ebb8b21be417b0d17cdc4ace34c8c82e558f2b5e kate Thu Oct 22 21:49:39 2015 -0700 Fix map boxes on non-log display. refs #15645 diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c index d481cc7..5d8f1da 100644 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@ -376,30 +376,45 @@ 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, gtexGraphHeight(), doLogTransform); +} + static void drawGraphBase(struct hvGfx *hvg, int x, int y, struct gtexGeneInfo *geneInfo) /* Draw faint line under graph to delineate extent when bars are missing (tissue w/ 0 expression) */ { Color lightGray = MAKECOLOR_32(0xD1, 0xD1, 0xD1); int graphWidth = gtexGraphWidth(geneInfo); hvGfxBox(hvg, x, y, graphWidth, 1, lightGray); } static void gtexGeneDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis) /* Draw tissue expression bar graph over gene model. Optionally, draw a second graph under gene, to compare sample sets */ { struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; struct gtexGeneBed *geneBed = geneInfo->geneBed; @@ -429,70 +444,63 @@ int keepX = x1; // FIXME: Too many X's! drawGraphBase(hvg, keepX, yZero+1, geneInfo); int startX = x1; 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); 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; - -double viewMax = (double)cartUsualIntClosestToHome(cart, tg->tdb, FALSE, GTEX_MAX_LIMIT, GTEX_MAX_LIMIT_DEFAULT); +double viewMax = (double)cartUsualIntClosestToHome(cart, tg->tdb, FALSE, + GTEX_MAX_LIMIT, GTEX_MAX_LIMIT_DEFAULT); // add labels to comparison graphs // TODO: generalize if (geneInfo->medians2) { hvGfxText(hvg, x1, yZero - tl.fontHeight, labelColor, font, "F"); hvGfxText(hvg, x1, yZero + gtexGeneHeight() + gtexGeneMargin(), labelColor, font, "M"); startX = startX + tl.mWidth+2; x1 = startX; } // draw bar graph // TODO: share this code with other 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 fillColor = gtexTissueBrightenColor(fillColor); } int fillColorIx = hvGfxFindColorIx(hvg, fillColor.r, fillColor.g, fillColor.b); - double expScore = (geneInfo->medians1 ? geneInfo->medians1[i] : geneBed->expScores[i]); - double useScore = expScore; - double useMax = maxMedian; - if (!doLogTransform) - { - useMax = viewMax; - if (expScore > viewMax) - useScore = viewMax; - } - int height = valToHeight(useScore, useMax, gtexGraphHeight(), doLogTransform); + int height = valToClippedHeight(expScore, maxMedian, viewMax, + gtexGraphHeight(), 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); - if (useScore != expScore) + // mark clipped bar with magenta tip + if (!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 = gtexGeneHeight()+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; @@ -503,44 +511,36 @@ yZero = yGene + gtexGeneHeight() + 1; // yZero is at top of graph drawGraphBase(hvg, keepX, yZero-1, geneInfo); 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]; - double useScore = expScore; - double useMax = maxMedian; - if (!doLogTransform) - { - useMax = viewMax; - if (expScore > viewMax) - useScore = viewMax; - } - int height = valToHeight(useScore, useMax, gtexGraphHeight(), doLogTransform); + int height = valToClippedHeight(expScore, maxMedian, viewMax, gtexGraphHeight(), 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 (useScore != expScore) + if (!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 @@ -677,42 +677,42 @@ int graphX = gtexGraphX(geneBed); if (graphX < 0) return; // x1 is at left of graph int x1 = insideX + graphX; if (geneInfo->medians2) { // skip over labels in comparison graphs x1 = x1 + tl.mWidth+ 2; } int i = 0; int yZero = gtexGraphHeight() + y - 1; boolean doLogTransform = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, GTEX_LOG_TRANSFORM, GTEX_LOG_TRANSFORM_DEFAULT); +double viewMax = (double)cartUsualIntClosestToHome(cart, tg->tdb, FALSE, + GTEX_MAX_LIMIT, GTEX_MAX_LIMIT_DEFAULT); for (tissue = tissues; tissue != NULL; tissue = tissue->next, i++) { - double expScore = geneBed->expScores[i]; - int height = valToHeight(expScore, maxMedian, gtexGraphHeight(), doLogTransform); - int yMedian = yZero - height; -// FIXME: need proper scaling for clipped (non-log) display - mapBoxHc(hvg, start, end, x1, yMedian+1, barWidth, height, tg->track, mapItemName, tissue->description); + int height = valToClippedHeight(geneBed->expScores[i], maxMedian, viewMax, + gtexGraphHeight(), doLogTransform); + mapBoxHc(hvg, start, end, x1, yZero-height, barWidth, height, tg->track, mapItemName, tissue->description); // add map box to comparison graph if (geneInfo->medians2) { double expScore = geneInfo->medians2[i]; - int height = valToHeight(expScore, maxMedian, gtexGraphHeight(), doLogTransform); + int height = valToClippedHeight(expScore, maxMedian, viewMax, gtexGraphHeight(), doLogTransform); int y = yZero + gtexGeneHeight() + gtexGeneMargin(); mapBoxHc(hvg, start, end, x1, y, barWidth, height, tg->track, mapItemName, tissue->description); } x1 = x1 + barWidth + padding; } } static char *gtexGeneItemName(struct track *tg, void *item) /* Return gene name */ { struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item; struct gtexGeneBed *geneBed = geneInfo->geneBed; return geneBed->name; }