight(struct track *tg, enum trackVisibility vis) /* calculate height of all the interactions being displayed */ { if ( tg->visibility == tvDense) return tl.fontHeight; int min, max, deflt, current; cartTdbFetchMinMaxPixels(cart, tg->tdb, INTERACT_MINHEIGHT, INTERACT_MAXHEIGHT, atoi(INTERACT_DEFHEIGHT), &min, &max, &deflt, ¤t); return tg->height = current; } static Color interactItemColor(struct track *tg, void *item, struct hvGfx *hvg) /* Return color to draw an interaction */ { struct interact *inter = item; struct rgbColor itemRgb; // There must be a better way... itemRgb.r = (inter->color & 0xff0000) >> 16; itemRgb.g = (inter->color & 0xff00) >> 8; itemRgb.b = inter->color & 0xff; return hvGfxFindColorIx(hvg, itemRgb.r, itemRgb.g, itemRgb.b); } void interactLoadItems(struct track *tg) /* Load all interact items in region */ { loadSimpleBedWithLoader(tg, (bedItemLoader)interactLoad); + +// filters +char buf[1024]; +safef(buf, sizeof buf, "%s.%s", tg->tdb->track, INTERACT_MINSCORE); +int minScore = cartUsualInt(cart, buf, INTERACT_DEFMINSCORE); +struct interact *inter, *next, *filteredItems = NULL; +for (inter = tg->items; inter; inter = next) + { + next = inter->next; + if (inter->score < minScore) + continue; + slAddHead(&filteredItems, inter); + } +slReverse(&filteredItems); +tg->items = filteredItems; } static void interactDrawItems(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 interact structures. */ { #define DRAW_LINE 0 #define DRAW_CURVE 1 #define DRAW_ELLIPSE 2 int draw = DRAW_LINE; if (vis != tvDense) { char *drawMode = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, INTERACT_DRAW, INTERACT_DRAW_DEFAULT); if (sameString(drawMode, INTERACT_DRAW_CURVE)) draw = DRAW_CURVE; else if (sameString(drawMode, INTERACT_DRAW_ELLIPSE)) draw = DRAW_ELLIPSE; } boolean isDirectional = interactUiDirectional(tg->tdb); double scale = scaleForWindow(width, seqStart, seqEnd); struct interact *inters = tg->items; unsigned int maxWidth = 0; struct interact *inter; char buffer[1024]; char itemBuf[2048]; -safef(buffer, sizeof buffer, "%s.%s", tg->tdb->track, INTERACT_MINSCORE); // Determine if there are mixed inter and intra-chromosomal // Suppress interchromosomal labels if they overlap int nSame = 0, nOther = 0; int prevLabelEnd = 0, prevLabelStart = 0; char *prevLabel = 0; boolean doOtherLabels = TRUE; char *otherChrom = NULL; for (inter=inters; inter; inter=inter->next) { int width = inter->chromEnd - inter->chromStart; if (width > maxWidth) maxWidth = width; } for (inter=inters; inter; inter=inter->next) { otherChrom = interactOtherChrom(inter); if (otherChrom == NULL) nSame++; else { nOther++; if (!doOtherLabels) continue; int labelWidth = vgGetFontStringWidth(hvg->vg, font, otherChrom); // TODO: simplify now that center approach is abandoned int sx = ((inter->chromStart - seqStart) + .5) * scale + xOff; // x coord of center int labelStart = (double)sx - labelWidth/2; int labelEnd = labelStart + labelWidth - 1; if (labelStart <= prevLabelEnd && !(labelStart == prevLabelStart && labelEnd == prevLabelEnd && sameString(otherChrom, prevLabel))) doOtherLabels = FALSE; prevLabelStart = labelStart; prevLabelEnd = labelEnd; prevLabel = otherChrom; } } int fontHeight = vgGetFontPixelHeight(hvg->vg, font); int otherHeight = (nOther) ? 3 * fontHeight : 0; int sameHeight = (nSame) ? tg->height - otherHeight: 0; // Draw items for (inter=inters; inter; inter=inter->next) { char *otherChrom = interactOtherChrom(inter); safef(itemBuf, sizeof itemBuf, "%s", inter->name); struct dyString *ds = dyStringNew(0); - if (isEmpty(inter->name)) + if (isEmpty(inter->name) || sameString(".", inter->name)) { - if (isNotEmpty(inter->exp)) + if (isNotEmpty(inter->exp) && differentString(".", inter->name)) dyStringPrintf(ds, "%s ", inter->exp); if (otherChrom) dyStringPrintf(ds, "%s", otherChrom); else { char buf[4096]; sprintLongWithCommas(buf, inter->chromEnd - inter->chromStart); dyStringPrintf(ds, "%s bp", buf); } } else dyStringPrintf(ds, "%s", inter->name); if (inter->score) dyStringPrintf(ds, " %d", inter->score); if (inter->value != 0.0) dyStringPrintf(ds, " %0.2f", inter->value); char *statusBuf = dyStringCannibalize(&ds); color = interactItemColor(tg, inter, hvg); if (vis == tvDense && interactOtherChrom(inter) && color == MG_BLACK) color = MG_MAGENTA; // TODO: simplify by using start/end instead of center and width // This is a holdover from longRange track implementation unsigned lowStart, lowEnd, highStart, highEnd; if (otherChrom) { lowStart = highStart = inter->chromStart; lowEnd = highEnd = inter->chromEnd; } else if (inter->sourceStart < inter->targetStart) { lowStart = inter->sourceStart; lowEnd = inter->sourceEnd; highStart = inter->targetStart; highEnd = inter->targetEnd; } else { lowStart = inter->targetStart; lowEnd = inter->targetEnd; highStart = inter->sourceStart; highEnd = inter->sourceEnd; } unsigned s = lowStart + ((double)(lowEnd - lowStart + .5) / 2); int sx = ((s - seqStart) + .5) * scale + xOff; // x coord of center (lower region) unsigned sw = lowEnd - lowStart; int sFootWidth = scale * (double)sw / 2; // width in pixels of half foot (lower) if (sFootWidth == 0) sFootWidth = 1; unsigned e = highStart + (double)(highEnd - highStart + .5) / 2; int ex = ((e - seqStart) + .5) * scale + xOff; unsigned ew = highEnd - highStart; int eFootWidth = scale * (double)ew / 2; if (eFootWidth == 0) eFootWidth = 1; if (otherChrom) { // different chromosomes // draw below same chrom items, if any unsigned yPos = 0; int height = 0; int yOffOther = yOff; if (tg->visibility == tvDense) { height = tg->height; } else { height = otherHeight/2; yOffOther = yOff + sameHeight; } yPos = yOffOther + height; // draw the foot hvGfxLine(hvg, sx - sFootWidth, yOffOther, sx + sFootWidth, yOffOther, color); // draw the vertical // TODO: modularize directional/non-directional draws if (differentString(inter->chrom, inter->sourceChrom) && isDirectional) hvGfxDottedLine(hvg, sx, yOffOther, sx, yPos, color, TRUE); else hvGfxLine(hvg, sx, yOffOther, sx, yPos, color); if (tg->visibility == tvFull) { // add map box to foot char *nameBuf = (inter->chromStart == inter->sourceStart ? inter->sourceName : inter->targetName); mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, sx - sFootWidth, yOffOther, sFootWidth * 2, 4, tg->track, itemBuf, nameBuf, NULL, TRUE, NULL); // add map box to vertical mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, sx - 2, yOffOther, 4, height, tg->track, itemBuf, statusBuf, NULL, TRUE, NULL); if (doOtherLabels) { safef(buffer, sizeof buffer, "%s", sameString(inter->chrom, inter->sourceChrom) ? inter->targetChrom : inter->sourceChrom); hvGfxTextCentered(hvg, sx, yPos + 2, 4, 4, MG_BLUE, font, buffer); int width = vgGetFontStringWidth(hvg->vg, font, buffer); // add mapBox to label mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, sx - width/2, yPos, width, fontHeight, tg->track, itemBuf, statusBuf, NULL, TRUE, NULL); } } continue; } // draw same chromosome interaction boolean sOnScreen = (s >= seqStart) && (s < seqEnd); boolean eOnScreen = (e >= seqStart) && (e < seqEnd); double interWidth = e - s; int peakHeight = (sameHeight - 15) * ((double)interWidth / maxWidth) + 10; int peak = yOff + peakHeight; if (tg->visibility == tvDense) peak = yOff + tg->height; if (sOnScreen) { // draw foot of lower region hvGfxLine(hvg, sx - sFootWidth, yOff, sx + sFootWidth, yOff, color); // draw vertical if (!eOnScreen || draw == DRAW_LINE) { if (inter->chromStart == inter->targetStart && isDirectional) hvGfxDottedLine(hvg, sx, yOff, sx, peak, color, TRUE); else hvGfxLine(hvg, sx, yOff, sx, peak, color); } } if (eOnScreen) { // draw foot of upper region hvGfxLine(hvg, ex - eFootWidth, yOff, ex + eFootWidth, yOff, color); // draw vertical if (!sOnScreen || draw == DRAW_LINE) { if (inter->chromStart == inter->targetStart && isDirectional) hvGfxDottedLine(hvg, ex, yOff, ex, peak, color, TRUE); else hvGfxLine(hvg, ex, yOff, ex, peak, color); } } if (tg->visibility == tvFull) { char *nameBuf = NULL; if (sOnScreen) { /* add mapbox to lower region */ nameBuf = (inter->chromStart == inter->sourceStart ? inter->sourceName : inter->targetName); mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, sx - sFootWidth, yOff, sFootWidth * 2, 4, tg->track, itemBuf, nameBuf, NULL, TRUE, NULL); } if (eOnScreen) { /* add mapbox to upper region */ nameBuf = (inter->chromEnd == inter->targetEnd ? inter->targetName : inter->sourceName); mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, ex - eFootWidth, yOff, eFootWidth * 2, 4, tg->track, itemBuf, nameBuf, NULL, TRUE, NULL); } if (sOnScreen && eOnScreen && draw != DRAW_LINE) { boolean isDashed = (inter->sourceStart > inter->targetStart); if (draw == DRAW_CURVE) { int peakX = ((ex - sx + 1) / 2) + sx; int peakY = peak + 30; hvGfxCurve(hvg, sx, yOff, peakX, peakY, ex, yOff, color, isDashed); // map box on peak // FIXME: not working /*mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, peakX - 2, peakY - 2, 4, 4, tg->track, itemBuf, statusBuf, NULL, TRUE, NULL); */ } else if (draw == DRAW_ELLIPSE) { int yLeft = yOff + peakHeight; int yTop = yOff - peakHeight; hvGfxEllipseDraw(hvg, sx, yLeft, ex, yTop, color, ELLIPSE_BOTTOM, isDashed); // map box on peak // FIXME: not working /*mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, sx - sFootWidth - 2, yOff + peakHeight, 4, 4, tg->track, itemBuf, statusBuf, NULL, TRUE, NULL); */ } } else { // draw link horizontal line between regions (dense mode just shows feet ??) unsigned ePeak = eOnScreen ? ex : xOff + width; unsigned sPeak = sOnScreen ? sx : xOff; if (inter->sourceStart > inter->targetStart && isDirectional) hvGfxDottedLine(hvg, sPeak, peak, ePeak, peak, color, TRUE); else hvGfxLine(hvg, sPeak, peak, ePeak, peak, color); // map box on horizontal line mapBoxHgcOrHgGene(hvg, s, e, sPeak, peak-2, ePeak - sPeak, 4, tg->track, itemBuf, statusBuf, NULL, TRUE, NULL); // map boxes on verticals if (sOnScreen) mapBoxHgcOrHgGene(hvg, s, e, sx - 2, yOff, 4, peak - yOff, tg->track, itemBuf, statusBuf, NULL, TRUE, NULL); if (eOnScreen) mapBoxHgcOrHgGene(hvg, s, e, ex - 2, yOff, 4, peak - yOff, tg->track, itemBuf, statusBuf, NULL, TRUE, NULL); } } } } void interactDrawLeftLabels(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) /* Override default */ { } void interactMethods(struct track *tg) /* Interact track type methods */ { tg->loadItems = interactLoadItems; tg->drawItems = interactDrawItems; tg->drawLeftLabels = interactDrawLeftLabels; tg->totalHeight = interactTotalHeight; tg->mapsSelf = TRUE; } void interactCtMethods(struct track *tg) /* Interact track methods for custom track */ { interactMethods(tg); }