4bb2602dc32b56e79cc661b7c546a05284f9581a
kate
  Wed Jul 22 11:47:30 2015 -0700
Add squished gene model under expression graph (address concern of SAB and others re anchoring to genome. refs #15645

diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c
index c883554..8c96182 100644
--- src/hg/hgTracks/gtexTracks.c
+++ src/hg/hgTracks/gtexTracks.c
@@ -1,355 +1,407 @@
 /* GTEX 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 "gtexGeneBed.h"
 #include "gtexTissue.h"
 #include "gtexUi.h"
 
 #define WIN_MAX_GRAPH 20000
 #define MAX_GRAPH_HEIGHT 100
 #define MAX_BAR_WIDTH 5
 #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
 
 //#define GENCODE_CODING_COLOR 0x0c0c78    // rgb(12,12,120)
 //#define GENCODE_NONCODING_COLOR 0x006400 // rgb(0,100,0)
 //#define GENCODE_PROBLEM_COLOR 0xfe000  //rgb(254,0,0)  
 
 #define GENCODE_CODING_COLOR "12,12,120"
 #define GENCODE_NONCODING_COLOR "0,100,0"
 #define GENCODE_PROBLEM_COLOR "254,0,0"
 
 #define UNKNOWN_COLOR "1,1,1"
 
 static struct statusColors
     {
     Color coding;
     Color nonCoding;
     Color problem;
     Color unknown;
     } statusColors = {0,0,0};
 
 static int findColorIx(struct hvGfx *hvg, char *rgb)
 {
 unsigned char red, green, blue;
 parseColor(rgb, &red, &green, &blue);
 return (hvGfxFindColorIx(hvg, red, green, blue));
 //return MAKECOLOR_32(red, green, blue);
 }
 
 static void initGeneColors(struct hvGfx *hvg)
 {
 if (statusColors.coding != 0)
     return;
 statusColors.coding = findColorIx(hvg, GENCODE_CODING_COLOR);
 statusColors.nonCoding = findColorIx(hvg, GENCODE_NONCODING_COLOR);
 statusColors.problem = findColorIx(hvg, GENCODE_PROBLEM_COLOR);
 statusColors.unknown = findColorIx(hvg, UNKNOWN_COLOR);
 }
 
 static int gtexBarWidth()
 {
 int winSize = winEnd - winStart;
 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()
 {
 int winSize = winEnd - winStart;
 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 gtexGraphHeight()
 {
 int winSize = winEnd - winStart;
 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 valToY(double val, double maxVal, int height)
 /* Convert a value from 0 to maxVal to 0 to height-1 */
 {
 double scaled = val/maxVal;
-int y = scaled * (height-1);
-return height - 1 - y;
+int y = scaled * (height);
+return (height-1) - y;
+//int y = scaled * (height-1);
+//return (height - 1) - y;
 }
 
 struct gtexGeneExtras 
     {
     double maxExp;
     };
 
 
 /* Cache tissue metadata */
 
 struct gtexTissue *getGtexTissues()
 /* Get tissue metadata from database */
 {
 static struct gtexTissue *gtexTissues = NULL;
 if (gtexTissues == NULL)
     {
     char query[1024];
     struct sqlConnection *conn = sqlConnect("hgFixed");
     sqlSafef(query, sizeof(query), "select * from gtexTissue order by id");
     gtexTissues = gtexTissueLoadByQuery(conn, query);
     }
 return gtexTissues;
 }
 
 struct rgbColor *getGtexTissueColors()
 /* Get RGB colors from tissue table */
 {
 struct gtexTissue *tissues = getGtexTissues();
 struct gtexTissue *tissue = NULL;
 int count = slCount(tissues);
 struct rgbColor *colors;
 AllocArray(colors, count);
 int i = 0;
 for (tissue = tissues; tissue != NULL; tissue = tissue->next)
     {
     // TODO: reconcile 
     colors[i] = (struct rgbColor){.r=COLOR_32_BLUE(tissue->color), .g=COLOR_32_GREEN(tissue->color), .b=COLOR_32_RED(tissue->color)};
     //colors[i] = mgColorIxToRgb(NULL, tissue->color);
     i++;
     }
 return colors;
 }
 
 static int gtexGraphWidth(struct gtexGeneBed *gtex)
 /* Width of GTEx graph in pixels */
 {
 int barWidth = gtexBarWidth();
 int padding = gtexGraphPadding();
 int count = gtex->expCount;
 return (barWidth * count) + (padding * (count-1));
 }
 
 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 void gtexGeneDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, 
                     double scale, MgFont *font, Color color, enum trackVisibility vis)
 {
 struct gtexGeneBed *geneBed = item;
-//warn("item: %s, xOff=%d\n", geneBed->name, xOff);
-if (vis != tvFull && vis != tvPack)
-    {
 initGeneColors(hvg);
+//warn("item: %s, xOff=%d\n", geneBed->name, xOff);
 // Color using transcriptClass
+Color statusColor;
 if (geneBed->transcriptClass == NULL)
-        color = statusColors.unknown;
-    if (sameString(geneBed->transcriptClass, "coding"))
-        color = statusColors.coding;
+    statusColor = statusColors.unknown;
+else if (sameString(geneBed->transcriptClass, "coding"))
+    statusColor = statusColors.coding;
 else if (sameString(geneBed->transcriptClass, "nonCoding"))
-        color = statusColors.nonCoding;
+    statusColor = statusColors.nonCoding;
 else if (sameString(geneBed->transcriptClass, "problem"))
-        color = statusColors.problem;
+    statusColor = statusColors.problem;
 else 
-        color = statusColors.unknown;
+    statusColor = statusColors.unknown;
 
-    bedDrawSimpleAt(tg, item, hvg, xOff, y, scale, font, color, vis);
+if (vis != tvFull && vis != tvPack)
+    {
+    bedDrawSimpleAt(tg, item, hvg, xOff, y, scale, font, statusColor, vis);
     return;
     }
 int i;
 int expCount = geneBed->expCount;
 double maxExp = ((struct gtexGeneExtras *)tg->extraUiData)->maxExp;
 struct rgbColor lineColor = {.r=0};
 int lineColorIx = hvGfxFindColorIx(hvg, lineColor.r, lineColor.g, lineColor.b);
 int heightPer = tg->heightPer;
 
-////int start = max(geneBed->chromStart, winStart);
-
-//int geneEnd = min(geneBed->chromEnd, winEnd);
-//int width = expCount * (BAR_WIDTH + PADDING);
-//int end = min(expCount*(BAR_WIDTH + PADDING), winEnd);
-//if (start > end)
-    //return;
-////int x1 = round((start-winStart)*scale) + xOff;
+// x1 is at left of graph
 int x1 = gtexGraphX(geneBed) + xOff;
-//warn("gtexGeneDrawAt: x1=%d, labelWidth=%d.  ",
-        //x1, mgFontStringWidth(font, geneBed->name));
-//int x2 = round((e-winStart)*scale) + xOff;
 
-int yBase = valToY(0, maxExp, heightPer) + y;
-//int yZero = yBase - 5;
+// yZero is at bottom of graph
+int yZero = gtexGraphHeight() + y - 1;
+
+//uglyf("DRAW: xOff=%d, x1=%d, y=%d, yZero=%d<br>", xOff, x1, y, yZero);
 
-//int firstX = x1;
 int barWidth = gtexBarWidth();
 int graphPadding = gtexGraphPadding();
 char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS, 
                         GTEX_COLORS_DEFAULT);
 struct rgbColor *colors;
 if (sameString(colorScheme, GTEX_COLORS_GTEX))
     {
     // retrieve from table
     // TODO: cache this
     colors = getGtexTissueColors();
     }
 else
     {
     // currently the only other choice
     // TODO: cache this
     colors = getRainbow(&saturatedRainbowAtPos, expCount);
     //colors = getRainbow(&lightRainbowAtPos, expCount);
     }
 for (i=0; i<expCount; i++)
     {
     struct rgbColor fillColor = 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];
-    int yMedian = valToY(expScore, maxExp, heightPer) + y;
+    int yMedian = valToY(expScore, maxExp, gtexGraphHeight()) + y;
+    //int height = yZero - yMedian + 1;
+    int height = yZero - yMedian;
+    // TODO: adjust yGene instead of yMedian+1 to get gene track distance as desired
+    //if (i ==0) uglyf("DRAW: expScore=%.2f, maxExp=%.2f, graphHeight=%d, y=%d<br>", expScore, maxExp, 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, yMedian, barWidth, yBase - yMedian, fillColorIx);
+        hvGfxBox(hvg, x1, yMedian+1, barWidth, height, fillColorIx);
     else
-        hvGfxOutlinedBox(hvg, x1, yMedian, barWidth, yBase - yMedian, fillColorIx, lineColorIx);
-    //warn("x1=%d, yMedian=%d, height=%d\n", x1, yMedian, yBase-yMedian);
+        hvGfxOutlinedBox(hvg, x1, yMedian+1, barWidth, height, fillColorIx, lineColorIx);
     x1 = x1 + barWidth + graphPadding;
     }
-// underline gene extent
-//hvGfxBox(hvg, firstX, yBase, round((geneEnd - start)*scale), 3, lineColorIx);
+// mark gene extent
+int yGene = yZero + gtexGeneMargin() - 1;
+
+#ifdef NO_GENE
+// underline
+int start = max(geneBed->chromStart, winStart);
+int end = min(geneBed->chromEnd, winEnd);
+if (start > end)
+    return;
+int xStart = round((start - winStart) * scale)+xOff;
+int width = round((end-start)*scale);
+hvGfxBox(hvg, xStart, yGene, width, gtexGeneHeight(), lineColorIx);
+//uglyf("DRAW: xStart=%d, yGene=%d, width=%d, height=%d<br> ", xStart, yGene, width, gtexGeneHeight());
+#endif
+
+// load & draw gene model
 
-// TODO: replace with cached table hash
-//char *tissueTable = "gtexTissue";
-//struct sqlConnection *conn = hAllocConn("hgFixed");
-//hFreeConn(&conn);
+char query[1024];
+char **row;
+sqlSafef(query, sizeof query, "select * from gtexGeneModel where name='%s'", geneBed->geneId);
+struct sqlConnection *conn = hAllocConn(database);
+if (conn == NULL)
+    return;
+//uglyf("query: %s<br>", query);
+struct sqlResult *sr = sqlGetResult(conn, query);
+struct genePred *geneModel = NULL;
+if (sr != NULL)
+    {
+    if ((row = sqlNextRow(sr)) != NULL)
+        geneModel = genePredLoad(row);
+    sqlFreeResult(&sr);
+    }
+if (geneModel == NULL)
+    return;
+struct linkedFeatures *lf = linkedFeaturesFromGenePred(tg, geneModel, FALSE);
+tg->heightPer = gtexGeneHeight()+1;
+lf->filterColor = statusColor;
+linkedFeaturesDrawAt(tg, lf, hvg, xOff, yGene, scale, font, color, tvSquish);
+tg->heightPer = heightPer;
+hFreeConn(&conn);
 }
 
 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) */
 {
 //uglyf("map item: itemName=%s, mapItemName=%s, start=%d, end=%d, x=%d, y=%d, width=%d, height=%d, insideX=%d",
         //itemName, mapItemName, start, end, x, y, width, height, insideX);
 struct gtexTissue *tissues = getGtexTissues();
 struct gtexTissue *tissue = NULL;
 struct gtexGeneBed *gtex = item;
 int barWidth = gtexBarWidth();
 int padding = gtexGraphPadding();
-int heightPer = tg->heightPer;
 double maxExp = ((struct gtexGeneExtras *)tg->extraUiData)->maxExp;
-int i = 0;
+
 //int start1 = max(start, winStart);
 // TODO: support reverse display (hvg->rc)
 //double scale = scaleForWindow(width, start, end);
 //int x1 = round((start-winStart)*scale) + x;
 
 // skip over label.  TODO: check w/ different modes, and look for a better way
 // map box on label
 int labelWidth = mgFontStringWidth(tl.font, gtex->name) + 3;
-mapBoxHc(hvg, start, end, x, y, labelWidth, height, tg->track, mapItemName, mapItemName);
+//mapBoxHc(hvg, start, end, x, y, labelWidth, height, tg->track, mapItemName, mapItemName);
 int x1 = x + labelWidth;
+
+int i = 0;
+int yZero = gtexGraphHeight() + y - 1;
 for (tissue = tissues; tissue != NULL; tissue = tissue->next, i++)
     {
-    //hvGfxBox(hvg, x1, yMedian, barWidth, yBase - yMedian, fillColorIx);
     double expScore = gtex->expScores[i];
-    int yBase = valToY(0, maxExp, heightPer) + y;
-    int yMedian = valToY(expScore, maxExp, heightPer) + y;
-    int height = yBase - yMedian;
+    int yMedian = valToY(expScore, maxExp, gtexGraphHeight()) + y;
+    int height = yZero - yMedian;
+    //hvGfxBox(hvg, x1, yMedian, barWidth, yBase - yMedian, fillColorIx);
+    //int yBase = valToY(0, maxExp, heightPer) + y;
+    //int height = yBase - yMedian;
     // TODO: call genericMapItem
     //genericMapItem(tg, hvg, item, itemName, tissue->description, start, end, x1, y, barWidth, height);
-    mapBoxHc(hvg, start, end, x1, yMedian, barWidth, height, tg->track, mapItemName, tissue->description);
     //uglyf("id=%d, mapItemName= %s, start=%d, end=%d, x1=%d, y=%d (expScore=%.2f, yMedian=%d, yBase=%d), height=%d.  ",
                 //i, mapItemName, start, end, x1, y1, expScore, yMedian, yBase, height);
+    mapBoxHc(hvg, start, end, x1, yMedian+1, barWidth, height, tg->track, mapItemName, tissue->description);
+    #ifdef DEBUG
+    if (i ==0)
+        {
+        uglyf("MAP: expScore=%.2f, maxExp=%.2f, graphHeight=%d, y=%d<br>", expScore, maxExp, gtexGraphHeight(), y);
+        uglyf("MAP: yZero=%d, yMedian=%d, height=%d<br>", yZero, yMedian, height); 
+        break;
+        }
+    #endif
     x1 = x1 + barWidth + padding;
     }
 }
 
 static struct gtexGeneBed *loadGtexGeneBed(char **row)
 {
 return gtexGeneBedLoad(row);
 }
 
 static void gtexGeneLoadItems(struct track *track)
 {
 bedLoadItem(track, track->table, (ItemLoader)loadGtexGeneBed);
 double maxExp = 0.0;
 int i;
 struct gtexGeneBed *geneBed;
 for (geneBed = track->items; geneBed != NULL; geneBed = geneBed->next)
     for (i=0; i<geneBed->expCount; i++)
         maxExp = (geneBed->expScores[i] > maxExp ? geneBed->expScores[i] : maxExp);
 struct gtexGeneExtras *extras;
 AllocVar(extras);
 extras->maxExp = maxExp;
 track->extraUiData = extras;
 }
 
 static int gtexGeneItemHeight(struct track *track, void *item)
 {
 if ((item == NULL) || (track->visibility == tvSquish) || (track->visibility == tvDense))
     return 0;
-return gtexGraphHeight();
+return gtexGraphHeight() + + gtexGeneMargin() + gtexGeneHeight();
 }
 
 static int gtexTotalHeight(struct track *track, enum trackVisibility vis)
 /* Figure out total height of track */
 {
 int height;
 if (track->visibility == tvSquish || track->visibility == tvDense)
     height = 10;
 else 
-    height = gtexGraphHeight();
+    height = gtexGraphHeight() + gtexGeneMargin() + gtexGeneHeight();
 return tgFixedTotalHeightOptionalOverflow(track, vis, height, height, FALSE);
 }
 
 void gtexGeneMethods(struct track *track)
 {
 track->drawItemAt = gtexGeneDrawAt;
 track->loadItems = gtexGeneLoadItems;
 track->mapItem = gtexGeneMapItem;
 track->itemHeight = gtexGeneItemHeight;
 track->totalHeight = gtexTotalHeight;
 }