static Color goldColor(struct track *tg, void *item, struct hvGfx *hvg)
/* Return color to draw known gene in. */
{
struct agpFrag *frag = item;
Color pink = hvGfxFindColorIx(hvg, 240, 140, 140);
Color color = (sameString(frag->type, "A") ? pink : tg->ixColor);
return color;
}
Color encodeRnaColor(struct track *tg, void *item, struct hvGfx *hvg)
/* Return color of encodeRna track item. */
{
struct encodeRna *el = item;
if(el->isRmasked) return MG_BLACK;
if(el->isTranscribed) return hvGfxFindColorIx(hvg, 0x79, 0xaa, 0x3d);
if(el->isPrediction) return MG_RED;
return MG_BLUE;
}
void makeGrayShades(struct hvGfx *hvg, int maxShade, Color shadesOfGray[])
/* Make eight shades of gray in display. */
{
int i;
for (i=0; i<=maxShade; ++i)
{
int level = 255 - (255*i/maxShade);
if (level < 0) level = 0;
shadesOfGray[i] = hvGfxFindColorIx(hvg, level, level, level);
}
shadesOfGray[maxShade+1] = MG_RED;
}
Color colorFromAscii(struct hvGfx *hvg, char *asciiColor)
/* Get color index for a named color. */
/* Copy/pasted from hgGenome/mainPage.c ... should be in a library */
/* somewhere! */
{
if (sameWord("red", asciiColor))
return MG_RED;
else if (sameWord("blue", asciiColor))
return MG_BLUE;
else if (sameWord("yellow", asciiColor))
return hvGfxFindColorIx(hvg, 220, 220, 0);
else if (sameWord("purple", asciiColor))
return hvGfxFindColorIx(hvg, 150, 0, 200);
else if (sameWord("orange", asciiColor))
return hvGfxFindColorIx(hvg, 230, 120, 0);
else if (sameWord("green", asciiColor))
return hvGfxFindColorIx(hvg, 0, 180, 0);
else if (sameWord("gray", asciiColor))
return MG_GRAY;
else
return MG_BLACK;
}
Color encodeStanfordNRSFColor(struct track *tg, void *item, struct hvGfx *hvg)
/* color by strand */
{
struct bed *thisItem = item;
int r = tg->color.r;
int g = tg->color.g;
int b = tg->color.b;
if (thisItem->strand[0] == '-')
{
r = g;
g = b;
b = tg->color.r;
}
return hvGfxFindColorIx(hvg, r, g, b);
}
void hvGfxMakeColorGradient(struct hvGfx *hvg,
struct rgbColor *start, struct rgbColor *end,
int steps, Color *colorIxs)
/* Make a color gradient that goes smoothly from start to end colors in given
* number of steps. Put indices in color table in colorIxs */
{
double scale = 0, invScale;
double invStep;
int i;
int r,g,b;
steps -= 1; /* Easier to do the calculation in an inclusive way. */
invStep = 1.0/steps;
for (i=0; i<=steps; ++i)
{
invScale = 1.0 - scale;
r = invScale * start->r + scale * end->r;
g = invScale * start->g + scale * end->g;
b = invScale * start->b + scale * end->b;
colorIxs[i] = hvGfxFindColorIx(hvg, r, g, b);
scale += invStep;
}
}
Color hCytoBandCentromereColor(struct hvGfx *hvg)
/* Get the color used traditionally to draw centromere */
{
return hvGfxFindColorIx(hvg, 150, 50, 50);
}
static void goldDrawDense(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw golden path items. */
{
int baseWidth = seqEnd - seqStart;
struct agpFrag *frag;
struct agpGap *gap;
int y = yOff;
int heightPer = tg->heightPer;
int lineHeight = tg->lineHeight;
int x1,x2,w;
int midLineOff = heightPer/2;
boolean isFull = (vis == tvFull);
Color brown = color;
Color gold = tg->ixAltColor;
Color pink = 0;
Color pink1 = hvGfxFindColorIx(hvg, 240, 140, 140);
Color pink2 = hvGfxFindColorIx(hvg, 240, 100, 100);
int ix = 0;
double scale = scaleForPixels(width);
/* Draw gaps if any. */
if (!isFull)
{
int midY = y + midLineOff;
for (gap = tg->customPt; gap != NULL; gap = gap->next)
{
if (!sameWord(gap->bridge, "no"))
{
drawScaledBox(hvg, gap->chromStart, gap->chromEnd, scale, xOff, midY, 1, brown);
}
}
}
for (frag = tg->items; frag != NULL; frag = frag->next)
{
x1 = round((double)((int)frag->chromStart-winStart)*scale) + xOff;
x2 = round((double)((int)frag->chromEnd-winStart)*scale) + xOff;
w = x2-x1;
color = ((ix&1) ? gold : brown);
pink = ((ix&1) ? pink1 : pink2);
if (w < 1)
w = 1;
if (sameString(frag->type, "A")) color = pink;
hvGfxBox(hvg, x1, y, w, heightPer, color);
if (isFull)
y += lineHeight;
else if (baseWidth < 10000000)
{
char status[256];
sprintf(status, "%s:%d-%d %s %s:%d-%d",
frag->frag, frag->fragStart, frag->fragEnd,
frag->strand,
frag->chrom, frag->chromStart, frag->chromEnd);
mapBoxHc(hvg, frag->chromStart, frag->chromEnd, x1,y,w,heightPer, tg->track,
frag->frag, status);
}
++ix;
}
}
void genoLayDrawBandedChroms(struct genoLay *gl, struct hvGfx *hvg, char *db,
struct sqlConnection *conn, Color *shadesOfGray, int maxShade,
int defaultColor)
/* Draw chromosomes with centromere and band glyphs.
* Get the band data from the database. If the data isn't
* there then draw simple chroms in default color instead */
{
char *bandTable = "cytoBandIdeo";
int yOffset = gl->chromOffsetY;
genoLayDrawSimpleChroms(gl, hvg, defaultColor);
if (sqlTableExists(conn, bandTable) && !gl->allOneLine)
{
int centromereColor = hCytoBandCentromereColor(hvg);
double pixelsPerBase = 1.0/gl->basesPerPixel;
int height = gl->chromHeight;
int innerHeight = gl->chromHeight-2;
struct genoLayChrom *chrom;
boolean isDmel = hCytoBandDbIsDmel(db);
boolean bColor = hvGfxFindColorIx(hvg, 200, 150, 150);
int fontPixelHeight = mgFontPixelHeight(gl->font);
for (chrom = gl->chromList; chrom != NULL; chrom = chrom->next)
{
boolean gotAny = FALSE;
struct sqlResult *sr;
char **row;
char query[256];
int cenX1=BIGNUM, cenX2=0;
int y = chrom->y + yOffset;
/* Fetch bands from database and draw them. */
safef(query, sizeof(query), "select * from %s where chrom='%s'",
bandTable, chrom->fullName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
struct cytoBand band;
int x1, x2;
cytoBandStaticLoad(row, &band);
x1 = pixelsPerBase*band.chromStart;
x2 = pixelsPerBase*band.chromEnd;
if (sameString(band.gieStain, "acen"))
{
/* Centromere is represented as two adjacent bands.
* We'll just record the extents of it here, and draw it
* in one piece later. */
if (x1 < cenX1)
cenX1 = x1;
if (x2 > cenX2)
cenX2 = x2;
}
else
{
/* Draw band */
hCytoBandDrawAt(&band, hvg, x1+chrom->x, y+1, x2-x1, innerHeight,
isDmel, gl->font, fontPixelHeight, MG_BLACK, bColor,
shadesOfGray, maxShade);
gotAny = TRUE;
}
}
sqlFreeResult(&sr);
/* Draw box around chromosome */
hvGfxBox(hvg, chrom->x, y, chrom->width, 1, MG_BLACK);
hvGfxBox(hvg, chrom->x, y+height-1, chrom->width, 1, MG_BLACK);
hvGfxBox(hvg, chrom->x, y, 1, height, MG_BLACK);
hvGfxBox(hvg, chrom->x+chrom->width-1, y, 1, height, MG_BLACK);
/* Draw centromere if we found one. */
if (cenX2 > cenX1)
{
hCytoBandDrawCentromere(hvg, cenX1+chrom->x, y, cenX2-cenX1, height,
MG_WHITE, centromereColor);
}
}
}
}
void initializeColors(struct hvGfx *hvg)
{
LLshadesOfCOGS['J'-'A']=hvGfxFindColorIx(hvg, 252, 204,252);
LLshadesOfCOGS['A'-'A']=hvGfxFindColorIx(hvg, 252, 220,252);
LLshadesOfCOGS['K'-'A']=hvGfxFindColorIx(hvg, 252, 220,236);
LLshadesOfCOGS['L'-'A']=hvGfxFindColorIx(hvg, 252, 220,220);
LLshadesOfCOGS['B'-'A']=hvGfxFindColorIx(hvg, 252, 220,204);
LLshadesOfCOGS['D'-'A']=hvGfxFindColorIx(hvg, 252, 252,220);
LLshadesOfCOGS['Y'-'A']=hvGfxFindColorIx(hvg, 252, 252,204);
LLshadesOfCOGS['V'-'A']=hvGfxFindColorIx(hvg, 252, 252,188);
LLshadesOfCOGS['T'-'A']=hvGfxFindColorIx(hvg, 252, 252,172);
LLshadesOfCOGS['M'-'A']=hvGfxFindColorIx(hvg, 236, 252,172);
LLshadesOfCOGS['N'-'A']=hvGfxFindColorIx(hvg, 220, 252,172);
LLshadesOfCOGS['Z'-'A']=hvGfxFindColorIx(hvg, 204, 252,172);
LLshadesOfCOGS['W'-'A']=hvGfxFindColorIx(hvg, 188, 252,172);
LLshadesOfCOGS['U'-'A']=hvGfxFindColorIx(hvg, 172, 252,172);
LLshadesOfCOGS['O'-'A']=hvGfxFindColorIx(hvg, 156, 252,172);
LLshadesOfCOGS['C'-'A']=hvGfxFindColorIx(hvg, 188, 252,252); /* light blue 133, 233,204); */
LLshadesOfCOGS['G'-'A']=hvGfxFindColorIx(hvg, 204, 252,252);
LLshadesOfCOGS['E'-'A']=hvGfxFindColorIx(hvg, 220, 252,252);
LLshadesOfCOGS['F'-'A']=hvGfxFindColorIx(hvg, 220, 236,252);
LLshadesOfCOGS['H'-'A']=hvGfxFindColorIx(hvg, 220, 220,252);
LLshadesOfCOGS['I'-'A']=hvGfxFindColorIx(hvg, 220, 204,252);
LLshadesOfCOGS['P'-'A']=hvGfxFindColorIx(hvg, 204, 204,252);
LLshadesOfCOGS['Q'-'A']=hvGfxFindColorIx(hvg, 188, 204,252);
LLshadesOfCOGS['R'-'A']=hvGfxFindColorIx(hvg, 224, 224,224); /* general function prediction */
LLshadesOfCOGS['S'-'A']=hvGfxFindColorIx(hvg, 204, 204,204);
LLshadesOfCOGS['-'-'A']=hvGfxFindColorIx(hvg, 224, 224,224);/* no cog - same as R (general function prediction) */
}
void bamDrawAt(struct track *tg, void *item,
struct hvGfx *hvg, int xOff, int y, double scale,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw a single bam linkedFeatures item. Borrows a lot from linkedFeaturesDrawAt,
* but cuts a lot of unneeded features (like coding region) and adds a couple
* additional sources of color. */
{
struct linkedFeatures *lf = item;
struct simpleFeature *sf;
int heightPer = tg->heightPer;
int x1 = round((double)((int)lf->start-winStart)*scale) + xOff;
int x2 = round((double)((int)lf->end-winStart)*scale) + xOff;
int w = x2-x1;
int midY = y + (heightPer>>1);
char *exonArrowsDense = trackDbSettingClosestToHome(tg->tdb, "exonArrowsDense");
boolean exonArrowsEvenWhenDense = (exonArrowsDense != NULL && SETTING_IS_ON(exonArrowsDense));
boolean exonArrows = (tg->exonArrows &&
(vis != tvDense || exonArrowsEvenWhenDense));
struct dnaSeq *mrnaSeq = NULL;
enum baseColorDrawOpt drawOpt = baseColorDrawOff;
boolean indelShowDoubleInsert, indelShowQueryInsert, indelShowPolyA;
struct psl *psl = (struct psl *)(lf->original);
char *colorMode = cartOrTdbString(cart, tg->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
char *grayMode = cartOrTdbString(cart, tg->tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_DEFAULT);
bool baseQualMode = (sameString(colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(grayMode, BAM_GRAY_MODE_BASE_QUAL));
char *qSeq = lf->extra;
if (vis != tvDense && isNotEmpty(qSeq) && !sameString(qSeq, "*"))
{
drawOpt = baseColorDrawSetup(hvg, tg, lf, &mrnaSeq, &psl);
if (drawOpt > baseColorDrawOff)
exonArrows = FALSE;
}
static Color darkBlueColor = 0;
static Color darkRedColor = 0;
if (darkRedColor == 0)
{
darkRedColor = hvGfxFindColorIx(hvg, 100,0,0);
darkBlueColor = hvGfxFindColorIx(hvg, 0,0,100);
}
if (sameString(colorMode, BAM_COLOR_MODE_STRAND))
color = (lf->orientation < 0) ? darkRedColor : darkBlueColor;
else if (lf->filterColor != 0)
{
// In bamTrack, lf->filterColor is an RGBA value
color = lf->filterColor;
}
else if (tg->colorShades)
color = tg->colorShades[lf->grayIx];
else
color = tg->ixColor;
indelEnabled(cart, tg->tdb, basesPerPixel, &indelShowDoubleInsert, &indelShowQueryInsert,
&indelShowPolyA);
if (!indelShowDoubleInsert)
innerLine(hvg, x1, midY, w, color);
for (sf = lf->components; sf != NULL; sf = sf->next)
{
int s = sf->start, e = sf->end;
if (e <= s || e < winStart || s > winEnd)
continue;
if (baseQualMode)
color = tg->colorShades[sf->grayIx];
baseColorDrawItem(tg, lf, sf->grayIx, hvg, xOff, y, scale, font, s, e, heightPer,
zoomedToCodonLevel, mrnaSeq, sf, psl, drawOpt, MAXPIXELS, winStart, color);
if (tg->exonArrowsAlways ||
(exonArrows &&
(sf->start <= winStart || sf->start == lf->start) &&
(sf->end >= winEnd || sf->end == lf->end)))
{
Color barbColor = hvGfxContrastingColor(hvg, color);
x1 = round((double)((int)s-winStart)*scale) + xOff;
x2 = round((double)((int)e-winStart)*scale) + xOff;
w = x2-x1;
clippedBarbs(hvg, x1+1, midY, x2-x1-2, tl.barbHeight, tl.barbSpacing, lf->orientation,
barbColor, TRUE);
}
}
if (indelShowDoubleInsert && psl)
{
int intronGap = 0;
if (vis != tvDense)
intronGap = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "intronGap", "0"));
lfDrawSpecialGaps(lf, intronGap, TRUE, 0, tg, hvg, xOff, y, scale, color, color, vis);
}
if (vis != tvDense)
{
/* If highlighting differences between aligned sequence and genome when
* zoomed way out, this must be done in a separate pass after exons are
* drawn so that exons sharing the pixel don't overdraw differences. */
if ((indelShowQueryInsert || indelShowPolyA) && psl)
baseColorOverdrawQInsert(tg, lf, hvg, xOff, y, scale, heightPer, mrnaSeq, psl, winStart,
drawOpt, indelShowQueryInsert, indelShowPolyA);
baseColorOverdrawDiff(tg, lf, hvg, xOff, y, scale, heightPer, mrnaSeq, psl, winStart, drawOpt);
baseColorDrawCleanup(lf, &mrnaSeq, &psl);
}
}
static void vcfHapClusterDraw(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Split samples' chromosomes (haplotypes), cluster them by center-weighted
* alpha similarity, and draw in the order determined by clustering. */
{
struct vcfFile *vcff = tg->extraUiData;
if (vcff->records == NULL)
return;
purple = hvGfxFindColorIx(hvg, 0x99, 0x00, 0xcc);
undefYellow = hvGfxFindRgb(hvg, &undefinedYellowColor);
enum hapColorMode colorMode = getColorMode(tg->tdb);
pushWarnHandler(ignoreEm);
struct vcfRecord *rec;
for (rec = vcff->records; rec != NULL; rec = rec->next)
vcfParseGenotypes(rec);
popWarnHandler();
unsigned short gtHapCount = 0;
int nRecords = slCount(vcff->records);
int centerIx = getCenterVariantIx(tg, seqStart, seqEnd, vcff->records);
// Limit the number of variants that we compare, to keep from timing out:
// (really what we should limit is the number of distinct haplo's passed to hacTree!)
// In the meantime, this should at least be a cart var...
int maxVariantsPerSide = 50;
int startIx = max(0, centerIx - maxVariantsPerSide);
int endIx = min(nRecords, centerIx+1 + maxVariantsPerSide);
struct hacTree *ht = NULL;
unsigned short *gtHapOrder = clusterHaps(vcff, centerIx, startIx, endIx, >HapCount, &ht);
struct vcfRecord *centerRec = NULL;
int ix;
// Unlike drawing order (last drawn is on top), the first mapBox gets priority,
// so map center variant before drawing & mapping other variants!
for (rec = vcff->records, ix=0; rec != NULL; rec = rec->next, ix++)
{
if (ix == centerIx)
{
centerRec = rec;
mapBoxForCenterVariant(rec, hvg, tg, xOff, yOff, width);
break;
}
}
for (rec = vcff->records, ix=0; rec != NULL; rec = rec->next, ix++)
{
boolean isClustered = (ix >= startIx && ix < endIx);
if (ix != centerIx)
drawOneRec(rec, gtHapOrder, gtHapCount, tg, hvg, xOff, yOff, width, isClustered, FALSE,
colorMode);
}
// Draw the center rec on top, outlined with black lines, to make sure it is very visible:
drawOneRec(centerRec, gtHapOrder, gtHapCount, tg, hvg, xOff, yOff, width, TRUE, TRUE,
colorMode);
// Draw as much of the tree as can fit in the left label area:
int extraPixel = (colorMode == altOnlyMode) ? 1 : 0;
int hapHeight = tg->height- CLIP_PAD - 2*extraPixel;
struct yFromNodeHelper yHelper = {0, NULL, NULL};
initYFromNodeHelper(&yHelper, yOff+extraPixel, hapHeight, gtHapCount, gtHapOrder,
vcff->genotypeCount);
struct titleHelper titleHelper = { NULL, 0, 0, 0, 0, NULL, NULL };
initTitleHelper(&titleHelper, tg->track, startIx, centerIx, endIx, nRecords, vcff);
char *treeAngle = cartOrTdbString(cart, tg->tdb, VCF_HAP_TREEANGLE_VAR, VCF_DEFAULT_HAP_TREEANGLE);
boolean drawRectangle = sameString(treeAngle, VCF_HAP_TREEANGLE_RECTANGLE);
drawTreeInLabelArea(ht, hvg, yOff+extraPixel, hapHeight+CLIP_PAD, &yHelper, &titleHelper,
drawRectangle);
}
static Color gvfColor(struct track *tg, void *item, struct hvGfx *hvg)
/* Color item by var_type attribute, according to Deanna Church's document
* SvRepresentation2.doc attached to redmine #34. */
{
struct bed8Attrs *gvf = item;
Color dbVarUnknown = hvGfxFindColorIx(hvg, 0xb2, 0xb2, 0xb2);
int ix = stringArrayIx("var_type", gvf->attrTags, gvf->attrCount);
if (ix < 0)
return dbVarUnknown;
char *varType = gvf->attrVals[ix];
if (sameString(varType, "CNV") || sameString(varType, "copy_number_variation"))
return MG_BLACK;
else if (strstrNoCase(varType, "Gain"))
return hvGfxFindColorIx(hvg, 0x00, 0x00, 0xff);
else if (strstrNoCase(varType, "Loss"))
return hvGfxFindColorIx(hvg, 0xff, 0x00, 0x00);
else if (strstrNoCase(varType, "Insertion"))
return hvGfxFindColorIx(hvg, 0xff, 0xcc, 0x00);
else if (strstrNoCase(varType, "Complex"))
return hvGfxFindColorIx(hvg, 0x99, 0xcc, 0xff);
else if (strstrNoCase(varType, "Unknown"))
return dbVarUnknown;
else if (strstrNoCase(varType, "Other"))
return hvGfxFindColorIx(hvg, 0xcc, 0x99, 0xff);
else if (strstrNoCase(varType, "Inversion"))
return hvGfxFindColorIx(hvg, 0x99, 0x33, 0xff); // Needs pattern
else if (strstrNoCase(varType, "LOH"))
return hvGfxFindColorIx(hvg, 0x00, 0x00, 0xff); // Needs pattern
else if (strstrNoCase(varType, "Everted"))
return hvGfxFindColorIx(hvg, 0x66, 0x66, 0x66); // Needs pattern
else if (strstrNoCase(varType, "Transchr"))
return hvGfxFindColorIx(hvg, 0xb2, 0xb2, 0xb2); // Plus black vert. bar at broken end
else if (strstrNoCase(varType, "UPD"))
return hvGfxFindColorIx(hvg, 0x00, 0xff, 0xff); // Needs pattern
return dbVarUnknown;
}
