7d70cdf40567dbcfd3a190c844d99046aced5637 kate Thu Apr 9 13:58:39 2020 -0700 Add settings to define window sizes for small/medium/large graphs. Useful for small (e.g. virus) genomes. Prompted by Max barCharts on wuhCor1. refs #25339 diff --git src/hg/hgTracks/barChartTrack.c src/hg/hgTracks/barChartTrack.c index 88e249a..56a4913 100644 --- src/hg/hgTracks/barChartTrack.c +++ src/hg/hgTracks/barChartTrack.c @@ -1,802 +1,810 @@ /* 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: can't find id %d\n", id); 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 = cartUsualBooleanClosestToHome(cart, tdb, FALSE, BAR_CHART_LOG_TRANSFORM, BAR_CHART_LOG_TRANSFORM_DEFAULT); extras->maxMedian = barChartUiMaxMedianScore(tdb); extras->noWhiteout = cartUsualBooleanClosestToHome(cart, tdb, FALSE, BAR_CHART_NO_WHITEOUT, BAR_CHART_NO_WHITEOUT_DEFAULT); extras->maxViewLimit = (double)cartUsualIntClosestToHome(cart, tg->tdb, FALSE, BAR_CHART_MAX_VIEW_LIMIT, BAR_CHART_MAX_VIEW_LIMIT_DEFAULT); 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 WIN_MAX_GRAPH 50000 -#define WIN_MED_GRAPH 500000 #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 50000 +#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 500000 +#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 +char *setting = trackDbSetting(tdb, BAR_CHART_WIN_MAX_GRAPH); +extras->winMaxGraph = isNotEmpty(setting) ? atoi(setting) : WIN_MAX_GRAPH_DEFAULT; +setting = trackDbSetting(tdb, BAR_CHART_WIN_MED_GRAPH); +extras->winMedGraph = isNotEmpty(setting) ? atoi(setting) : WIN_MED_GRAPH_DEFAULT; + int scale = (getCategoryCount(tg) < 15 ? 2 : 1); long winSize = virtWinBaseCount; -if (winSize < WIN_MAX_GRAPH && sameString(extras->maxGraphSize, BAR_CHART_MAX_GRAPH_SIZE_LARGE)) +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 < WIN_MED_GRAPH && differentString(extras->maxGraphSize, BAR_CHART_MAX_GRAPH_SIZE_SMALL)) +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; } 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, 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; } 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; tg->nonPropDrawItemAt = barChartNonPropDrawAt; tg->nonPropPixelWidth = barChartNonPropPixelWidth; } void barChartCtMethods(struct track *tg) /* Bar Chart track methods for custom track */ { barChartMethods(tg); }