4f14572c392ef39b38df827df7adba1a36a75cd1 kent Wed Feb 3 08:21:48 2021 -0800 Removing barChartFitGene tag and associated code since have integrated the best part of it into the existing code. diff --git src/hg/hgTracks/barChartTrack.c src/hg/hgTracks/barChartTrack.c index 41166c4..65ee121 100644 --- src/hg/hgTracks/barChartTrack.c +++ src/hg/hgTracks/barChartTrack.c @@ -12,31 +12,30 @@ #include "fieldedTable.h" #include "facetedTable.h" #include "barChartBed.h" #include "barChartCategory.h" #include "barChartUi.h" // If a category contributes more than this percentage, its color is displayed in squish mode // Could be a trackDb setting struct barChartTrack /* Track extras */ { boolean noWhiteout; /* Suppress whiteout of graph background (allow highlight, blue lines) */ double maxMedian; /* Maximum median across all categories */ boolean doLogTransform; /* Log10(x+1) */ - boolean fitToGene; /* Fit our width to gene */ char *unit; /* Units for category values (e.g. RPKM) */ struct barChartCategory *categories; /* Category names, colors, etc. */ int categCount; /* Count of categories - derived from above */ char **categNames; /* Category names - derived from above */ char **categLabels; /* Category labels - derived from above */ struct rgbColor *colors; /* Colors for all categories */ struct hash *categoryFilter; /* NULL out excluded factors */ int maxViewLimit; // dimensions for drawing char *maxGraphSize; /* optionally limit graph size (override semantic zoom) small, medium, or large (default) */ int winMaxGraph; /* Draw large graphs if window size smaller than this */ int winMedGraph; /* Draw medium graphs if window size greater than this and smaller than winMaxGraph */ @@ -341,32 +340,32 @@ static int barChartItemHeight(struct track *tg, void *item) { int height = chartItemHeightOptionalMax(tg, item, FALSE); return height; } static int chartStandardWidth(struct track *tg, struct barChartItem *itemInfo) /* How wide is chart if we go by standard bar chart size? */ { struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; int count = filteredCategoryCount(extras); return (extras->barWidth * count) + (extras->padding * (count-1)) + 2; } -int windowsTotalIntersection(struct window *list, char *chrom, int chromStart, int chromEnd) -/* Return total size all bits of region that intersects windows list */ +static int windowsTotalIntersection(struct window *list, char *chrom, int chromStart, int chromEnd) +/* Return total size all bits of region defined by chrom/start/end that intersects windows list */ { if (list == NULL || list->next == NULL) return (double)insideWidth * (chromEnd - chromStart) / (winEnd - winStart); long long totalGenoSize = 0; int totalPixelSize = 0; struct window *w; int totalIntersect = 0; for (w = list; w != NULL; w = w->next) { totalPixelSize += w->insideWidth;; totalGenoSize += w->winEnd - w->winStart; if (sameString(w->chromName, chrom)) { int single = rangeIntersection(w->winStart, w->winEnd, chromStart, chromEnd); @@ -374,68 +373,59 @@ totalIntersect += single; } } if (totalIntersect == 0) return 0; else { return totalPixelSize * (double)totalIntersect / totalGenoSize; } } static int chartWidth(struct track *tg, struct barChartItem *itemInfo) /* How wide is the chart? */ { struct bed *bed = itemInfo->bed; -struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; int geneSize = windowsTotalIntersection(windows, bed->chrom, bed->chromStart, bed->chromEnd); -if (extras->fitToGene) - { - return geneSize; - } -else - { int standardSize = chartStandardWidth(tg, itemInfo); return max(standardSize, geneSize); } -} static void barChartLoadItems(struct track *tg) /* Load method for track items */ { /* Initialize colors for visibilities that don't display actual barchart */ if (tg->visibility == tvSquish || tg->limitedVis == tvSquish) tg->itemColor = barChartItemColor; tg->colorShades = shadesOfGray; /* Get track UI info */ struct barChartTrack *extras; if (!tg->extraUiData) { AllocVar(extras); tg->extraUiData = extras; } extras = (struct barChartTrack *)tg->extraUiData; extras->colors = getCategoryColors(tg); struct trackDb *tdb = tg->tdb; extras->doLogTransform = barChartIsLogTransformed(cart, tdb->track, tdb); extras->maxMedian = barChartUiMaxMedianScore(tdb); extras->noWhiteout = cartUsualBooleanClosestToHome(cart, tdb, FALSE, BAR_CHART_NO_WHITEOUT, BAR_CHART_NO_WHITEOUT_DEFAULT); -extras->fitToGene = trackDbSettingClosestToHomeOn(tdb, BAR_CHART_FIT_TO_GENE); extras->maxViewLimit = barChartCurViewMax(cart, tg->track, tg->tdb); extras->maxGraphSize = trackDbSettingClosestToHomeOrDefault(tdb, BAR_CHART_MAX_GRAPH_SIZE, BAR_CHART_MAX_GRAPH_SIZE_DEFAULT); extras->unit = trackDbSettingClosestToHomeOrDefault(tdb, BAR_CHART_UNIT, ""); /* Set barchart dimensions to draw. For three window sizes */ #define MAX_BAR_CHART_MODEL_HEIGHT 2 #define MED_BAR_CHART_MODEL_HEIGHT 2 #define SMALL_BAR_CHART_MODEL_HEIGHT 1 #define MIN_BAR_CHART_MODEL_HEIGHT 1 #define WIN_MAX_GRAPH_DEFAULT 50000 #define MAX_GRAPH_HEIGHT 175 #define MAX_BAR_WIDTH 5 @@ -603,77 +593,51 @@ struct barChartItem *itemInfo = (struct barChartItem *)item; struct bed *bed = itemInfo->bed; if (vis == tvDense) { bedDrawSimpleAt(tg, bed, hvg, xOff, y, scale, font, MG_WHITE, vis); // color ignored (using grayscale) return; } if (vis == tvSquish) { Color color = barChartItemColor(tg, bed, hvg); int height = extras->squishHeight; drawScaledBox(hvg, bed->chromStart, bed->chromEnd, scale, xOff, y, height, color); return; } -int graphX = barChartX(bed); -if (graphX < 0) - return; - // draw line to show range of item on the genome (since chart is fixed width) int topGraphHeight = chartHeight(tg, itemInfo); topGraphHeight = max(topGraphHeight, tl.fontHeight); int yZero = topGraphHeight + y - 1; // yZero is bottom of graph int yGene = yZero + extras->margin; int heightPer = tg->heightPer; tg->heightPer = extras->modelHeight; int height = extras->boxModelHeight; drawScaledBox(hvg, bed->chromStart, bed->chromEnd, scale, xOff, yGene+1, height, MG_GRAY); tg->heightPer = heightPer; } static int barChartNonPropPixelWidth(struct track *tg, void *item) /* Return end chromosome coordinate of item, including graph */ { struct barChartItem *itemInfo = (struct barChartItem *)item; int graphWidth = chartWidth(tg, itemInfo); return graphWidth; } -static void findBarPosX(int chromStart, int chromEnd, double scale, int barIx, int barCount, int *pStart, int *pEnd) -/* Figure out start/end position of our bar's region */ -{ -int baseWidth = chromEnd - chromStart; -double scaledSize = baseWidth *scale; -double oneWidth = scaledSize/barCount; -double barThinner = 1.0; -if (oneWidth >= 5.0) - { - if (oneWidth > 7.0) - barThinner = 0.8; - else - barThinner = 0.75; - } - -int iStart = baseWidth*barIx/barCount; -int iEnd = baseWidth*(barIx+1)/barCount; -int iWidth = iEnd - iStart; -int start = *pStart = iStart + chromStart; -*pEnd = start + iWidth*barThinner; -} - static void barChartNonPropDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis) { if (vis != tvFull && vis != tvPack) return; struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; struct barChartItem *itemInfo = (struct barChartItem *)item; struct bed *bed = itemInfo->bed; int topGraphHeight = chartHeight(tg, itemInfo); int graphWidth = chartWidth(tg, itemInfo); #ifdef OLD #endif /* OLD */ topGraphHeight = max(topGraphHeight, tl.fontHeight); int yZero = topGraphHeight + y - 1; // yZero is bottom of graph @@ -804,52 +768,49 @@ int labelWidth = mgFontStringWidth(tl.font, itemName); getItemX(start, end, &x1, &x2); if (x1-labelWidth <= insideX) labelWidth = 0; // map over label int itemHeight = itemInfo->height; mapBoxHc(hvg, itemStart, itemEnd, x1-labelWidth, y, labelWidth, itemHeight-3, tg->track, mapItemName, itemName); // add maps to category bars struct barChartCategory *categs = getCategories(tg); struct barChartCategory *categ = NULL; int graphX = barChartX(bed); -if (graphX < 0) - return; int graphWidth = chartWidth(tg, itemInfo); int x0 = insideX + graphX; int barCount = filteredCategoryCount(extras); double invCount = 1.0/barCount; int i = 0, barsDrawn = 0; for (categ = categs; categ != NULL; categ = categ->next, i++) { if (!filterCategory(extras, categ->name)) continue; x1 = barsDrawn * graphWidth * invCount; barsDrawn += 1; x2 = barsDrawn * graphWidth * invCount; - int width = x2-x1; + int width = max(1, x2-x1); double expScore = bed->expScores[i]; int height = valToClippedHeight(expScore, extras->maxMedian, extras->maxViewLimit, extras->maxHeight, extras->doLogTransform); mapBoxHc(hvg, itemStart, itemEnd, x0 + x1, yZero-height, width, height, tg->track, mapItemName, chartMapText(tg, categ, expScore)); - x1 = x1 + extras->barWidth + extras->padding; } // map over background of chart getItemX(start, end, &x1, &x2); mapBoxHc(hvg, itemStart, itemEnd, x1, y, graphWidth, itemHeight-3, tg->track, mapItemName, itemName); } /* This is lifted nearly wholesale from gtexGene track. Could be shared */ static int getBarChartHeight(void *item) { struct barChartItem *itemInfo = (struct barChartItem *)item; assert(itemInfo->height != 0); return itemInfo->height; @@ -939,144 +900,40 @@ struct bed *bed = chartItem->bed; return bed->name; } static char *barChartItemName(struct track *tg, void *item) /* Return item name for labeling */ { struct barChartItem *chartItem = (struct barChartItem *)item; struct bed *bed = chartItem->bed; if (tg->isBigBed) return bigBedItemName(tg, bed); return bed->name; } -static void barsToGeneDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, - double scale, MgFont *font, Color color, enum trackVisibility vis) -/* Draw bar chart over item in proportional to gene way*/ -{ -if (vis != tvFull && vis != tvPack) - { - barChartDrawAt(tg, item, hvg, xOff, y, scale, font, color, vis); - return; - } - -/* Fetch our item and the bed from it */ -struct barChartItem *itemInfo = (struct barChartItem *)item; -struct bed *bed = itemInfo->bed; - -/* Figure out where to draw things in Y dimension */ -struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; -int topGraphHeight = chartHeight(tg, itemInfo); -topGraphHeight = max(topGraphHeight, tl.fontHeight); -int yZero = topGraphHeight + y - 1; // yZero is bottom of graph -int yGene = yZero + extras->margin; - -/* Figure out width between bars */ -int barCount = filteredCategoryCount(extras); -int expCount = bed->expCount; - - -int i; -Color clipColor = MG_MAGENTA; -int outBarIx = 0; -struct barChartCategory *categ; -for (i=0, categ=extras->categories; i<expCount && categ != NULL; ++i, categ=categ->next) - { - if (!filterCategory(extras, categ->name)) - continue; - struct rgbColor rgb = extras->colors[i]; - int color = hvGfxFindColorIx(hvg, rgb.r, rgb.g, rgb.b); - int cStart, cEnd; - findBarPosX(bed->chromStart, bed->chromEnd, scale, outBarIx, barCount, &cStart, &cEnd); - double expScore = bed->expScores[i]; - int height = valToClippedHeight(expScore, extras->maxMedian, extras->maxViewLimit, - extras->maxHeight, extras->doLogTransform); - drawScaledBox(hvg, cStart, cEnd, scale, xOff, y+topGraphHeight-height, height, color); - if (!extras->doLogTransform && expScore > extras->maxViewLimit) - drawScaledBox(hvg, cStart, cEnd, scale, xOff, yZero-height+1, 2, clipColor); - ++outBarIx; - } - - -// Draw the line our graph sits on top of -drawScaledBox(hvg, bed->chromStart, bed->chromEnd, scale, xOff, yGene+1, extras->boxModelHeight, - MG_GRAY); -} - -static void barsToGeneMapItem(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 on item and label, and one for each category (bar in the graph) */ -{ -enum trackVisibility vis = trackVisAfterLimit(tg); -if (vis != tvFull && vis != tvPack) - { - barChartMapItem(tg, hvg, item, itemName, mapItemName, start, end, x, y, width, height); - return; - } -struct barChartTrack *extras = tg->extraUiData; -struct barChartItem *itemInfo = item; -struct bed *bed = itemInfo->bed; -int barCount = filteredCategoryCount(extras); -if (width > barCount) // When get down to less than a pixel suppress the bar-by-bar map boxes*/ - { - int i = 0; - int outBarIx = 0; - struct barChartCategory *categs = getCategories(tg); - struct barChartCategory *categ; - int topGraphHeight = chartHeight(tg, itemInfo); - double scale = scaleForWindow(insideWidth, winStart, winEnd); - for (categ = categs; categ != NULL; categ = categ->next, i++) - { - if (!filterCategory(extras, categ->name)) - continue; - int cStart, cEnd; - findBarPosX(bed->chromStart, bed->chromEnd, scale, outBarIx, barCount, &cStart, &cEnd); - int x1,x2; - if (scaledBoxToPixelCoords(cStart, cEnd, scale, 0, &x1, &x2)) - { - double expScore = bed->expScores[i]; - int height = valToClippedHeight(expScore, extras->maxMedian, extras->maxViewLimit, - extras->maxHeight, extras->doLogTransform); - mapBoxHc(hvg, bed->chromStart, bed->chromEnd, x1+insideX, y+topGraphHeight-height, x2-x1, height, - tg->track, mapItemName, chartMapText(tg, categ, expScore)); - } - ++outBarIx; - } - } -mapBoxHc(hvg, bed->chromStart, bed->chromEnd, x, y, width, height, tg->track, itemName, NULL); -} - void barChartMethods(struct track *tg) /* Bar Chart track type: draw fixed width chart of colored bars over a BED item */ { tg->bedSize = 8; bedMethods(tg); tg->canPack = TRUE; tg->loadItems = barChartLoadItems; tg->itemName = barChartItemName; tg->mapItemName = barChartMapItemName; tg->itemHeight = barChartItemHeight; tg->itemStart = barChartItemStart; tg->itemEnd = barChartItemEnd; tg->totalHeight = barChartTotalHeight; -if (trackDbSettingClosestToHomeOn(tg->tdb, BAR_CHART_FIT_TO_GENE)) - { - tg->drawItemAt = barsToGeneDrawAt; - tg->mapItem = barsToGeneMapItem; - } -else - { tg->preDrawItems = barChartPreDrawItems; tg->drawItemAt = barChartDrawAt; tg->mapItem = barChartMapItem; tg->nonPropDrawItemAt = barChartNonPropDrawAt; tg->nonPropPixelWidth = barChartNonPropPixelWidth; } -} void barChartCtMethods(struct track *tg) /* Bar Chart track methods for custom track */ { barChartMethods(tg); }