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
@@ -1,849 +1,762 @@
 /* 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"
 
 // NOTE: Sections to change for multi-region (vertical slice) display 
 //       are marked with #ifdef MULTI_REGION
 
 struct gtexGeneExtras 
 /* Track info */
     {
     double maxMedian;           /* Maximum median rpkm for all tissues */
     boolean isComparison;       /* Comparison of two sample sets (e.g. male/female).
                                        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 */
     };
 
 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)
 /* Get and cache indexes for color values */
 {
 if (statusColors.coding != 0)
     return;
 statusColors.coding = hvGfxFindColorIx(hvg, codingColor.r, codingColor.g, codingColor.b);
 statusColors.noncoding = hvGfxFindColorIx(hvg, noncodingColor.r, noncodingColor.g, noncodingColor.b);
 statusColors.problem = hvGfxFindColorIx(hvg, problemColor.r, problemColor.g, problemColor.b);
 statusColors.unknown = hvGfxFindColorIx(hvg, unknownColor.r, unknownColor.g, unknownColor.b);
 }
 
 static Color getTranscriptStatusColor(struct hvGfx *hvg, struct gtexGeneBed *geneBed)
 /* Find GENCODE color for transcriptClass  of canonical transcript */
 {
 initGeneColors(hvg);
 if (geneBed->transcriptClass == NULL)
     return statusColors.unknown;
 if (sameString(geneBed->transcriptClass, "coding"))
     return statusColors.coding;
 if (sameString(geneBed->transcriptClass, "nonCoding"))
     return statusColors.noncoding;
 if (sameString(geneBed->transcriptClass, "problem"))
     return statusColors.problem;
 return statusColors.unknown;
 }
 
 /***********************************************/
 /* Cache tissue info */
 
 struct gtexTissue *getTissues()
 /* Get and cache tissue metadata from database */
 {
 static struct gtexTissue *gtexTissues = NULL;
 
 if (!gtexTissues)
     gtexTissues = gtexGetTissues();
 return gtexTissues;
 }
 
 int getTissueCount()
 /* Get and cache the number of tissues in GTEx tissue table */
 {
 static int tissueCount = 0;
 
 if (!tissueCount)
     tissueCount = slCount(getTissues());
 return tissueCount;
 }
 
 char *getTissueName(int id)
 /* Get tissue name from id, cacheing */
 {
 static char **tissueNames = NULL;
 
 struct gtexTissue *tissue;
 int count = getTissueCount();
 if (!tissueNames)
     {
     struct gtexTissue *tissues = getTissues();
     AllocArray(tissueNames, count);
     for (tissue = tissues; tissue != NULL; tissue = tissue->next)
         tissueNames[tissue->id] = cloneString(tissue->name);
     }
 if (id >= count)
     errAbort("GTEx tissue table problem: can't find id %d\n", id);
 return tissueNames[id];
 }
 
 struct rgbColor *getGtexTissueColors()
 /* Get RGB colors from tissue table */
 {
 struct gtexTissue *tissues = getTissues();
 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;
 }
 
 /*****************************************************************/
 /* Load sample data, gene info, and anything else needed to draw */
 
 static struct hash *loadGeneModels(char *table)
 /* Load gene models from table */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 int rowOffset;
 sr = hRangeQuery(conn, table, chromName, winStart, winEnd, NULL, &rowOffset);
 
 struct hash *modelHash = newHash(0);
 struct genePred *model = NULL;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     model = genePredLoad(row+rowOffset);
     hashAdd(modelHash, model->name, model);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return modelHash;
 }
 
 static void loadComputedMedians(struct gtexGeneInfo *geneInfo, struct gtexGeneExtras *extras)
 /* Compute medians based on graph type.  Returns a list of 2 for comparison graph types */
 {
 struct gtexGeneBed *geneBed = geneInfo->geneBed;
 int expCount = geneBed->expCount;
 if (extras->isComparison)
     {
     // create two score hashes, one for each sample subset
     struct hash *scoreHash1 = hashNew(0), *scoreHash2 = hashNew(0);
     struct sqlConnection *conn = hAllocConn("hgFixed");
     char query[1024];
     char **row;
     sqlSafef(query, sizeof(query), "select gtexSampleData.sample, gtexDonor.gender, gtexSampleData.tissue, gtexSampleData.score from gtexSampleData, gtexSample, gtexDonor where gtexSampleData.geneId='%s' and gtexSampleData.sample=gtexSample.sampleId and gtexSample.donor=gtexDonor.name", geneBed->geneId);
     struct sqlResult *sr = sqlGetResult(conn, query);
     while ((row = sqlNextRow(sr)) != NULL)
         {
         char gender = *row[1];
         // TODO: generalize for other comparison graphs (this code just for M/F comparison)
         struct hash *scoreHash = ((gender == 'F') ? scoreHash1 : scoreHash2);
         char *tissue = cloneString(row[2]);
         struct slDouble *score = slDoubleNew(sqlDouble(row[3]));
 
         // create hash of lists of scores, keyed by tissue name
         double *tissueScores = hashFindVal(scoreHash, tissue);
         if (tissueScores)
             slAddHead(tissueScores, score);
         else
             hashAdd(scoreHash, tissue, score);
         }
     sqlFreeResult(&sr);
     hFreeConn(&conn);
 
     // get tissue medians for each sample subset
     double *medians1;
     double *medians2;
     AllocArray(medians1, expCount);
     AllocArray(medians2, expCount);
     int i;
     for (i=0; i<geneBed->expCount; i++)
         {
         //medians1[i] = -1, medians2[i] = -1;       // mark missing tissues ?
         struct slDouble *scores;
         scores = hashFindVal(scoreHash1, getTissueName(i));
         if (scores)
             medians1[i] = slDoubleMedian(scores);
         scores = hashFindVal(scoreHash2, getTissueName(i));
         if (scores)
             medians2[i] = slDoubleMedian(scores);
         }
     geneInfo->medians1 = medians1;
     geneInfo->medians2 = medians2;
     }
 else
     {
     // TODO: compute median for single graph based on filtering of sample set
     }
 }
 
 static void gtexGeneLoadItems(struct track *tg)
 /* Load method for track items */
 {
 /* Get track UI info */
 struct gtexGeneExtras *extras;
 AllocVar(extras);
 tg->extraUiData = extras;
 char *samples = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, 
                                                 GTEX_SAMPLES, GTEX_SAMPLES_DEFAULT);
 extras->graphType = cloneString(samples);
 if (sameString(samples, GTEX_SAMPLES_COMPARE_SEX))
     extras->isComparison = TRUE;
 extras->maxMedian = gtexMaxMedianScore(NULL);
 
 /* Get geneModels in range */
 //TODO: version the table name, move to lib
 char *modelTable = "gtexGeneModel";
 struct hash *modelHash = loadGeneModels(modelTable);
 
 /* Get geneBeds (names and all-sample tissue median scores) in range */
 bedLoadItem(tg, tg->table, (ItemLoader)gtexGeneBedLoad);
 
 /* Create geneInfo items with BED and geneModels */
 struct gtexGeneInfo *geneInfo = NULL, *list = NULL;
 struct gtexGeneBed *geneBed = (struct gtexGeneBed *)tg->items;
 
 /* Load tissue colors: GTEx or rainbow */
 char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS, 
                         GTEX_COLORS_DEFAULT);
 if (sameString(colorScheme, GTEX_COLORS_GTEX))
     {
     extras->colors = getGtexTissueColors();
     }
 else
     {
     int expCount = geneBed->expCount;
     extras->colors = getRainbow(&saturatedRainbowAtPos, expCount);
     }
 while (geneBed != NULL)
     {
     AllocVar(geneInfo);
     geneInfo->geneBed = geneBed;
     geneInfo->geneModel = hashFindVal(modelHash, geneBed->geneId);
     slAddHead(&list, geneInfo);
     geneBed = geneBed->next;
     geneInfo->geneBed->next = NULL;
     }
 slReverse(&list);
 tg->items = list;
 }
 
 /***********************************************/
 /* Draw */
 
 /* Bargraph layouts for three window sizes */
 #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
 
 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 gtexGraphHeight()
 {
 #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 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);
 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;
     }
-
 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))
     return 0;
 int extra = 0;
 if (((struct gtexGeneExtras *)tg->extraUiData)->isComparison)
     extra = gtexGraphHeight() + 2;
 //uglyf("GTEX itemHeight extra = %d<br>", extra);
 return gtexGraphHeight() + gtexGeneMargin() + gtexGeneHeight() + extra;
 }
 
 static int gtexTotalHeight(struct track *tg, enum trackVisibility vis)
 /* Figure out total height of track */
 {
 int height;
 int extra = 0;
 if (((struct gtexGeneExtras *)tg->extraUiData)->isComparison)
     extra = gtexGraphHeight() + 2;
 if (tg->visibility == tvSquish || tg->visibility == tvDense)
     height = 10;
 else 
     height = gtexGraphHeight() + gtexGeneMargin() + gtexGeneHeight() + extra;
 //uglyf("GTEX totalHeight = %d<br>", height);
 return tgFixedTotalHeightOptionalOverflow(tg, vis, height, height, FALSE);
 }
 
 static int gtexGeneItemStart(struct track *tg, void *item)
 /* Return end chromosome coordinate of item, including graph */
 {
 struct gtexGeneInfo *geneInfo = (struct gtexGeneInfo *)item;
 struct gtexGeneBed *geneBed = geneInfo->geneBed;
 return geneBed->chromStart;
 }
 
 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(geneInfo);
 return max(geneBed->chromEnd, max(winStart, geneBed->chromStart) + graphWidth/scale);
 }
 
 void gtexGeneMethods(struct track *tg)
 {
 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 = gtexTotalHeight;
 #ifdef MULTI_REGION
 tg->nonPropDrawItemAt = gtexGeneNonPropDrawAt;
 tg->nonPropPixelWidth = gtexGeneNonPropPixelWidth;
 #endif
 }