5bfb32fdfc639f9bffb5435044cef164bdde0b28
kent
  Sun Dec 12 08:02:13 2021 -0800
Implementing barChartMerge trackDb option for faceted bar charts.

diff --git src/hg/hgc/barChartClick.c src/hg/hgc/barChartClick.c
index c311843..70a0426 100644
--- src/hg/hgc/barChartClick.c
+++ src/hg/hgc/barChartClick.c
@@ -1,618 +1,618 @@
 /* Details pages for barChart tracks */
 
 /* Copyright (C) 2015 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "hdb.h"
 #include "hvGfx.h"
 #include "trashDir.h"
 #include "hCommon.h"
 #include "hui.h"
 #include "asParse.h"
 #include "hgc.h"
 #include "trackHub.h"
 #include "memgfx.h"
 #include "hgColors.h"
 #include "fieldedTable.h"
 
 #include "barChartBed.h"
 #include "barChartCategory.h"
 #include "barChartData.h"
 #include "barChartSample.h"
 #include "barChartUi.h"
 #include "hgConfig.h"
 #include "facetedBar.h"
 #include "pipeline.h"
 
 #define EXTRA_FIELDS_SIZE 256
 
 struct barChartItemData
 /* Measured value for a sample and the sample category at a locus.
  * Used for barChart track details (boxplot) */
     {
     struct barChartItemData *next;  /* Next in singly linked list. */
     char *sample;	/* Sample identifier */
     char *category;     /* Sample category (from barChartSample table  or barChartSampleUrl file) */
     double value;	/* Measured value (e.g. expression level) */
     };
 
 static struct barChartBed *getBarChartFromFile(struct trackDb *tdb, char *file, 
                                                 char *item, char *chrom, int start, int end, 
                                                 struct asObject **retAs, char **extraFieldsRet,
                                                 int *extraFieldsCountRet)
 /* Retrieve barChart BED item from big file */
 {
 boolean hasOffsets = TRUE;
 struct bbiFile *bbi = bigBedFileOpen(file);
 struct asObject *as = bigBedAsOrDefault(bbi);
 if (retAs != NULL)
     *retAs = as;
 hasOffsets = (
     asColumnFind(as, BARCHART_OFFSET_COLUMN) != NULL && 
     asColumnFind(as, BARCHART_LEN_COLUMN) != NULL);
 struct lm *lm = lmInit(0);
 struct bigBedInterval *bb, *bbList =  bigBedIntervalQuery(bbi, chrom, start, end, 0, lm);
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     char *rest = cloneString(bb->rest);
     char startBuf[16], endBuf[16];
     char *row[32];
     bigBedIntervalToRow(bb, chrom, startBuf, endBuf, row, ArraySize(row));
     struct barChartBed *barChart = barChartBedLoadOptionalOffsets(row, hasOffsets);
     if (barChart == NULL)
         continue;
     if (sameString(barChart->name, item))
         {
         char *restFields[EXTRA_FIELDS_SIZE];
         int restCount = chopTabs(rest, restFields);
         int restBedFields = (6 + (hasOffsets ? 2 : 0));
         if (restCount > restBedFields)
             {
             int i;
             for (i = 0; i < restCount - restBedFields; i++)
                 extraFieldsRet[i] = restFields[restBedFields + i];
             *extraFieldsCountRet = (restCount - restBedFields);
             }
         return barChart;
         }
     }
 return NULL;
 }
 
 static struct barChartBed *getBarChartFromTable(struct trackDb *tdb, char *table, 
                                                 char *item, char *chrom, int start, int end)
 /* Retrieve barChart BED item from track table */
 {
 struct sqlConnection *conn = NULL;
 struct customTrack *ct = lookupCt(tdb->track);
 if (ct == NULL)
     conn = hAllocConnTrack(database, tdb);
 else
     {
     conn = hAllocConn(CUSTOM_TRASH);
     table = ct->dbTableName;
     }
 if (conn == NULL)
     return NULL;
 struct barChartBed *barChart = NULL;
 char **row;
 char query[512];
 struct sqlResult *sr;
 if (sqlTableExists(conn, table))
     {
     boolean hasOffsets = (sqlColumnExists(conn, table, BARCHART_OFFSET_COLUMN) &&
                          sqlColumnExists(conn, table, BARCHART_LEN_COLUMN));
     sqlSafef(query, sizeof query, 
                 "SELECT * FROM %s WHERE name='%s'"
                     "AND chrom='%s' AND chromStart=%d AND chromEnd=%d", 
                                 table, item, chrom, start, end);
     sr = sqlGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row != NULL)
         {
         barChart = barChartBedLoadOptionalOffsets(row, hasOffsets);
         }
     sqlFreeResult(&sr);
     }
 hFreeConn(&conn);
 return barChart;
 }
 
 static struct barChartBed *getBarChart(struct trackDb *tdb, char *item, char *chrom, int start, int end,
                                         struct asObject **retAs, char **extraFieldsReg, int *extraFieldsCountRet)
 /* Retrieve barChart BED item from track */
 {
 struct barChartBed *barChart = NULL;
 char *file = trackDbSetting(tdb, "bigDataUrl");
 if (file != NULL)
     barChart = getBarChartFromFile(tdb, file, item, chrom, start, end, retAs, extraFieldsReg, extraFieldsCountRet);
 else
     barChart = getBarChartFromTable(tdb, tdb->table, item, chrom, start, end);
 return barChart;
 }
 
 static struct barChartItemData *getSampleValsFromFile(struct trackDb *tdb, 
                         struct hash *categoryHash, struct barChartBed *bed, 
                         char *dataFile, char *sampleFile)
 /* Get all data values in a file for this item (locus) */
 {
 // Get sample categories from sample file
 // Format: id, category, extras
 struct lineFile *lf = udcWrapShortLineFile(sampleFile, NULL, 0);
 struct hash *sampleHash = hashNew(0);
 char *words[2];
 int sampleCt = 0;
 while (lineFileChopNext(lf, words, sizeof words))
     {
     hashAdd(sampleHash, words[0], words[1]);
     sampleCt++;
     }
 lineFileClose(&lf);
 
 // Open matrix file
 struct udcFile *f = udcFileOpen(dataFile, NULL);
 
 // Get header line with sample ids
 char *header = udcReadLine(f);
 int wordCt = sampleCt+1;        // initial field is label or empty 
 char **samples;
 AllocArray(samples, wordCt);
 chopByWhite(header, samples, wordCt);
 
 // Get data values
 // Format: id, category, extras
 bits64 offset = (bits64)bed->_dataOffset;
 bits64 size = (bits64)bed->_dataLen;
 udcSeek(f, offset);
 bits64 seek = udcTell(f);
 if (udcTell(f) != offset)
     warn("UDC seek mismatch: expecting %Lx, got %Lx. ", offset, seek);
 char *buf = needMem(size+1);
 bits64 count = udcRead(f, buf, size);
 if (count != size)
     warn("UDC read mismatch: expecting %Ld bytes, got %Ld. ", size, count);
 
 char **vals;
 AllocArray(vals, wordCt);
 buf[size]=0; // in case that size does not include the trailing newline
 chopByWhite(buf, vals, wordCt);
 
 udcFileClose(&f);
 
 // Construct list of sample data with category
 struct barChartItemData *sampleVals = NULL, *data = NULL;
 int i;
 for (i=1; i<wordCt && samples[i] != NULL; i++)
     {
     char *sample = samples[i];
     char *categ = (char *)hashFindVal(sampleHash, sample);
     if (categ == NULL)
         warn("barChart track %s: unknown category for sample %s", tdb->track, sample);
     else if (hashLookup(categoryHash, categ))
         {
         AllocVar(data);
         data->sample = cloneString(sample);
         data->category = cloneString(categ);
         data->value = sqlDouble(vals[i]);
         slAddHead(&sampleVals, data);
         }
     else
         {
         // we may have subbed out '_' for ' ' in barChartUiGetCategories earlier so try
         // searching for them in the hash here instead of straight from the data file
         subChar(categ, '_', ' ');
         if (hashLookup(categoryHash, categ))
             {
             AllocVar(data);
             data->sample = cloneString(sample);
             data->category = cloneString(categ);
             data->value = sqlDouble(vals[i]);
             slAddHead(&sampleVals, data);
             }
         }
     }
 return sampleVals;
 }
 
 static struct sqlConnection *getConnectionAndTable(struct trackDb *tdb, char *suffix,
                                                          char **retTable)
 /* Look for <table><suffix> in database or hgFixed and set up connection */
 {
 char table[256];
 if (trackHubDatabase(database))
     return NULL;
 
 assert(retTable);
 safef(table, sizeof(table), "%s%s", tdb->table, suffix);
 *retTable = cloneString(table);
 struct sqlConnection *conn = hAllocConn(database);
 if (!sqlTableExists(conn, table))
     {
     hFreeConn(&conn);
     conn = hAllocConn("hgFixed");
     if (!sqlTableExists(conn, table))
         {
         hFreeConn(&conn);
         return NULL;
         }
     }
 return conn;
 }
 
 static struct barChartItemData *getSampleValsFromTable(struct trackDb *tdb, 
                                                         struct hash *categoryHash,
                                                         struct barChartBed *bed)
 /* Get data values for this item (locus) from all samples */
 {
 char *table = NULL;
 struct sqlConnection *conn = getConnectionAndTable(tdb, "Data", &table);
 if (conn == NULL)
     return NULL;
 struct barChartData *val, *vals = barChartDataLoadForLocus(conn, table, bed->name);
 
 // Get category for samples 
 conn = getConnectionAndTable(tdb, "Sample", &table);
 char query[512];
 sqlSafef(query, sizeof(query), "SELECT * FROM %s", table);
 struct barChartSample *sample, *samples = barChartSampleLoadByQuery(conn, query);
 hFreeConn(&conn);
 
 struct hash *sampleHash = hashNew(0);
 for (sample = samples; sample != NULL; sample = sample->next)
     {
     hashAdd(sampleHash, sample->sample, sample);
     }
 
 // Construct list of sample data with category
 struct barChartItemData *sampleVals = NULL, *data = NULL;
 for (val = vals; val != NULL; val = val->next)
     {
     struct barChartSample *sample = hashFindVal(sampleHash, val->sample);
     if (sample == NULL)
         warn("barChart track %s: unknown category for sample %s", tdb->track, val->sample);
     else if (hashLookup(categoryHash, sample->category))
         {
         AllocVar(data);
         data->sample = cloneString(val->sample);
         data->category = cloneString(sample->category);
         data->value = val->value;
         slAddHead(&sampleVals, data);
         }
     }
 return sampleVals;
 }
 
 static struct barChartItemData *getSampleVals(struct trackDb *tdb, struct barChartBed *chartItem,
                                                 char **retMatrixUrl, char **retSampleUrl)
 /* Get data values for this item (locus) from all samples */
 {
 struct barChartItemData *vals = NULL;
 char *dataFile = trackDbSetting(tdb, "barChartMatrixUrl");
 // for backwards compatibility during qa review
 if (dataFile == NULL)
     dataFile = trackDbSetting(tdb, "barChartDataUrl");
 // for backwards compatibility during qa review
 struct barChartCategory *categories = barChartUiGetCategories(database, tdb);
 struct hash *categoryHash = barChartCategoriesToHash(categories);
 if (dataFile != NULL)
     {
     char *sampleFile = trackDbSetting(tdb, "barChartSampleUrl");
     if (sampleFile == NULL)
         return NULL;
     if (retMatrixUrl != NULL)
         *retMatrixUrl = dataFile;
     if (retSampleUrl != NULL)
         *retSampleUrl = sampleFile;
     vals = getSampleValsFromFile(tdb, categoryHash, chartItem, dataFile, sampleFile);
     }
 else
     vals = getSampleValsFromTable(tdb, categoryHash, chartItem);
 return vals;
 }
 
 static char *makeDataFrame(char *track, struct barChartItemData *vals)
 /* Create R data frame from sample data.  This is a tab-sep file, one row per sample.
    Return filename. */
 {
 
 // Create data frame with columns for sample, category, value */
 struct tempName dfTn;
 trashDirFile(&dfTn, "hgc", "barChart", ".df.txt");
 FILE *f = fopen(dfTn.forCgi, "w");
 if (f == NULL)
     errAbort("can't create temp file %s", dfTn.forCgi);
 fprintf(f, "sample\tcategory\tvalue\n");
 struct barChartItemData *val;
 for (val = vals; val != NULL; val = val->next)
     {
     fprintf(f, "%s\t%s\t%0.3f\n", val->sample, val->category, val->value);
     }
 fclose(f);
 return cloneString(dfTn.forCgi);
 }
 
 char *makeColorFile(struct trackDb *tdb)
 /* Make a file with category + color */
 {
 struct tempName colorTn;
 trashDirFile(&colorTn, "hgc", "barChartColors", ".txt");
 FILE *f = fopen(colorTn.forCgi, "w");
 if (f == NULL)
     errAbort("can't create temp file %s", colorTn.forCgi);
 struct barChartCategory *categs = barChartUiGetCategories(database, tdb);
 struct barChartCategory *categ;
 fprintf(f, "%s\t%s\n", "category", "color");
 for (categ = categs; categ != NULL; categ = categ->next)
     {
     //fprintf(f, "%s\t#%06X\n", categ->label, categ->color);
     fprintf(f, "%s\t%d\n", categ->label, categ->color);
     }
 fclose(f);
 return cloneString(colorTn.forCgi);
 }
 
 static void printBoxplot(char *df, char *item, char *name2, char *units, char *colorFile)
 /* Plot data frame to image file and include in HTML */
 {
 struct tempName pngTn;
 trashDirFile(&pngTn, "hgc", "barChart", ".png");
 
 // to help with QAing the change, we add the "oldFonts" CGI parameter so QA can compare
 // old and new fonts to make sure that things are still readible on mirrors and servers
 // without the new fonts installed. This only needed during the QA phase
 bool useOldFonts = cgiBoolean("oldFonts");
 
 /* Exec R in quiet mode, without reading/saving environment or workspace */
 char *pipeCmd[] = {"Rscript","--vanilla","--slave","hgcData/barChartBoxplot.R", 
     item, units, colorFile, df, pngTn.forHtml, 
     isEmpty(name2) ? "n/a" : name2, useOldFonts ? "1" : "0", NULL};
 struct pipeline *pl = pipelineOpen1(pipeCmd, pipelineWrite | pipelineNoAbort, "/dev/null", NULL, 0);
 int ret = pipelineWait(pl);
 
 if (ret == 0)
     printf("<img src = \"%s\" border=1><br>\n", pngTn.forHtml);
 else
     warn("Error creating boxplot from sample data with command: %s", pipelineDesc(pl));
 }
 
 static double estimateStringWidth(char *s)
 /* Get estimate of string width based on a memory font that is about the
  * same size as svg will be using.  After much research I don't think we
  * can get the size from the server, would have to be in Javascript to get
  * more precise */
 {
 MgFont *font = mgHelvetica14Font();
 return mgFontStringWidth(font, s);
 }
 
 static double longestLabelSize(struct barChartCategory *categList)
 /* Get estimate of longest label in pixels */
 {
 int longest = 0;
 struct barChartCategory *categ;
 for (categ = categList; categ != NULL; categ = categ->next)
     {
     int size = estimateStringWidth(categ->label);
     if (size > longest)
         longest = size;
     }
 return longest * 1.02;
 }
 
 void deunderbarColumn(struct fieldedTable *ft, int fieldIx)
 /* Ununderbar all of a column inside table because space/underbar gets
  * so confusing */
 {
 struct fieldedRow *row;
 for (row = ft->rowList; row != NULL; row = row->next)
     replaceChar(row->row[fieldIx], '_', ' ');
 }
 
 static void svgBarChart(struct barChartBed *chart, struct trackDb *tdb, double maxVal, char *metric)
 /* Plot bar chart without quartiles or anything fancy just using SVG */
 {
+puts("<p>");
 /* Load up input labels, color, and data */
 struct barChartCategory *categs = barChartUiGetCategories(database, tdb);
 int categCount = slCount(categs);
 if (categCount != chart->expCount)
     {
     warn("Problem in %s barchart track. There are %d categories in trackDb and %d in data",
 	tdb->track, categCount, chart->expCount);
     return;
     }
 
 char *statsFile = trackDbSetting(tdb, "barChartStatsUrl");
 struct hash *statsHash = NULL;
 int countStatIx = 0;
 double statsSize = 0.0;
 if (statsFile != NULL)
     {
     char *required[] = { "count", "total"};
     struct fieldedTable *ft = fieldedTableFromTabFile(
 	statsFile, statsFile, required, ArraySize(required));
     deunderbarColumn(ft, 0);
     statsHash = fieldedTableIndex(ft, ft->fields[0]);
     countStatIx = fieldedTableFindFieldIx(ft, "count");
     statsSize = 8*(fieldedTableMaxColChars(ft, countStatIx)+1);
     }
 
 /* Some constants that control layout */
 double heightPer=18.0;
 double totalWidth=1250.0;
 double borderSize = 1.0;
 
 double headerHeight = heightPer + 2*borderSize;
 double innerHeight=heightPer-borderSize;
 double labelWidth = longestLabelSize(categs) + 9;  // Add some because size is just estimate
 if (labelWidth > totalWidth/2) labelWidth = totalWidth/2;  // Don't let labels take up more than half
 double patchWidth = heightPer;
 double labelOffset = patchWidth + 2*borderSize;
 double statsOffset = labelOffset + labelWidth;
 double barOffset = statsOffset + statsSize;
 double statsRightOffset = barOffset - 9;
 double barNumLabelWidth = estimateStringWidth(" 1234.000"); 
 double barMaxWidth = totalWidth-barOffset -barNumLabelWidth ;
 double totalHeight = headerHeight + heightPer * categCount + borderSize;
 
 printf("<svg width=\"%g\" height=\"%g\">\n", totalWidth, totalHeight);
 
 /* Draw header */
 printf("<rect width=\"%g\" height=\"%g\" style=\"fill:#%s\"/>\n", totalWidth, headerHeight, HG_COL_HEADER);
 char *sampleLabel = trackDbSettingOrDefault(tdb, "barChartLabel", "Sample");
 printf("<text x=\"%g\" y=\"%g\" font-size=\"%g\">%s</text>\n", 
     labelOffset, innerHeight-1, innerHeight-1, sampleLabel);
 if (statsSize > 0.0)
     printf("<text x=\"%g\" y=\"%g\" font-size=\"%g\" text-anchor=\"end\">%s</text>\n", 
 	statsRightOffset, innerHeight-1, innerHeight-1, "N");
 printf("<text x=\"%g\" y=\"%g\" font-size=\"%g\">%s %s</text>\n", 
     barOffset, innerHeight-1, innerHeight-1, metric, "Value");
 
 /* Set up clipping path for the pesky labels, which may be too long */
 printf("<clipPath id=\"labelClip\"><rect x=\"%g\" y=\"0\" width=\"%g\" height=\"%g\"/></clipPath>\n",
     labelOffset, barOffset-labelOffset, totalHeight);
 
 double yPos = headerHeight;
 struct barChartCategory *categ;
 int i;
 for (i=0, categ=categs; i<categCount; ++i , categ=categ->next, yPos += heightPer)
     {
     double score = chart->expScores[i];
     double barWidth = 0;
     if (maxVal > 0.0)
 	barWidth = barMaxWidth * score/maxVal;
     char *deunder = cloneString(categ->label);
     replaceChar(deunder, '_', ' ');
     printf("<rect x=\"0\" y=\"%g\" width=\"15\" height=\"%g\" style=\"fill:#%06X\"/>\n",
 	yPos, innerHeight, categ->color);
     printf("<rect x=\"%g\" y=\"%g\" width=\"%g\" height=\"%g\" style=\"fill:#%06X\"/>\n",
 	barOffset, yPos, barWidth, innerHeight, categ->color);
     if (i&1)  // every other time
 	printf("<rect x=\"%g\" y=\"%g\" width=\"%g\" height=\"%g\" style=\"fill:#%06X\"/>\n",
 	    labelOffset, yPos, labelWidth+statsSize, innerHeight, 0xFFFFFF);
     printf("<text x=\"%g\" y=\"%g\" font-size=\"%g\" clip-path=\"url(#labelClip)\"\">%s</text>\n", 
  	labelOffset, yPos+innerHeight-1, innerHeight-1, deunder);
     if (statsSize > 0.0)
 	{
 	struct fieldedRow *fr = hashFindVal(statsHash, deunder);
 	if (fr != NULL)
 	    {
 	    printf("<text x=\"%g\" y=\"%g\" font-size=\"%g\" text-anchor=\"end\">%s</text>\n", 
 		statsRightOffset, yPos+innerHeight-1, innerHeight-1, fr->row[countStatIx]);
 	    }
 	}
     printf("<text x=\"%g\" y=\"%g\" font-size=\"%g\">%5.3f</text>\n", 
 	barOffset+barWidth+2, yPos+innerHeight-1, innerHeight-1, score);
     }
 printf("</svg>");
 }
 
 
 static void printBarChart(char *item, struct barChartBed *chart, struct trackDb *tdb, 
     double maxVal, char *metric)
 /* Plot bar chart without expressionMatrix or R plots*/
 {
 char *statsFile = trackDbSetting(tdb, "barChartStatsUrl");
 char *facets = trackDbSetting(tdb, "barChartFacets");
 if (facets != NULL && statsFile != NULL)
     facetedBarChart(item, chart, tdb, maxVal, statsFile, facets, metric);
 else
     svgBarChart(chart, tdb, maxVal, metric);
 }
 
 struct asColumn *asFindColByIx(struct asObject *as, int ix)
 /* Find AS column by index */
 {
 struct asColumn *asCol;
 int i;
 for (i=0, asCol = as->columnList; asCol != NULL && i<ix; asCol = asCol->next, i++);
     return asCol;
 }
 
 void doBarChartDetails(struct trackDb *tdb, char *item)
 /* Details of barChart item */
 {
 int start = cartInt(cart, "o");
 int end = cartInt(cart, "t");
 struct asObject *as = NULL;
 char *extraFields[EXTRA_FIELDS_SIZE];
 int extraFieldCount = 0;
 int numColumns = 0;
 struct barChartBed *chartItem = getBarChart(tdb, item, seqName, start, end, &as, extraFields, &extraFieldCount);
 if (chartItem == NULL)
     errAbort("Can't find item %s in barChart table/file %s\n", item, tdb->table);
 
 genericHeader(tdb, item);
 
 // get name and name2 from trackDb, .as file, or use defaults
 struct asColumn *nameCol = NULL, *name2Col = NULL;
 //struct asColumn *name2Col;
 char *nameLabel = NULL, *name2Label = NULL;
 if (as != NULL)
     {
     numColumns = slCount(as->columnList);
     nameCol = asFindColByIx(as, BARCHART_NAME_COLUMN_IX);
     name2Col = asFindColByIx(as, BARCHART_NAME2_COLUMN_IX);
     }
 nameLabel = trackDbSettingClosestToHomeOrDefault(tdb, "bedNameLabel", nameCol ? nameCol->comment : "Item");
 if (trackDbSettingClosestToHomeOrDefault(tdb, "url", NULL) != NULL)
     printCustomUrl(tdb, item, TRUE);
 else
     printf("<b>%s: </b>%s ", nameLabel, chartItem->name);
 name2Label = name2Col ? name2Col->comment : "Alternative name";
 if (differentString(chartItem->name2, "")) 
     {
     if (trackDbSettingClosestToHomeOrDefault(tdb, "url2", NULL) != NULL)
         printOtherCustomUrl(tdb, chartItem->name2, "url2", TRUE);
     else
         printf("(%s: %s)<br>\n", name2Label, chartItem->name2);
     }
 else
     printf("<br>\n");
 
 int categId;
 float highLevel = barChartMaxValue(chartItem, &categId);
 char *units = trackDbSettingClosestToHomeOrDefault(tdb, BAR_CHART_UNIT, "units");
 char *metric = trackDbSettingClosestToHomeOrDefault(tdb, BAR_CHART_METRIC, "");
 printf("<b>Maximum %s value: </b> %0.2f %s in %s<br>\n", 
                 metric, highLevel, units, barChartUiGetCategoryLabelById(categId, database, tdb));
-printf("<b>Score: </b> %d<br>\n", chartItem->score); 
-printf("<b>Genomic position: "
-                "</b>%s <a href='%s&db=%s&position=%s%%3A%d-%d'>%s:%d-%d</a><br>\n", 
+printf("<b>Gene position: "
+                "</b>%s <a href='%s&db=%s&position=%s%%3A%d-%d'>%s:%d-%d</a>\n", 
                     database, hgTracksPathAndSettings(), database, 
                     chartItem->chrom, chartItem->chromStart+1, chartItem->chromEnd,
                     chartItem->chrom, chartItem->chromStart+1, chartItem->chromEnd);
-printf("<b>Strand: </b> %s\n", chartItem->strand); 
+printf("&nbsp;&nbsp;<b>Strand: </b> %s\n", chartItem->strand); 
 
 // print any remaining extra fields
 if (numColumns > 0)
     {
     extraFieldsPrint(tdb, NULL, extraFields, extraFieldCount);
     }
 
 char *matrixUrl = NULL, *sampleUrl = NULL;
 struct barChartItemData *vals = getSampleVals(tdb, chartItem, &matrixUrl, &sampleUrl);
-puts("<p>");
 if (vals != NULL)
     {
+    puts("<p>");
     // Print boxplot
     char *df = makeDataFrame(tdb->table, vals);
     char *colorFile = makeColorFile(tdb);
     printBoxplot(df, item, chartItem->name2, units, colorFile);
     printf("<br><a href='%s'>View all data points for %s%s%s%s</a>\n", df, 
                         chartItem->name, 
                         chartItem->name2 ? " (" : "",
                         chartItem->name2 ? chartItem->name2 : "",
                         chartItem->name2 ? ")" : "");
     }
 else
     {
     if (cfgOptionBooleanDefault("svgBarChart", FALSE))
 	{
 	printBarChart(item, chartItem, tdb, highLevel, metric);
 	}
     }
 puts("<br>");
 }