f4aba74550dea6d8548ba891cb9d057eaf6de43e
kate
Wed Mar 22 12:30:24 2017 -0700
Fix bogus color cacheing. Its now per-track
diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c
index 31a2434..d7e5a9e 100644
--- src/hg/hgTracks/gtexTracks.c
+++ src/hg/hgTracks/gtexTracks.c
@@ -36,31 +36,35 @@
struct gtexGeneExtras
/* Track info */
{
char *version; /* Suffix to table name, e.g. 'V6' */
boolean codingOnly; /* User filter to limit display to coding genes */
boolean showExons; /* Show gene model exons */
boolean noWhiteout; /* Suppress whiteout of graph background (allow highlight, blue lines) */
enum geneLabelStyle labelStyle; /* Show gene symbol, accession, or both */
double maxMedian; /* Maximum median rpkm for all tissues */
boolean isComparison; /* Comparison of two sample sets (e.g. male/female). */
boolean isDifference; /* True if comparison is shown as a single difference graph.
False if 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 */
boolean doLogTransform; /* Log10(x+1) */
- struct gtexTissue *tissues; /* Cache tissue names, descriptions */
+ struct gtexTissue *tissues; /* Tissue names, descriptions */
+ int tissueCount; /* Tissue count - derived from above */
+ char **tissueNames; /* Tissue names by id - derived from above */
+ char **tissueLabels; /* Tissue labels by id - derived from above */
+ char **tissueDescriptions; /* Tissue descriptions by id - derived from above */
struct hash *tissueFilter; /* For filter. NULL out excluded tissues */
};
struct gtexGeneInfo
/* GTEx gene model, names, and expression medians */
{
struct gtexGeneInfo *next; /* Next in singly linked list */
struct gtexGeneBed *geneBed;/* Gene name, id, type, exp count and medians
from BED table */
struct genePred *geneModel; /* Gene structure from model table */
char *label; /* Name, accession, or both */
char *description; /* Gene description */
double *medians1; /* Computed medians */
double *medians2; /* Computed medians for comparison (inverse) graph */
int height; /* Item height in pixels */
@@ -107,134 +111,136 @@
char *geneClass = gtexGeneClass(geneBed);
if (geneClass == NULL)
return statusColors.unknown;
if (sameString(geneClass, "coding"))
return statusColors.coding;
if (sameString(geneClass, "nonCoding"))
return statusColors.nonCoding;
if (sameString(geneClass, "pseudo"))
return statusColors.pseudo;
return statusColors.unknown;
}
/***********************************************/
/* Cache tissue info */
-struct gtexTissue *getTissues(char *version)
+struct gtexTissue *getTissues(struct track *tg, char *version)
/* Get and cache tissue metadata from database */
{
-static struct gtexTissue *gtexTissues = NULL;
-
-if (!gtexTissues)
- gtexTissues = gtexGetTissues(version);
-return gtexTissues;
+struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData;
+if (!extras->tissues)
+ extras->tissues = gtexGetTissues(version);
+return extras->tissues;
}
-int getTissueCount(char *version)
+int getTissueCount(struct track *tg, char *version)
/* Get and cache the number of tissues in GTEx tissue table */
{
-static int tissueCount = 0;
-
-if (!tissueCount)
- tissueCount = slCount(getTissues(version));
-return tissueCount;
+struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData;
+if (!extras->tissueCount)
+ extras->tissueCount = slCount(getTissues(tg, version));
+return extras->tissueCount;
}
-char *getTissueName(int id, char *version)
+char *getTissueName(struct track *tg, int id, char *version)
/* Get tissue name from id, cacheing */
{
-static char **tissueNames = NULL;
struct gtexTissue *tissue;
-int count = getTissueCount(version);
-if (!tissueNames)
+int count = getTissueCount(tg, version);
+struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData;
+if (!extras->tissueNames)
{
- struct gtexTissue *tissues = getTissues(version);
- AllocArray(tissueNames, count);
+ struct gtexTissue *tissues = getTissues(tg, version);
+ AllocArray(extras->tissueNames, count);
for (tissue = tissues; tissue != NULL; tissue = tissue->next)
- tissueNames[tissue->id] = cloneString(tissue->name);
+ extras->tissueNames[tissue->id] = cloneString(tissue->name);
}
if (id >= count)
errAbort("GTEx tissue table problem: can't find id %d\n", id);
-return tissueNames[id];
+return extras->tissueNames[id];
}
-char *getTissueDescription(int id, char *version)
+char *getTissueDescription(struct track *tg, int id, char *version)
/* Get tissue description from id, cacheing */
{
-static char **tissueDescriptions = NULL;
struct gtexTissue *tissue;
-int count = getTissueCount(version);
-if (!tissueDescriptions)
+int count = getTissueCount(tg, version);
+struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData;
+if (!extras->tissueDescriptions)
{
- struct gtexTissue *tissues = getTissues(version);
- AllocArray(tissueDescriptions, count);
+ struct gtexTissue *tissues = getTissues(tg, version);
+ AllocArray(extras->tissueDescriptions, count);
for (tissue = tissues; tissue != NULL; tissue = tissue->next)
- tissueDescriptions[tissue->id] = cloneString(tissue->description);
+ extras->tissueDescriptions[tissue->id] = cloneString(tissue->description);
}
if (id >= count)
errAbort("GTEx tissue table problem: can't find id %d\n", id);
-return tissueDescriptions[id];
+return extras->tissueDescriptions[id];
}
-struct rgbColor *getGtexTissueColors(char *version)
+struct rgbColor *getGtexTissueColors(struct track *tg, char *version)
/* Get RGB colors from tissue table */
{
-struct gtexTissue *tissues = getTissues(version);
+struct gtexTissue *tissues = getTissues(tg, version);
struct gtexTissue *tissue = NULL;
-int count = slCount(tissues);
-struct rgbColor *colors;
-AllocArray(colors, count);
+int count = getTissueCount(tg, version);
+struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData;
+if (!extras->colors)
+ {
+ AllocArray(extras->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)};
+ extras->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;
+ }
+return extras->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)
+static void loadComputedMedians(struct track *tg, struct gtexGeneInfo *geneInfo)
/* Compute medians based on graph type. Returns a list of 2 for comparison graph types */
{
struct gtexGeneBed *geneBed = geneInfo->geneBed;
int expCount = geneBed->expCount;
+struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData;
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]);
@@ -248,34 +254,34 @@
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, extras->version));
+ scores = hashFindVal(scoreHash1, getTissueName(tg, i, extras->version));
if (scores)
medians1[i] = slDoubleMedian(scores);
- scores = hashFindVal(scoreHash2, getTissueName(i, extras->version));
+ scores = hashFindVal(scoreHash2, getTissueName(tg, i, extras->version));
if (scores)
medians2[i] = slDoubleMedian(scores);
}
if (extras->isDifference)
{
for (i=0; i<geneBed->expCount; i++)
{
if (medians1[i] >= medians2[i])
{
medians1[i] -= medians2[i];
medians2[i] = 0;
}
else
{
medians2[i] -= medians1[i];
@@ -309,31 +315,31 @@
if (winSize < WIN_MAX_GRAPH)
return MAX_GENE_BOX_HEIGHT;
else if (winSize < WIN_MED_GRAPH)
return MED_GENE_BOX_HEIGHT;
else
return MIN_GENE_BOX_HEIGHT;
}
static int gtexGeneItemHeight(struct track *tg, void *item);
static void filterTissues(struct track *tg)
/* Check cart for tissue selection. NULL out unselected tissues in tissue list */
{
struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData;
struct gtexTissue *tis = NULL;
-extras->tissues = getTissues(extras->version);
+extras->tissues = getTissues(tg, extras->version);
extras->tissueFilter = hashNew(0);
if (cartListVarExistsAnyLevel(cart, tg->tdb, FALSE, GTEX_TISSUE_SELECT))
{
struct slName *selectedValues = cartOptionalSlNameListClosestToHome(cart, tg->tdb,
FALSE, GTEX_TISSUE_SELECT);
if (selectedValues != NULL)
{
struct slName *name;
for (name = selectedValues; name != NULL; name = name->next)
hashAdd(extras->tissueFilter, name->name, name->name);
return;
}
}
/* no filter */
for (tis = extras->tissues; tis != NULL; tis = tis->next)
@@ -432,33 +438,34 @@
/* Get geneBeds (names and all-sample tissue median scores) in range */
char *filter = getScoreFilterClause(cart, tg->tdb, NULL);
bedLoadItemWhere(tg, tg->table, filter, (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 */
#ifdef COLOR_SCHEME
char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS,
GTEX_COLORS_DEFAULT);
#else
char *colorScheme = GTEX_COLORS_DEFAULT;
#endif
+
if (sameString(colorScheme, GTEX_COLORS_GTEX))
{
- extras->colors = getGtexTissueColors(extras->version);
+ extras->colors = getGtexTissueColors(tg, extras->version);
}
else
{
if (geneBed)
{
int expCount = geneBed->expCount;
extras->colors = getRainbow(&saturatedRainbowAtPos, expCount);
}
}
filterTissues(tg);
while (geneBed != NULL)
{
if (extras->codingOnly && !gtexGeneIsCoding(geneBed))
{
@@ -503,31 +510,31 @@
// also strip 'homo sapiens' prefix
#define SPECIES_PREFIX "Homo sapiens "
if (startsWith(SPECIES_PREFIX, desc))
desc += strlen(SPECIES_PREFIX);
geneInfo->description = desc;
}
else
geneInfo->description = geneInfo->geneBed->name;
slAddHead(&list, geneInfo);
geneBed = geneBed->next;
geneInfo->geneBed->next = NULL;
if (extras->isComparison && (tg->visibility == tvFull || tg->visibility == tvPack))
// compute medians based on configuration (comparisons, and later, filters)
- loadComputedMedians(geneInfo, extras);
+ loadComputedMedians(tg, geneInfo);
geneInfo->height = gtexGeneItemHeight(tg, geneInfo);
}
slReverse(&list);
tg->items = list;
}
/***********************************************/
/* Draw */
/* Bargraph layouts for three window sizes */
#define WIN_MAX_GRAPH 50000
#define MAX_GRAPH_HEIGHT 175
#define MAX_BAR_WIDTH 5
#define MAX_GRAPH_PADDING 2
@@ -651,31 +658,31 @@
return valToHeight(useVal, useMax, gtexMaxGraphHeight(), doLogTransform);
}
static int gtexGeneGraphHeight(struct track *tg, struct gtexGeneInfo *geneInfo, boolean doTop)
/* Determine height in pixels of graph. This will be the box for tissue with highest expression
If doTop is false, compute height of bottom graph of comparison */
{
struct gtexGeneBed *geneBed = geneInfo->geneBed;
struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData;
int i;
double maxExp = 0.0;
int expCount = geneBed->expCount;
double expScore;
for (i=0; i<expCount; i++)
{
- if (!filterTissue(tg, getTissueName(i, extras->version)))
+ if (!filterTissue(tg, getTissueName(tg, i, extras->version)))
continue;
if (doTop)
expScore = (geneInfo->medians1 ? geneInfo->medians1[i] : geneBed->expScores[i]);
else
expScore = geneInfo->medians2[i];
maxExp = max(maxExp, expScore);
}
double viewMax = (double)cartUsualIntClosestToHome(cart, tg->tdb, FALSE,
GTEX_MAX_LIMIT, GTEX_MAX_LIMIT_DEFAULT);
double maxMedian = ((struct gtexGeneExtras *)tg->extraUiData)->maxMedian;
return valToClippedHeight(maxExp, maxMedian, viewMax, gtexMaxGraphHeight(), extras->doLogTransform);
}
static void drawGraphBox(struct track *tg, struct gtexGeneInfo *geneInfo, struct hvGfx *hvg, int x, int y)
/* Draw white background for graph */
@@ -962,48 +969,48 @@
if (tg->limitedVis == tvDense)
{
genericMapItem(tg, hvg, item, itemName, itemName, start, end, x, y, width, height);
return;
}
struct gtexGeneInfo *geneInfo = item;
struct gtexGeneBed *geneBed = geneInfo->geneBed;
struct gtexGeneExtras *extras = (struct gtexGeneExtras *)tg->extraUiData;
int geneStart = geneBed->chromStart;
int geneEnd = geneBed->chromEnd;
if (tg->limitedVis == tvSquish)
{
int tisId = maxTissueForGene(geneBed);
char *maxTissue = "";
if (tisId > 1)
- maxTissue = getTissueDescription(tisId, extras->version);
+ maxTissue = getTissueDescription(tg, tisId, extras->version);
char buf[128];
safef(buf, sizeof buf, "%s %s", geneBed->name, maxTissue);
int x1, x2;
getItemX(geneStart, geneEnd, &x1, &x2);
int width = max(1, x2-x1);
mapBoxHc(hvg, geneStart, geneEnd, x1, y, width, height,
tg->track, mapItemName, buf);
return;
}
int topGraphHeight = gtexGeneGraphHeight(tg, geneInfo, TRUE);
topGraphHeight = max(topGraphHeight, tl.fontHeight); // label
int yZero = topGraphHeight + y - 1; // yZero is bottom of graph
int x1 = insideX;
// add maps to tissue bars in expresion graph
-struct gtexTissue *tissues = getTissues(extras->version);
+struct gtexTissue *tissues = getTissues(tg, extras->version);
struct gtexTissue *tissue = NULL;
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
x1 = insideX + graphX;
if (geneInfo->medians2)
{
// skip over labels in comparison graphs