ef14e76a5a86847e16542058cd2845f7693a7b84
kate
Thu Oct 22 15:46:17 2015 -0700
Add map box to comparison graph. Code cleanup. refs #15645
diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c
index bbc9f92..02fe007 100644
--- src/hg/hgTracks/gtexTracks.c
+++ src/hg/hgTracks/gtexTracks.c
@@ -29,30 +29,31 @@
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 */
};
/***********************************************/
/* 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)
@@ -336,244 +337,188 @@
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 gtexGeneInfo *geneInfo)
/* Width of GTEx graph in pixels */
{
int barWidth = gtexBarWidth();
int padding = gtexGraphPadding();
struct gtexGeneBed *geneBed = geneInfo->geneBed;
int count = geneBed->expCount;
-// TODO: save labels in extras
-int labelWidth = geneInfo->medians2 ? 5 : 0;
+int labelWidth = geneInfo->medians2 ? tl.mWidth : 0;
return (barWidth * count) + (padding * (count-1)) + labelWidth + 2;
-;
}
static int gtexGraphX(struct gtexGeneBed *gtex)
/* Locate graph on X, relative to viewport. Return -1 if it won't fit */
{
int start = max(gtex->chromStart, winStart);
//int end = min(gtex->chromEnd, winEnd);
//if (start > end)
//return -1;
double scale = scaleForWindow(insideWidth, winStart, winEnd);
int x1 = round((start - winStart) * scale);
//int x2 = round((end - winStart) * scale);
//int width = gtexGraphWidth(gtex);
//if (x1 + width > x2)
//return -1;
return x1;
}
static int gtexGeneHeight()
{
return 8;
}
static int gtexGeneMargin()
{
return 1;
}
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 */
-// TODO: support linear or log scale
+/* 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);
-//uglyf("%.2f -> %.2f height %d", val, scaled, (int)scaled * (maxHeight-1));
return (scaled * (maxHeight-1));
}
-// TODO: whack this
-static int valToY(double val, double maxVal, int maxHeight)
-/* Convert a value from 0 to maxVal to 0 to height-1 */
+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) */
{
-if (val == 0.0)
- return 0;
-//double scaled = (log10(val)+3.001)/(log10(maxVal)+3.001);
-double scaled = log10(val+1.0) / log10(maxVal+1.0);
-if (scaled < 0)
- warn("scaled=%f\n", scaled);
-int y = scaled * (maxHeight);
-//uglyf("%.2f -> %.2f height %d", val, scaled, (int)scaled * (maxHeight-1));
-return (maxHeight-1) - y;
+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;
boolean doLogTransform = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, GTEX_LOG_TRANSFORM,
GTEX_LOG_TRANSFORM_DEFAULT);
-
// Color in dense mode using transcriptClass
Color statusColor = getTranscriptStatusColor(hvg, geneBed);
if (vis != tvFull && vis != tvPack)
{
bedDrawSimpleAt(tg, geneBed, hvg, xOff, y, scale, font, statusColor, vis);
return;
}
-
struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData;
if (extras->isComparison && (tg->visibility == tvFull || tg->visibility == tvPack))
//&& gtexGraphHeight() != MIN_GRAPH_HEIGHT)
// compute medians based on configuration (comparisons, and later, filters)
loadComputedMedians(geneInfo, extras);
-int heightPer = tg->heightPer;
+int heightPer = tg->heightPer;
int graphX = gtexGraphX(geneBed);
if (graphX < 0)
return;
-
-// yZero is at bottom of graph
-int yZero = gtexGraphHeight() + y - 1;
-
-// draw faint line under graph to delineate extent when bars are missing (tissue w/ 0 expression)
-// TODO: skip missing bars -- then we can lose the gray line (at least for non-comparison mode)
-
-//uglyf("DRAW: xOff=%d, x1=%d, y=%d, yZero=%d<br>", xOff, x1, y, yZero);
+int yZero = gtexGraphHeight() + y-1; // yZero is bottom of graph
#ifndef MULTI_REGION
-// x1 is at left of graph
-int x1 = xOff + graphX;
-int startX = x1;
-Color lightGray = MAKECOLOR_32(0xD1, 0xD1, 0xD1);
-int graphWidth = gtexGraphWidth(geneInfo);
-hvGfxBox(hvg, x1, yZero+1, graphWidth, 1, lightGray);
+int x1 = xOff + graphX; // x1 is at left of graph
+int keepX = x1;
+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;
+// add labels to comparison graphs
// TODO: generalize
if (geneInfo->medians2)
{
- // add labels to comparison graphs
- //FIXME: compute these
- int charHeight = 5;
- int labelWidth = 5;
- hvGfxText(hvg, x1, yZero-charHeight, labelColor, font, "F");
+ hvGfxText(hvg, x1, yZero - tl.fontHeight, labelColor, font, "F");
hvGfxText(hvg, x1, yZero + gtexGeneHeight() + gtexGeneMargin(), labelColor, font, "M");
- startX = startX + labelWidth + 2;
+ startX = startX + tl.mWidth+2;
x1 = startX;
}
-
-/* TODO: Remove DEBUG code here */
-struct gtexTissue *tissues = getTissues();
-struct gtexTissue *tissue = tissues;
-/* DEBUG */
-
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 expScore = geneBed->expScores[i];
- /*
- if (expScore < 1)
- expScore = 0.0;
- */
- // DEBUG code here
- //uglyf("%s: score=%.2f<br>", tissue->description, expScore);
- tissue = tissue->next;
- // END DEBUG
int height = valToHeight(expScore, maxMedian, gtexGraphHeight(), doLogTransform);
- // TODO: adjust yGene to get gene track distance as desired
- //if (i ==0) uglyf("DRAW: expScore=%.2f, maxMedian=%.2f, graphHeight=%d, y=%d<br>", expScore, maxMedian, gtexGraphHeight(), y);
- //if (i ==0) uglyf("DRAW: yZero=%d, yMedian=%d, height=%d<br>", yZero, yMedian, height);
if (graphPadding == 0 || sameString(colorScheme, GTEX_COLORS_GTEX))
- hvGfxBox(hvg, x1, yZero-height, barWidth, height, fillColorIx);
+ hvGfxBox(hvg, x1, yZero-height+1, barWidth, height, fillColorIx);
else
- hvGfxOutlinedBox(hvg, x1, yZero-height, barWidth, height, fillColorIx, lineColorIx);
+ hvGfxOutlinedBox(hvg, x1, yZero-height+1, barWidth, height, fillColorIx, lineColorIx);
x1 = x1 + barWidth + graphPadding;
}
#endif
-// mark gene extent
-int yGene = yZero + gtexGeneMargin() - 1;
-
// 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;
#ifndef MULTI_REGION
// draw comparison graph (upside down)
-
x1 = startX;
-// yZero is at top of graph
-yZero = yGene + gtexGeneHeight();
+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 = geneBed->expScores[i];
double expScore = geneInfo->medians2[i];
- //if (expScore < 1)
- //expScore = 0.0;
int height = valToHeight(expScore, maxMedian, gtexGraphHeight(), doLogTransform);
- // TODO: adjust yGene instead of yMedian+1 to get gene track distance as desired
- //if (i ==0) uglyf("DRAW2: expScore=%.2f, maxMedian=%.2f, graphHeight=%d, y=%d<br>", expScore, maxMedian, gtexGraphHeight(), y);
- //if (i ==0) uglyf("DRAW2: yZero=%d, height=%d<br>", yZero, height);
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
}
#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);
@@ -583,206 +528,174 @@
#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;
}
-
struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData;
if (extras->isComparison && (tg->visibility == tvFull || tg->visibility == tvPack))
//&& gtexGraphHeight() != MIN_GRAPH_HEIGHT)
// compute medians based on configuration (comparisons, and later, filters)
loadComputedMedians(geneInfo, extras);
-
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;
-// x1 is at left of graph
-int x1 = xOff + graphX;
+int x1 = xOff + graphX; // x1 is at left of graph
int startX = x1;
-
-// yZero is at bottom of graph
-int yZero = gtexGraphHeight() + y - 1;
+int yZero = gtexGraphHeight() + 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 -- then we can lose the gray line (at least for non-comparison mode)
+// TODO: skip missing bars
Color lightGray = MAKECOLOR_32(0xD1, 0xD1, 0xD1);
int graphWidth = gtexGraphWidth(geneInfo);
hvGfxBox(hvg, x1, yZero+1, graphWidth, 1, lightGray);
-//uglyf("DRAW: xOff=%d, x1=%d, y=%d, yZero=%d<br>", xOff, x1, y, yZero);
-
int barWidth = gtexBarWidth();
int graphPadding = gtexGraphPadding();
char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS,
GTEX_COLORS_DEFAULT);
Color labelColor = MG_GRAY;
-// TODO: generalize
if (geneInfo->medians2)
{
// add labels to comparison graphs
- //FIXME: compute these
- int charHeight = 5;
- int labelWidth = 5;
- hvGfxText(hvg, x1, yZero-charHeight, labelColor, font, "F");
+ // TODO: generalize
+ hvGfxText(hvg, x1, yZero-tl.fontHeight, labelColor, font, "F");
hvGfxText(hvg, x1, yZero + gtexGeneHeight() + gtexGeneMargin(), labelColor, font, "M");
- startX = startX + labelWidth + 2;
+ 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]);
- //double expScore = geneBed->expScores[i];
- /*
- if (expScore < 1)
- expScore = 0.0;
- */
int height = valToHeight(expScore, maxMedian, gtexGraphHeight(), doLogTransform);
- // TODO: adjust yGene to get gene track distance as desired
- //if (i ==0) uglyf("DRAW: expScore=%.2f, maxMedian=%.2f, graphHeight=%d, y=%d<br>", expScore, maxMedian, gtexGraphHeight(), y);
- //if (i ==0) uglyf("DRAW: yZero=%d, yMedian=%d, height=%d<br>", yZero, yMedian, height);
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 = gtexGeneHeight()+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 is at top of graph
-yZero = yGene + gtexGeneHeight();
+yZero = yGene + gtexGeneHeight(); // 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 = geneBed->expScores[i];
double expScore = geneInfo->medians2[i];
- //if (expScore < 1)
- //expScore = 0.0;
int height = valToHeight(expScore, maxMedian, gtexGraphHeight(), doLogTransform);
- // TODO: adjust yGene instead of yMedian+1 to get gene track distance as desired
- //if (i ==0) uglyf("DRAW2: expScore=%.2f, maxMedian=%.2f, graphHeight=%d, y=%d<br>", expScore, maxMedian, gtexGraphHeight(), y);
- //if (i ==0) uglyf("DRAW2: yZero=%d, height=%d<br>", yZero, height);
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 void gtexGeneMapItem(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 for each tissue (bar in the graph) or a single map for squish/dense modes */
{
-//uglyf("map item: itemName=%s, mapItemName=%s, start=%d, end=%d, x=%d, y=%d, width=%d, height=%d, insideX=%d<br>",
- //itemName, mapItemName, start, end, x, y, width, height, insideX);
-
if (tg->visibility == tvDense || tg->visibility == tvSquish)
{
genericMapItem(tg, hvg, item, itemName, itemName, start, end, x, y, width, height);
return;
}
-
struct gtexTissue *tissues = getTissues();
struct gtexTissue *tissue = NULL;
struct gtexGeneInfo *geneInfo = item;
struct gtexGeneBed *geneBed = geneInfo->geneBed;
int barWidth = gtexBarWidth();
int padding = gtexGraphPadding();
double maxMedian = ((struct gtexGeneExtras *)tg->extraUiData)->maxMedian;
int graphX = gtexGraphX(geneBed);
if (graphX < 0)
return;
// x1 is at left of graph
int x1 = insideX + graphX;
if (geneInfo->medians2)
{
- // add labels to comparison graphs
- //FIXME: compute these
- int labelWidth = 5;
- x1 = x1 + labelWidth + 2;
+ // 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);
for (tissue = tissues; tissue != NULL; tissue = tissue->next, i++)
{
double expScore = geneBed->expScores[i];
- //TODO: use valToHeight
- int yMedian = valToY(expScore, maxMedian, gtexGraphHeight()) + y;
- int height = yZero - yMedian;
- // TODO: call genericMapItem
- //genericMapItem(tg, hvg, item, itemName, tissue->description, start, end, x1, y, barWidth, height);
+ int height = valToHeight(expScore, maxMedian, gtexGraphHeight(), doLogTransform);
+ int yMedian = yZero - height;
mapBoxHc(hvg, start, end, x1, yMedian+1, barWidth, height, tg->track, mapItemName, tissue->description);
- //if (i==0) uglyf("MAP: expScore=%.2f, maxMedian=%.2f, graphHeight=%d, y=%d<br>", expScore, maxMedian, gtexGraphHeight(), y);
- //if (i==0) uglyf("MAP: x=%d, x1=%d, y=%d, yZero=%d<br>", x, x1, y, yZero);
- //if (i==0) uglyf("MAP: yZero=%d, yMedian=%d, height=%d<br>", yZero, yMedian, height);
+ // add map box to comparison graph
+ if (geneInfo->medians2)
+ {
+ double expScore = geneInfo->medians2[i];
+ int height = valToHeight(expScore, maxMedian, 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;
}
static int gtexGeneItemHeight(struct track *tg, void *item)
{
if ((item == NULL) || (tg->visibility == tvSquish) || (tg->visibility == tvDense))