4b572c8e95475106bbaf594bca1907c42bfb02fd kent Sat Jan 23 11:44:41 2021 -0800 First cut of barChartFitGene to look at. Showing correct colors and bars and stretching. Getting spacing between bars in still to be done and some other things, but it's looking good in a lot of ways. Will let us zoom into the bars for sure anyway. diff --git src/hg/hgTracks/barChartTrack.c src/hg/hgTracks/barChartTrack.c index e1a4dd6..f0a425d 100644 --- src/hg/hgTracks/barChartTrack.c +++ src/hg/hgTracks/barChartTrack.c @@ -1,841 +1,914 @@ /* barGraph tracks - display a colored bargraph across each region in a file */ /* Copyright (C) 2015 The Regents of the University of California * See README in this or parent directory for licensing extrasrmation. */ #include "common.h" #include "hgTracks.h" #include "bed.h" #include "hvGfx.h" #include "spaceSaver.h" #include "hubConnect.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 #define SPECIFICITY_THRESHOLD 10 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) */ 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 */ int squishHeight; /* Height of item in squish mode (larger than typical) */ int boxModelHeight; /* Height of indicator box drawn under graph to show gene extent */ int modelHeight; /* Height of box drawn under graph with padding */ int barWidth; /* Width of individual bar in pixels */ int margin; int padding; int maxHeight; }; struct barChartItem /* BED item plus computed values for display */ { struct barChartItem *next; /* Next in singly linked list */ struct bed *bed; /* Item coords, name, exp count and values */ int height; /* Item height in pixels */ }; /***********************************************/ /* Organize category info */ struct barChartCategory *getCategories(struct track *tg) /* Get and cache category extras */ { struct barChartTrack *extras; if (!tg->extraUiData) { AllocVar(extras); tg->extraUiData = extras; } extras = (struct barChartTrack *)tg->extraUiData; if (extras->categories == NULL) extras->categories = barChartUiGetCategories(database, tg->tdb); return extras->categories; } int getCategoryCount(struct track *tg) /* Get and cache the number of categories */ { struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; if (extras->categCount == 0) extras->categCount = slCount(getCategories(tg)); return extras->categCount; } char *getCategoryName(struct track *tg, int id) /* Get category name from id, cacheing */ { struct barChartCategory *categ; int count = getCategoryCount(tg); struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; if (!extras->categNames) { struct barChartCategory *categs = getCategories(tg); AllocArray(extras->categNames, count); for (categ = categs; categ != NULL; categ = categ->next) extras->categNames[categ->id] = cloneString(categ->name); } if (id >= count) { warn("Bar chart track '%s': can't find sample ID %d in category file with %d categories. The category file is a two-column file where sample IDs are associated to categories, specified with the setting 'barChartSampleUrl'.\n", tg->shortLabel, id, count); return NULL; // Exclude this category } return extras->categNames[id]; } char *getCategoryLabel(struct track *tg, int id) /* Get category descriptive label from id, cacheing */ { struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; struct barChartCategory *categ; int count = getCategoryCount(tg); if (!extras->categLabels) { struct barChartCategory *categs = getCategories(tg); AllocArray(extras->categLabels, count); for (categ = categs; categ != NULL; categ = categ->next) extras->categLabels[categ->id] = cloneString(categ->label); } if (id >= count) errAbort("Bar chart track: can't find id %d\n", id); return extras->categLabels[id]; } struct rgbColor *getCategoryColors(struct track *tg) /* Get RGB colors from category table */ { struct barChartCategory *categs = getCategories(tg); struct barChartCategory *categ = NULL; int count = slCount(categs); struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; if (!extras->colors) { AllocArray(extras->colors, count); int i = 0; for (categ = categs; categ != NULL; categ = categ->next) { extras->colors[i] = (struct rgbColor){.r=COLOR_32_BLUE(categ->color), .g=COLOR_32_GREEN(categ->color), .b=COLOR_32_RED(categ->color)}; i++; } } return extras->colors; } static void filterCategories(struct track *tg) /* Check cart for category selection. NULL out unselected categorys in category list */ { struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; struct barChartCategory *categ = NULL; extras->categories = getCategories(tg); extras->categoryFilter = hashNew(0); if (cartListVarExistsAnyLevel(cart, tg->tdb, FALSE, BAR_CHART_CATEGORY_SELECT)) { struct slName *selectedValues = cartOptionalSlNameListClosestToHome(cart, tg->tdb, FALSE, BAR_CHART_CATEGORY_SELECT); if (selectedValues != NULL) { struct slName *name; for (name = selectedValues; name != NULL; name = name->next) hashAdd(extras->categoryFilter, name->name, name->name); return; } } /* no filter */ for (categ = extras->categories; categ != NULL; categ = categ->next) hashAdd(extras->categoryFilter, categ->name, categ->name); } static int filteredCategoryCount(struct barChartTrack *extras) /* Count of categories to display */ { return hashNumEntries(extras->categoryFilter); } static boolean filterCategory(struct barChartTrack *extras, char *name) /* Does category pass filter */ { if (name == NULL) return FALSE; return (hashLookup(extras->categoryFilter, name) != NULL); } static int maxCategoryForItem(struct bed *bed, int threshold) /* Return id of highest valued category for an item, if significantly higher than median. * If none are over threshold, return -1 */ { double maxScore = 0.0, expScore; double totalScore = 0.0; int maxNum = 0, i; int expCount = bed->expCount; for (i=0; i<expCount; i++) { expScore = bed->expScores[i]; if (expScore > maxScore) { maxScore = max(maxScore, expScore); maxNum = i; } totalScore += expScore; } // threshold to consider this item category specific -- a category contributes > threshold % to // total level if (totalScore < 1 || maxScore <= (totalScore * threshold * .01)) return -1; return maxNum; } static Color barChartItemColor(struct track *tg, void *item, struct hvGfx *hvg) /* A bit of category-specific coloring in squish mode only, on bed item */ { struct bed *bed = (struct bed *)item; int id = maxCategoryForItem(bed, SPECIFICITY_THRESHOLD); if (id < 0) return MG_BLACK; struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; struct rgbColor color = extras->colors[id]; return hvGfxFindColorIx(hvg, color.r, color.g, color.b); } // Convenience functions for draw static int valToHeight(double val, double maxVal, int maxHeight, boolean doLogTransform) /* Log-scale and convert a value from 0 to maxVal to 0 to maxHeight-1 */ { if (val == 0.0) return 0; double scaled = 0.0; if (doLogTransform) scaled = log10(val+1.0) / log10(maxVal+1.0); else scaled = val/maxVal; if (scaled < 0) warn("scaled=%f\n", scaled); return (scaled * (maxHeight-1)); } static int valToClippedHeight(double val, double maxVal, int maxView, int maxHeight, boolean doLogTransform) /* Convert a value from 0 to maxVal to 0 to maxHeight-1, with clipping, or log transform the value */ { double useVal = val; double useMax = maxVal; if (!doLogTransform) { useMax = maxView; if (val > maxView) useVal = maxView; } return valToHeight(useVal, useMax, maxHeight, doLogTransform); } static int chartHeight(struct track *tg, struct barChartItem *itemInfo) /* Determine height in pixels of graph. This will be the box for category with highest value */ { struct bed *bed = (struct bed *)itemInfo->bed; struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; int i; double maxExp = 0.0; int expCount = bed->expCount; double expScore; for (i=0; i<expCount; i++) { if (!filterCategory(extras, getCategoryName(tg, i))) continue; expScore = bed->expScores[i]; maxExp = max(maxExp, expScore); } return valToClippedHeight(maxExp, extras->maxMedian, extras->maxViewLimit, extras->maxHeight, extras->doLogTransform); } static int chartItemHeightOptionalMax(struct track *tg, void *item, boolean isMax) { // It seems that this can be called early or late struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; enum trackVisibility vis = tg->visibility; if (tg->limitedVisSet) vis = tg->limitedVis; int height; if (vis == tvSquish || vis == tvDense) { if (vis == tvSquish) { tg->lineHeight = extras->squishHeight; tg->heightPer = tg->lineHeight; } height = tgFixedItemHeight(tg, item); return height; } if (isMax) { int extra = 0; height= extras->maxHeight + extras->margin + extras->modelHeight + extra; return height; } if (item == NULL) return 0; struct barChartItem *itemInfo = (struct barChartItem *)item; if (itemInfo->height != 0) { return itemInfo->height; } int topGraphHeight = chartHeight(tg, itemInfo); topGraphHeight = max(topGraphHeight, tl.fontHeight); int bottomGraphHeight = 0; height = topGraphHeight + bottomGraphHeight + extras->margin + extras->modelHeight; return height; } static int barChartItemHeight(struct track *tg, void *item) { int height = chartItemHeightOptionalMax(tg, item, FALSE); return height; } 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->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 MIN_BAR_CHART_MODEL_HEIGHT 1 #define WIN_MAX_GRAPH_DEFAULT 50000 #define MAX_GRAPH_HEIGHT 175 #define MAX_BAR_WIDTH 5 #define MAX_GRAPH_PADDING 2 #define WIN_MED_GRAPH_DEFAULT 500000 #define MED_GRAPH_HEIGHT 100 #define MED_BAR_WIDTH 3 #define MED_GRAPH_PADDING 1 #define MIN_BAR_WIDTH 1 #define MIN_GRAPH_PADDING 0 extras->winMaxGraph = WIN_MAX_GRAPH_DEFAULT; extras->winMedGraph = WIN_MED_GRAPH_DEFAULT; char *setting = trackDbSetting(tdb, BAR_CHART_SIZE_WINDOWS); if (isNotEmpty(setting)) { char *words[2]; int ct = chopLine(setting, words); if (ct == 2) { extras->winMaxGraph = atoi(words[0]); extras->winMedGraph = atoi(words[1]); } } int barCount = getCategoryCount(tg); double scale = 1.0; if (barCount <= 20) scale = 2.5; else if (barCount <= 40) scale = 1.6; else if (barCount <= 60) scale = 1.0; else if (barCount <= 120) scale = 0.9; else if (barCount <= 200) scale = 0.75; else scale = 0.5; long winSize = virtWinBaseCount; if (winSize < extras->winMaxGraph && sameString(extras->maxGraphSize, BAR_CHART_MAX_GRAPH_SIZE_LARGE)) { extras->boxModelHeight = MAX_BAR_CHART_MODEL_HEIGHT; extras->barWidth = MAX_BAR_WIDTH * scale; extras->padding = MAX_GRAPH_PADDING; extras->maxHeight = MAX_GRAPH_HEIGHT; } else if (winSize < extras->winMedGraph && differentString(extras->maxGraphSize, BAR_CHART_MAX_GRAPH_SIZE_SMALL)) { extras->boxModelHeight = MED_BAR_CHART_MODEL_HEIGHT; extras->barWidth = MED_BAR_WIDTH * scale; extras->padding = MED_GRAPH_PADDING; extras->maxHeight = MED_GRAPH_HEIGHT; } else { extras->boxModelHeight = MIN_BAR_CHART_MODEL_HEIGHT; extras->barWidth = MIN_BAR_WIDTH * scale; extras->padding = MIN_GRAPH_PADDING; extras->maxHeight = tl.fontHeight * 4; } if (extras->barWidth == 1 && extras->padding == 1) { extras->barWidth = 2; extras->padding = 0; } if (extras->barWidth < 1) { extras->barWidth = 1; extras->padding = 0; } extras->modelHeight = extras->boxModelHeight + 3; extras->margin = 1; extras->squishHeight = tl.fontHeight - tl.fontHeight/2; /* Get bed (names and all-sample category median scores) in range */ loadSimpleBedWithLoader(tg, (bedItemLoader)barChartSimpleBedLoad); /* Create itemInfo items with BED and geneModels */ struct barChartItem *itemInfo = NULL, *list = NULL; struct bed *bed = (struct bed *)tg->items; /* Test that configuration matches data file */ if (bed != NULL) { int categCount = getCategoryCount(tg); int expCount = bed->expCount; if (categCount != expCount) warn("Bar chart track: category count mismatch between trackDb (%d) and data file (%d)", categCount, expCount); } filterCategories(tg); while (bed != NULL) { AllocVar(itemInfo); itemInfo->bed = bed; slAddHead(&list, itemInfo); bed = bed->next; itemInfo->bed->next = NULL; itemInfo->height = barChartItemHeight(tg, itemInfo); } slReverse(&list); tg->items = list; } /***********************************************/ /* Draw */ static int chartWidth(struct track *tg, struct barChartItem *itemInfo) { struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; int count = filteredCategoryCount(extras); return (extras->barWidth * count) + (extras->padding * (count-1)) + 2; } static int barChartX(struct bed *bed) /* Locate chart on X, relative to viewport. */ { int start = max(bed->chromStart, winStart); double scale = scaleForWindow(insideWidth, winStart, winEnd); int x1 = round((start - winStart) * scale); return x1; } static void drawGraphBox(struct track *tg, struct barChartItem *itemInfo, struct hvGfx *hvg, int x, int y) /* Draw white background for graph */ { Color lighterGray = MAKECOLOR_32(0xF3, 0xF3, 0xF3); int width = chartWidth(tg, itemInfo); int height = chartHeight(tg, itemInfo); hvGfxOutlinedBox(hvg, x, y-height, width, height, MG_WHITE, lighterGray); } static void drawGraphBase(struct track *tg, struct barChartItem *itemInfo, struct hvGfx *hvg, int x, int y) /* Draw faint line under graph to delineate extent when bars are missing (category w/ 0 value) */ { Color lightGray = MAKECOLOR_32(0xD1, 0xD1, 0xD1); int graphWidth = chartWidth(tg, itemInfo); hvGfxBox(hvg, x, y, graphWidth, 1, lightGray); } static void barChartDrawAt(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 */ { struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; struct barChartItem *itemInfo = (struct barChartItem *)item; struct bed *bed = (struct 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 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 = (struct bed *)itemInfo->bed; int topGraphHeight = chartHeight(tg, itemInfo); topGraphHeight = max(topGraphHeight, tl.fontHeight); int yZero = topGraphHeight + y - 1; // yZero is bottom of graph int graphX = barChartX(bed); int x1 = xOff + graphX; // x1 is at left of graph int keepX = x1; drawGraphBase(tg, itemInfo, hvg, keepX, yZero+1); if (!extras->noWhiteout) drawGraphBox(tg, itemInfo, hvg, keepX, yZero+1); struct rgbColor lineColor = {.r=0}; int lineColorIx = hvGfxFindColorIx(hvg, lineColor.r, lineColor.g, lineColor.b); int barWidth = extras->barWidth; char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, BAR_CHART_COLORS, BAR_CHART_COLORS_DEFAULT); Color clipColor = MG_MAGENTA; // draw bar graph int i; int expCount = bed->expCount; 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 fillColor = extras->colors[i]; int fillColorIx = hvGfxFindColorIx(hvg, fillColor.r, fillColor.g, fillColor.b); double expScore = bed->expScores[i]; int height = valToClippedHeight(expScore, extras->maxMedian, extras->maxViewLimit, extras->maxHeight, extras->doLogTransform); if (extras->padding == 0 || sameString(colorScheme, BAR_CHART_COLORS_USER)) hvGfxBox(hvg, x1, yZero-height+1, barWidth, height, fillColorIx); else hvGfxOutlinedBox(hvg, x1, yZero-height+1, barWidth, height, fillColorIx, lineColorIx); // mark clipped bar with magenta tip if (!extras->doLogTransform && expScore > extras->maxViewLimit) hvGfxBox(hvg, x1, yZero-height+1, barWidth, 2, clipColor); x1 = x1 + barWidth + extras->padding; } } static char *chartMapText(struct track *tg, struct barChartCategory *categ, double expScore) /* Construct mouseover text for a chart bar */ { static char buf[128]; struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; safef(buf, sizeof(buf), "%s (%.1f %s)", categ->label, expScore, extras->unit); return buf; } static int barChartItemStart(struct track *tg, void *item) /* Return end chromosome coordinate of item, including graph */ { struct barChartItem *itemInfo = (struct barChartItem *)item; struct bed *bed = (struct bed *)itemInfo->bed; return bed->chromStart; } static int barChartItemEnd(struct track *tg, void *item) /* Return end chromosome coordinate of item, including graph */ { struct barChartItem *itemInfo = (struct barChartItem *)item; struct bed *bed = (struct bed *)itemInfo->bed; double scale = scaleForWindow(insideWidth, winStart, winEnd); int graphWidth = chartWidth(tg, itemInfo); return max(bed->chromEnd, max(winStart, bed->chromStart) + graphWidth/scale); } static void getItemX(int start, int end, int *x1, int *x2) /* Return startX, endX based on item coordinates and current window */ // Residual (largely replaced by drawScaledBox -- still used by gene model bmap box { int s = max(start, winStart); int e = min(end, winEnd); double scale = scaleForWindow(insideWidth, winStart, winEnd); assert(x1); *x1 = round((double)((int)s-winStart)*scale + insideX); assert(x2); *x2 = round((double)((int)e-winStart)*scale + insideX); } static void barChartMapItem(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) in * pack or full mode. Just single map for squish/dense modes */ { if (tg->limitedVis == tvDense) { genericMapItem(tg, hvg, item, itemName, itemName, start, end, x, y, width, height); return; } struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; struct barChartItem *itemInfo = (struct barChartItem *)item; struct bed *bed = (struct bed *)itemInfo->bed; int itemStart = bed->chromStart; int itemEnd = bed->chromEnd; int x1, x2; if (tg->limitedVis == tvSquish) { int categId = maxCategoryForItem(bed, SPECIFICITY_THRESHOLD); char *maxCateg = ""; if (categId > 1) maxCateg = getCategoryLabel(tg, categId); char buf[128]; safef(buf, sizeof buf, "%s %s", bed->name, maxCateg); getItemX(itemStart, itemEnd, &x1, &x2); int width = max(1, x2-x1); mapBoxHc(hvg, itemStart, itemEnd, x1, y, width, height, tg->track, mapItemName, buf); return; } int topGraphHeight = chartHeight(tg, itemInfo); topGraphHeight = max(topGraphHeight, tl.fontHeight); // label int yZero = topGraphHeight + y - 1; // yZero is bottom of graph // add map box to item label 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; // x1 is at left of graph x1 = insideX + graphX; int i = 0; for (categ = categs; categ != NULL; categ = categ->next, i++) { if (!filterCategory(extras, categ->name)) continue; double expScore = bed->expScores[i]; int height = valToClippedHeight(expScore, extras->maxMedian, extras->maxViewLimit, extras->maxHeight, extras->doLogTransform); mapBoxHc(hvg, itemStart, itemEnd, x1, yZero-height, extras->barWidth + extras->padding, height, tg->track, mapItemName, chartMapText(tg, categ, expScore)); x1 = x1 + extras->barWidth + extras->padding; } // map over background of chart int graphWidth = chartWidth(tg, itemInfo); 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; } /* This is lifted nearly wholesale from gtexGene track. Could be shared */ static int barChartTotalHeight(struct track *tg, enum trackVisibility vis) /* Figure out total height of track. Set in track and also return it */ { int height = 0; int lineHeight = 0; int heightPer = 0; if (vis == tvDense) { heightPer = tl.fontHeight; lineHeight=heightPer+1; } else if (vis == tvSquish) { // for visibility, set larger than the usual squish, which is half font height struct barChartTrack *extras = (struct barChartTrack *)tg->extraUiData; heightPer = extras->squishHeight * 2; // the squish packer halves this lineHeight=heightPer+1; } else if ((vis == tvPack) || (vis == tvFull)) { heightPer = tl.fontHeight; lineHeight=heightPer; } height = tgFixedTotalHeightOptionalOverflow(tg, vis, lineHeight, heightPer, FALSE); if ((vis == tvPack) || (vis == tvFull)) { // set variable height rows if (tg->ss && tg->ss->rowCount) { if (!tg->ss->rowSizes) { // collect the rowSizes data across all windows assert(currentWindow==windows); // first window assert(tg->ss->vis == vis); // viz matches, we have the right one struct spaceSaver *ssHold; AllocVar(ssHold); struct track *tgSave = tg; for(tg=tgSave; tg; tg=tg->nextWindow) { assert(tgSave->ss->vis == tg->ss->vis); // viz matches, we have the right one spaceSaverSetRowHeights(tg->ss, ssHold, getBarChartHeight); } // share the rowSizes data across all windows for(tg=tgSave; tg; tg=tg->nextWindow) { tg->ss->rowSizes = ssHold->rowSizes; } tg = tgSave; } struct spaceSaver *ss = findSpaceSaver(tg, vis); // ss is a list now assert(ss); // viz matches, we have the right one height = spaceSaverGetRowHeightsTotal(ss); } } tg->height = height; return height; } static void barChartPreDrawItems(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) { if (vis == tvSquish || vis == tvDense) { // NonProp routines not relevant to these modes, and they interfere // NOTE: they must be installed by barChartMethods() for pack mode tg->nonPropDrawItemAt = NULL; tg->nonPropPixelWidth = NULL; } } static char *barChartMapItemName(struct track *tg, void *item) /* Return item name for click handler */ { struct barChartItem *chartItem = (struct barChartItem *)item; struct bed *bed = (struct 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 = (struct 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*/ +{ +/* Fetch our item and the bed from it */ +struct barChartItem *itemInfo = (struct barChartItem *)item; +struct bed *bed = itemInfo->bed; +double baseWidth = bed->chromEnd - bed->chromStart; + +/* 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 */ +double xStart = (bed->chromStart- winStart) * scale; +double xEnd = (bed->chromEnd - winStart)* scale; +int pixelWidth = xEnd - xStart; +int barCount = bed->expCount; +double oneWidth = pixelWidth/barCount; + +/* Figure out how much space to leave between bars */ +int barSpacing = round(oneWidth/10); +if (barSpacing == 0) + { + if (oneWidth >= 3) + barSpacing = 1; + } + +// drawScaledBox(hvg, bed->chromStart, bed->chromEnd, scale, xOff, y, topGraphHeight, MG_YELLOW); // ugly debug + +int i; +// int lastEnd = xStart + xOff; +Color clipColor = MG_MAGENTA; +for (i=0; i<barCount; ++i) + { + struct rgbColor rgb = extras->colors[i]; + int color = hvGfxFindColorIx(hvg, rgb.r, rgb.g, rgb.b); + int cStart = bed->chromStart + baseWidth*i/barCount; + int cEnd = bed->chromStart + baseWidth*(i+1)/barCount; + 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); + } + + +// 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) */ +{ +struct barChartItem *chartItem = (struct barChartItem *)item; +struct bed *bed = (struct bed *)chartItem->bed; +genericMapItem(tg, hvg, item, bed->name, bed->name, start, end, x, y, width, height); +} + 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->drawItemAt = barChartDrawAt; -tg->preDrawItems = barChartPreDrawItems; tg->loadItems = barChartLoadItems; -tg->mapItem = barChartMapItem; tg->itemName = barChartItemName; tg->mapItemName = barChartMapItemName; tg->itemHeight = barChartItemHeight; tg->itemStart = barChartItemStart; tg->itemEnd = barChartItemEnd; tg->totalHeight = barChartTotalHeight; +if (trackDbSettingClosestToHomeOn(tg->tdb, "barChartFitGene")) + { + 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); }