fd877baf9f8076f760de6d00931347b9db2a7053 kate Wed Nov 25 11:31:38 2015 -0800 Remove ifdefs for multi-region. diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c index 2d12b65..30acd84 100644 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@ -1,67 +1,60 @@ /* GTEx (Genotype Tissue Expression) tracks */ /* Copyright (C) 2015 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "hgTracks.h" #include "hvGfx.h" #include "rainbow.h" #include "gtexInfo.h" #include "gtexGeneBed.h" #include "gtexTissue.h" #include "gtexTissueData.h" #include "gtexUi.h" -// TODO: move spaceSaver code to simpleTracks #include "spaceSaver.h" -// NOTE: Sections to change for multi-region (vertical slice) display -// are marked with #ifdef MULTI_REGION. WARNING: These sections -// are a bit out-of-date (refer to #ifndef MULTI code when integrating) - struct gtexGeneExtras /* Track info */ { double maxMedian; /* Maximum median rpkm for all tissues */ boolean isComparison; /* Comparison of two sample sets (e.g. male/female). */ boolean isDifference; /* True if comparison is shown as a single difference graph. False if displayed as two graphs, one oriented downward */ char *graphType; /* Additional info about graph (e.g. type of comparison graph */ struct rgbColor *colors; /* Color palette for tissues */ boolean doLogTransform; /* Log10(x+1) */ struct gtexTissue *tissues; /* Cache tissue names, descriptions */ struct hash *tissueFilter; /* For filter. NULL out excluded tissues */ }; struct gtexGeneInfo /* GTEx gene model, names, and expression medians */ { struct gtexGeneInfo *next; /* Next in singly linked list */ struct gtexGeneBed *geneBed;/* Gene name, id, canonical transcript, exp count and medians from BED table */ struct genePred *geneModel; /* Gene structure from model table */ double *medians1; /* Computed medians */ double *medians2; /* Computed medians for comparison (inverse) graph */ int height; /* Item height in pixels */ }; /***********************************************/ /* Color gene models using GENCODE conventions */ -// TODO: reuse GENCODE code for some/all of this ?? -// MAKE_COLOR_32 ? struct rgbColor codingColor = {12, 12, 120}; // #0C0C78 struct rgbColor noncodingColor = {0, 100, 0}; // #006400 struct rgbColor problemColor = {254, 0, 0}; // #FE0000 struct rgbColor unknownColor = {1, 1, 1}; static struct statusColors /* Color values for gene models */ { Color coding; Color noncoding; Color problem; Color unknown; } statusColors = {0,0,0,0}; static void initGeneColors(struct hvGfx *hvg) @@ -232,34 +225,30 @@ { medians1[i] -= medians2[i]; medians2[i] = 0; } else { medians2[i] -= medians1[i]; medians1[i] = 0; } } } geneInfo->medians1 = medians1; geneInfo->medians2 = medians2; } -else - { - // TODO: compute median for single graph based on filtering of sample set - } } static int gtexGeneItemHeight(struct track *tg, void *item); static void filterTissues(struct track *tg) /* Check cart for tissue selection. NULL out unselected tissues in tissue list */ { struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; struct gtexTissue *tis = NULL; extras->tissues = getTissues(); extras->tissueFilter = hashNew(0); if (cartListVarExistsAnyLevel(cart, tg->tdb, FALSE, GTEX_TISSUE_SELECT)) { struct slName *selectedValues = cartOptionalSlNameListClosestToHome(cart, tg->tdb, FALSE, GTEX_TISSUE_SELECT); @@ -362,66 +351,53 @@ #define MAX_GRAPH_PADDING 2 #define WIN_MED_GRAPH 500000 #define MED_GRAPH_HEIGHT 60 #define MED_BAR_WIDTH 3 #define MED_GRAPH_PADDING 1 #define MIN_GRAPH_HEIGHT 20 #define MIN_BAR_WIDTH 1 #define MIN_GRAPH_PADDING 0 #define MARGIN_WIDTH 1 static int gtexBarWidth() { -#ifdef MULTI_REGION -int winSize = virtWinBaseCount; // GALT CHANGED OLD winEnd - winStart; -#else int winSize = winEnd - winStart; -#endif if (winSize < WIN_MAX_GRAPH) return MAX_BAR_WIDTH; else if (winSize < WIN_MED_GRAPH) return MED_BAR_WIDTH; else return MIN_BAR_WIDTH; } static int gtexGraphPadding() { -#ifdef MULTI_REGION -int winSize = virtWinBaseCount; // GALT CHANGED OLD winEnd - winStart; -#else int winSize = winEnd - winStart; -#endif - if (winSize < WIN_MAX_GRAPH) return MAX_GRAPH_PADDING; else if (winSize < WIN_MED_GRAPH) return MED_GRAPH_PADDING; else return MIN_GRAPH_PADDING; } static int gtexMaxGraphHeight() { -#ifdef MULTI_REGION -int winSize = virtWinBaseCount; // GALT CHANGED OLD winEnd - winStart; -#else int winSize = winEnd - winStart; -#endif if (winSize < WIN_MAX_GRAPH) return MAX_GRAPH_HEIGHT; else if (winSize < WIN_MED_GRAPH) return MED_GRAPH_HEIGHT; else return MIN_GRAPH_HEIGHT; } static int gtexGraphWidth(struct track *tg, struct gtexGeneInfo *geneInfo) /* Width of GTEx graph in pixels */ { int barWidth = gtexBarWidth(); int padding = gtexGraphPadding(); int count = filteredTissueCount(tg); int labelWidth = geneInfo->medians2 ? tl.mWidth : 0; @@ -521,249 +497,126 @@ if (vis != tvFull && vis != tvPack) { bedDrawSimpleAt(tg, geneBed, hvg, xOff, y, scale, font, statusColor, vis); return; } int heightPer = tg->heightPer; int graphX = gtexGraphX(geneBed); if (graphX < 0) return; int topGraphHeight = gtexGeneGraphHeight(tg, geneInfo, TRUE); topGraphHeight = max(topGraphHeight, tl.fontHeight); int yZero = topGraphHeight + y - 1; // yZero is bottom of graph -#ifndef MULTI_REGION int x1 = xOff + graphX; // x1 is at left of graph -int keepX = x1; // FIXME: Too many X's! +int keepX = x1; drawGraphBase(tg, geneInfo, hvg, keepX, yZero+1); int startX = x1; struct rgbColor lineColor = {.r=0}; int lineColorIx = hvGfxFindColorIx(hvg, lineColor.r, lineColor.g, lineColor.b); int barWidth = gtexBarWidth(); int graphPadding = gtexGraphPadding(); char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS, GTEX_COLORS_DEFAULT); Color labelColor = MG_GRAY; Color clipColor = MG_MAGENTA; // add labels to comparison graphs -// TODO: generalize if (geneInfo->medians2) { hvGfxText(hvg, x1, yZero - tl.fontHeight + 1, labelColor, font, "F"); hvGfxText(hvg, x1, yZero + gtexGeneModelHeight() + gtexGeneMargin() + 1, labelColor, font, "M"); startX = startX + tl.mWidth+2; x1 = startX; } // draw bar graph -// TODO: share this code with other graph double viewMax = (double)cartUsualIntClosestToHome(cart, tg->tdb, FALSE, GTEX_MAX_LIMIT, GTEX_MAX_LIMIT_DEFAULT); double maxMedian = ((struct gtexGeneExtras *)tg->extraUiData)->maxMedian; int i; int expCount = geneBed->expCount; struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData; struct gtexTissue *tis; for (i=0, tis=extras->tissues; i<expCount; i++, tis=tis->next) { if (!filterTissue(tg, tis->name)) continue; struct rgbColor fillColor = extras->colors[i]; if (barWidth == 1 && sameString(colorScheme, GTEX_COLORS_GTEX)) { // brighten colors a bit so they'll be more visible at this scale fillColor = gtexTissueBrightenColor(fillColor); } int fillColorIx = hvGfxFindColorIx(hvg, fillColor.r, fillColor.g, fillColor.b); double expScore = (geneInfo->medians1 ? geneInfo->medians1[i] : geneBed->expScores[i]); int height = valToClippedHeight(expScore, maxMedian, viewMax, gtexMaxGraphHeight(), extras->doLogTransform); if (graphPadding == 0 || sameString(colorScheme, GTEX_COLORS_GTEX)) 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 > viewMax) hvGfxBox(hvg, x1, yZero-height+1, barWidth, 1, clipColor); x1 = x1 + barWidth + graphPadding; } -#endif // draw gene model int yGene = yZero + gtexGeneMargin() - 1; tg->heightPer = gtexGeneModelHeight() + 1; struct linkedFeatures *lf = linkedFeaturesFromGenePred(tg, geneInfo->geneModel, FALSE); lf->filterColor = statusColor; linkedFeaturesDrawAt(tg, lf, hvg, xOff, yGene, scale, font, color, tvSquish); tg->heightPer = heightPer; if (!geneInfo->medians2) return; -#ifndef MULTI_REGION // draw comparison bar graph (upside down) x1 = startX; yZero = yGene + gtexGeneModelHeight() + 1; // yZero is at top of graph drawGraphBase(tg, geneInfo, hvg, keepX, yZero-1); for (i=0, tis=extras->tissues; i<expCount; i++, tis=tis->next) { if (!filterTissue(tg, tis->name)) continue; struct rgbColor fillColor = extras->colors[i]; if (barWidth == 1 && sameString(colorScheme, GTEX_COLORS_GTEX)) { // brighten colors a bit so they'll be more visible at this scale struct hslColor hsl = mgRgbToHsl(fillColor); hsl.s = min(1000, hsl.s + 300); fillColor = mgHslToRgb(hsl); } int fillColorIx = hvGfxFindColorIx(hvg, fillColor.r, fillColor.g, fillColor.b); double expScore = geneInfo->medians2[i]; int height = valToClippedHeight(expScore, maxMedian, viewMax, gtexMaxGraphHeight(), extras->doLogTransform); if (graphPadding == 0 || sameString(colorScheme, GTEX_COLORS_GTEX)) hvGfxBox(hvg, x1, yZero, barWidth, height, fillColorIx); else hvGfxOutlinedBox(hvg, x1, yZero, barWidth, height, fillColorIx, lineColorIx); if (!extras->doLogTransform && expScore > viewMax) hvGfxBox(hvg, x1, yZero + height, barWidth, 1, clipColor); x1 = x1 + barWidth + graphPadding; } -#endif -} - -#ifdef MULTI_REGION -static int gtexGeneNonPropPixelWidth(struct track *tg, void *item) -/* Return end chromosome coordinate of item, including graph */ -{ -struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; -int graphWidth = gtexGraphWidth(geneInfo); -return graphWidth; -} -#endif - -#ifdef MULTI_REGION -static void gtexGeneNonPropDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, - double scale, MgFont *font, Color color, enum trackVisibility vis) -{ -struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; -struct gtexGeneBed *geneBed = geneInfo->geneBed; - -// Color in dense mode using transcriptClass -// GALT REMOVE Color statusColor = getTranscriptStatusColor(hvg, geneBed); -if (vis != tvFull && vis != tvPack) - { - //GALT bedDrawSimpleAt(tg, geneBed, hvg, xOff, y, scale, font, statusColor, vis); - return; - } -int i; -int expCount = geneBed->expCount; -double maxMedian = ((struct gtexGeneExtras *)tg->extraUiData)->maxMedian; -struct rgbColor lineColor = {.r=0}; -int lineColorIx = hvGfxFindColorIx(hvg, lineColor.r, lineColor.g, lineColor.b); -// GALT REMOVE int heightPer = tg->heightPer; - -int graphX = gtexGraphX(geneBed); -if (graphX < 0) - return; -int x1 = xOff + graphX; // x1 is at left of graph -int startX = x1; -int yZero = gtexMaxGraphHeight() + y - 1; // yZero is at bottom of graph - -// draw faint line under graph to delineate extent when bars are missing (tissue w/ 0 expression) -// TODO: skip missing bars -Color lightGray = MAKECOLOR_32(0xD1, 0xD1, 0xD1); -int graphWidth = gtexGraphWidth(geneInfo); -hvGfxBox(hvg, x1, yZero+1, graphWidth, 1, lightGray); - -int barWidth = gtexBarWidth(); -int graphPadding = gtexGraphPadding(); - -char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS, - GTEX_COLORS_DEFAULT); -Color labelColor = MG_GRAY; - -if (geneInfo->medians2) - { - // add labels to comparison graphs - // TODO: generalize - hvGfxText(hvg, x1, yZero-tl.fontHeight, labelColor, font, "F"); - hvGfxText(hvg, x1, yZero + gtexGeneModelHeight() + gtexGeneMargin(), labelColor, font, "M"); - startX = startX + tl.mWidth + 2; - x1 = startX; - } -for (i=0; i<expCount; i++) - { - struct rgbColor fillColor = extras->colors[i]; - if (barWidth == 1 && sameString(colorScheme, GTEX_COLORS_GTEX)) - { - // brighten colors a bit so they'll be more visible at this scale - fillColor = gtexTissueBrightenColor(fillColor); - } - int fillColorIx = hvGfxFindColorIx(hvg, fillColor.r, fillColor.g, fillColor.b); - - double expScore = (geneInfo->medians1 ? geneInfo->medians1[i] : geneBed->expScores[i]); - int height = valToHeight(expScore, maxMedian, gtexMaxGraphHeight(), extras->doLogTransform); - if (graphPadding == 0 || sameString(colorScheme, GTEX_COLORS_GTEX)) - hvGfxBox(hvg, x1, yZero-height, barWidth, height, fillColorIx); - else - hvGfxOutlinedBox(hvg, x1, yZero-height, barWidth, height, fillColorIx, lineColorIx); - x1 = x1 + barWidth + graphPadding; - } - -// mark gene extent -int yGene = yZero + gtexGeneMargin() - 1; - -/* GALT NOT DONE HERE NOW -// draw gene model -tg->heightPer = gtexGeneModelHeight()+1; -struct linkedFeatures *lf = linkedFeaturesFromGenePred(tg, geneInfo->geneModel, FALSE); -lf->filterColor = statusColor; -// GALT linkedFeaturesDrawAt(tg, lf, hvg, xOff, yGene, scale, font, color, tvSquish); -tg->heightPer = heightPer; -*/ -if (!geneInfo->medians2) - return; -// draw comparison graph (upside down) -x1 = startX; -yZero = yGene + gtexGeneModelHeight(); // yZero is at top of graph -for (i=0; i<expCount; i++) - { - struct rgbColor fillColor = extras->colors[i]; - if (barWidth == 1 && sameString(colorScheme, GTEX_COLORS_GTEX)) - { - // brighten colors a bit so they'll be more visible at this scale - struct hslColor hsl = mgRgbToHsl(fillColor); - hsl.s = min(1000, hsl.s + 300); - fillColor = mgHslToRgb(hsl); - } - int fillColorIx = hvGfxFindColorIx(hvg, fillColor.r, fillColor.g, fillColor.b); - double expScore = geneInfo->medians2[i]; - int height = valToHeight(expScore, maxMedian, gtexMaxGraphHeight(), extras->doLogTransform); - if (graphPadding == 0 || sameString(colorScheme, GTEX_COLORS_GTEX)) - hvGfxBox(hvg, x1, yZero, barWidth, height, fillColorIx); - else - hvGfxOutlinedBox(hvg, x1, yZero, barWidth, height, fillColorIx, lineColorIx); - x1 = x1 + barWidth + graphPadding; - } } -#endif static int gtexGeneItemHeightOptionalMax(struct track *tg, void *item, boolean isMax) { if (tg->visibility == tvSquish || tg->visibility == tvDense) return 0; if (isMax) { int extra = 0; if (((struct gtexGeneExtras *)tg->extraUiData)->isComparison) extra = gtexMaxGraphHeight() + 2; return gtexMaxGraphHeight() + gtexGeneMargin() + gtexGeneModelHeight() + extra; } if (item == NULL) return 0; struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; @@ -979,31 +832,26 @@ static int gtexGeneItemEnd(struct track *tg, void *item) /* Return end chromosome coordinate of item, including graph */ { struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; struct gtexGeneBed *geneBed = geneInfo->geneBed; double scale = scaleForWindow(insideWidth, winStart, winEnd); int graphWidth = gtexGraphWidth(tg, geneInfo); return max(geneBed->chromEnd, max(winStart, geneBed->chromStart) + graphWidth/scale); } void gtexGeneMethods(struct track *tg) { tg->drawItems = gtexGeneDrawItems; tg->drawItemAt = gtexGeneDrawAt; tg->loadItems = gtexGeneLoadItems; -//tg->freeItems = gtexGeneFreeItems; tg->mapItem = gtexGeneMapItem; tg->itemName = gtexGeneItemName; tg->mapItemName = gtexGeneItemName; tg->itemHeight = gtexGeneItemHeight; tg->itemStart = gtexGeneItemStart; tg->itemEnd = gtexGeneItemEnd; tg->totalHeight = gtexGeneTotalHeight; -#ifdef MULTI_REGION -tg->nonPropDrawItemAt = gtexGeneNonPropDrawAt; -tg->nonPropPixelWidth = gtexGeneNonPropPixelWidth; -#endif }