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#43 More work on gtf/gffs drawing. Fixed out-by-one GTF-GFF start loc…
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…ation. Better use of space for drawing bams
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@kcleal
kcleal committed Aug 21, 2024
1 parent 8b73ae6 commit e6c1427
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Showing 7 changed files with 138 additions and 115 deletions.
155 changes: 83 additions & 72 deletions src/drawing.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1380,7 +1380,6 @@ namespace Drawing {
}
if (nTracks > 0) {
float y = totalCovY + refSpace + (trackY*(float)nbams) + (gap * 0.5);
// float y = fb_height - totalTabixY - refSpace;
float step = totalTabixY / (float) nTracks;
path.reset();
for (int i = 0; i < (int) nTracks; ++i) {
Expand Down Expand Up @@ -1544,7 +1543,7 @@ namespace Drawing {
float padX, float padY,
float y, float h, float stepX, float stepY, float gap, float gap2, float xScaling,
Themes::IniOptions &opts, SkCanvas *canvas, const Themes::Fonts &fonts,
bool add_text, bool add_rect, bool v_line, bool shaded, float *labelsEnd, std::string &vartype,
bool add_text, bool add_rect, bool shaded, float *labelsEnd, std::string &vartype,
float monitorScale, std::vector<TextItem> &text, bool addArc, bool isRoi, SkPaint &faceColour, float pointSlop, float strand) {
float x = 0;
float w;
Expand Down Expand Up @@ -1586,23 +1585,16 @@ namespace Drawing {
// if (shaded) {
// faceColour2 = //&opts.theme.fcCoverage;
// } else {
faceColour2 = &faceColour;
// faceColour2 = &faceColour;
// faceColour = opts.theme.fcTrack;
// }
// }
}

if (addArc) {
v_line = false;
}

x = (float) (start - rgn.start) * xScaling;
w = std::fmax(monitorScale, (float) (stop - start) * xScaling);
rect.setXYWH(x + padX, y + padY, w, h);

// if (rect.bottom() == 0) {
// return;
// }
if (addArc) {
arcColour.setStyle(SkPaint::kStroke_Style);
arcColour.setStrokeWidth(monitorScale);
Expand Down Expand Up @@ -1644,22 +1636,24 @@ namespace Drawing {

}
else if (add_rect) {
if (strand == 1) { // +
drawRightPointedRectangleNoEdge(canvas, h, y + padY, x + padX, w, 0, opts.theme.lcBright, path, pointSlop);
} else if (strand == 2) { // -
drawLeftPointedRectangleNoEdge(canvas, h, y + padY, x + padX, w, 0, opts.theme.lcBright, path, pointSlop);
if (!shaded) {
if (strand == 1) { // +
drawRightPointedRectangleNoEdge(canvas, h, y + padY, x + padX, w, 0, opts.theme.bgPaint, path, pointSlop);
drawRightPointedRectangleNoEdge(canvas, h, y + padY, x + padX, w, 0, opts.theme.lcJoins, path, pointSlop);
} else if (strand == 2) { // -
drawLeftPointedRectangleNoEdge(canvas, h, y + padY, x + padX, w, 0, opts.theme.bgPaint, path, pointSlop);
drawLeftPointedRectangleNoEdge(canvas, h, y + padY, x + padX, w, 0, opts.theme.lcJoins, path, pointSlop);
}
canvas->drawRect(rect, *faceColour2);
} else {
if (strand == 1) { // +
drawRightPointedRectangleNoEdge(canvas, h, y + padY, x + padX, w, 0, *faceColour2, path, pointSlop);
} else if (strand == 2) { // -
drawLeftPointedRectangleNoEdge(canvas, h, y + padY, x + padX, w, 0, *faceColour2, path, pointSlop);
}
}
canvas->drawRect(rect, *faceColour2);

if (shaded) {
canvas->drawRect(rect, opts.theme.lcLightJoins);
}
}
// if (v_line && x != 0) {
// path.moveTo(x + padX, y + padY);
// path.lineTo(x + padX, y + h + padY);
// canvas->drawPath(path, opts.theme.lcLightJoins);
// }

if (!add_text) {
return;
Expand Down Expand Up @@ -1700,47 +1694,30 @@ namespace Drawing {
float gap, Utils::TrackBlock &trk, bool any_text, const Utils::Region &rgn, SkRect &rect,
SkPath &path, SkPath &path2, float padX, float padY, float stepX, float stepY,
float y, float h, float h2, float h4, float gap2, float xScaling, int nLevels,
float *labelsEnd, std::vector<TextItem> &text, bool vline, SkPaint &faceColour, SkPaint &shadedFaceColour,
float *labelsEnd, std::vector<TextItem> &text, SkPaint &faceColour, SkPaint &shadedFaceColour,
float pointSlop, int strand, float monitorScale) {

int target = (int) trk.s.size();
int stranded = trk.strand;
// int stranded = trk.strand;
float screenLeftEdge = padX;
float screenRightEdge = padX + (((float) rgn.end - (float) rgn.start) * xScaling);
std::string empty_str;
if (any_text) {
drawTrackBlock(trk.start, trk.end, trk.name, rgn, rect, path, padX, padY, y, h, stepX, stepY, gap, gap2,
xScaling, opts, canvas, fonts, true, false, false, false, labelsEnd, empty_str, monitorScale, text, false, false, faceColour, pointSlop, strand);
xScaling, opts, canvas, fonts, true, false, false, labelsEnd, empty_str, monitorScale, text, false, false, faceColour, pointSlop, strand);
}
for (int i = 0; i < target; ++i) {
int s, e;
float x, yy, w;
int s, e;
for (int i = 0; i < target; ++i) { // draw lines first and thickness == 1
s = trk.s[i];
e = trk.e[i];
if (e < rgn.start) {
continue;
}
bool add_line = (i == 0 && vline); // vertical line at start of interval
assert (i < trk.drawThickness.size());
uint8_t thickness = trk.drawThickness[i];
if (thickness && s < rgn.end && e > rgn.start) {

if (s < trk.coding_end && e > trk.coding_end) { //overlaps, split into two blocks!
drawTrackBlock(s, trk.coding_end, trk.name, rgn, rect, path, padX, padY, y, h, stepX, stepY, gap,
gap2, xScaling, opts, canvas, fonts, false, true, add_line, false, labelsEnd, empty_str, 0, text, false, false, faceColour, pointSlop, strand);
drawTrackBlock(trk.coding_end, e, trk.name, rgn, rect, path, padX, padY, y + (h * 0.25), h * 0.5, stepX, stepY, gap,
gap2, xScaling, opts, canvas, fonts, false, true, add_line, true, labelsEnd, empty_str, 0, text, false, false, shadedFaceColour, pointSlop, 0);
}

if (thickness == 1) {
drawTrackBlock(s, e, trk.name, rgn, rect, path, padX, padY, y + (h * 0.25), h * 0.5, stepX, stepY, gap, gap2, xScaling,
opts, canvas, fonts, false, true, add_line, true, labelsEnd, empty_str, 0, text, false, false, shadedFaceColour, pointSlop, 0);
} else {
drawTrackBlock(s, e, trk.name, rgn, rect, path, padX, padY, y, h, stepX, stepY, gap, gap2, xScaling,
opts, canvas, fonts, false, true, add_line, false, labelsEnd, empty_str, 0, text, false, false, faceColour, pointSlop, strand);
}
}
float x, yy, w;
yy = y + padY + (h / 2);
if (i == 0) {
continue;
}
int lastEnd = (i > 0) ? trk.e[i - 1] : trk.start;
if (lastEnd < s) { // add arrows
x = std::max(((float) (lastEnd - rgn.start) * xScaling) + padX, (float) screenLeftEdge);
Expand All @@ -1749,27 +1726,62 @@ namespace Drawing {
path2.reset();
path2.moveTo(x, yy);
path2.lineTo(w, yy);
canvas->drawPath(path2, opts.theme.lcLightJoins);
if (stranded != 0 && w - x > 50) {
while (x + 50 < w) {
x += 50;
path2.reset();
if (stranded == 1) {
path2.moveTo(x, yy);
path2.lineTo(x - 6, yy + 6);
path2.moveTo(x, yy);
path2.lineTo(x - 6, yy - 6);
} else {
path2.moveTo(x, yy);
path2.lineTo(x + 6, yy + 6);
path2.moveTo(x, yy);
path2.lineTo(x + 6, yy - 6);
}
canvas->drawPath(path2, opts.theme.lcJoins);
}
}
canvas->drawPath(path2, opts.theme.lcGTFJoins);
// if (stranded != 0 && w - x > 50) {
// while (x + 50 < w) {
// x += 50;
// path2.reset();
// if (stranded == 1) {
// path2.moveTo(x, yy);
// path2.lineTo(x - 6, yy + 6);
// path2.moveTo(x, yy);
// path2.lineTo(x - 6, yy - 6);
// } else {
// path2.moveTo(x, yy);
// path2.lineTo(x + 6, yy + 6);
// path2.moveTo(x, yy);
// path2.lineTo(x + 6, yy - 6);
// }
// canvas->drawPath(path2, opts.theme.lcJoins);
// }
// }
}
}
}
for (int i = 0; i < target; ++i) {
s = trk.s[i];
e = trk.e[i];
if (e < rgn.start) {
continue;
}
assert (i < trk.drawThickness.size());
uint8_t thickness = trk.drawThickness[i];
if (thickness && s < rgn.end && e > rgn.start) {
int left_cds = std::min(trk.coding_start, trk.coding_end);
int right_cds = std::max(trk.coding_start, trk.coding_end);
if (s < right_cds && e > right_cds) { //overlaps, split into two blocks!
drawTrackBlock(right_cds, e, trk.name, rgn, rect, path, padX, padY, y + (h * 0.25), h * 0.5, stepX, stepY, gap,
gap2, xScaling, opts, canvas, fonts, false, true, true, labelsEnd, empty_str, 0, text, false, false, shadedFaceColour, pointSlop / 2, strand);
drawTrackBlock(s, right_cds, trk.name, rgn, rect, path, padX, padY, y, h, stepX, stepY, gap,
gap2, xScaling, opts, canvas, fonts, false, true, false, labelsEnd, empty_str, 0, text, false, false, faceColour, pointSlop, strand);
continue;
} else if (s < left_cds && e > left_cds) {
drawTrackBlock(s, left_cds, trk.name, rgn, rect, path, padX, padY, y + (h * 0.25), h * 0.5, stepX, stepY, gap,
gap2, xScaling, opts, canvas, fonts, false, true, true, labelsEnd, empty_str, 0, text, false, false, shadedFaceColour, pointSlop / 2, strand);
drawTrackBlock(left_cds, e, trk.name, rgn, rect, path, padX, padY, y, h, stepX, stepY, gap,
gap2, xScaling, opts, canvas, fonts, false, true, false, labelsEnd, empty_str, 0, text, false, false, faceColour, pointSlop, strand);
continue;
}

if (thickness == 1) {
drawTrackBlock(s, e, trk.name, rgn, rect, path, padX, padY, y + (h * 0.25), h * 0.5, stepX, stepY, gap, gap2, xScaling,
opts, canvas, fonts, false, true, true, labelsEnd, empty_str, 0, text, false, false, shadedFaceColour, pointSlop / 2, strand);
} else if (thickness == 2) {
drawTrackBlock(s, e, trk.name, rgn, rect, path, padX, padY, y, h, stepX, stepY, gap, gap2, xScaling,
opts, canvas, fonts, false, true, false, labelsEnd, empty_str, 0, text, false, false, faceColour, pointSlop, strand);
}
}

}
}

Expand All @@ -1785,7 +1797,7 @@ namespace Drawing {

float stepX = fb_width / (float) regions.size();
float stepY = tabixY;
stepY -= sliderSpace - gap; // todo this should not be needed
stepY -= sliderSpace;

float y = fb_height - totalTabixY - sliderSpace; // + gap; // start of tracks on canvas
float t = (float) 0.005 * fb_width;
Expand All @@ -1799,7 +1811,6 @@ namespace Drawing {

for (auto &rgn: regions) {
bool any_text = true;
bool add_line = ((rgn.end - rgn.start) < opts.soft_clip_threshold);
float xScaling = (stepX - gap2) / (float) (rgn.end - rgn.start);
float padY = gap;
int trackIdx = 0;
Expand Down Expand Up @@ -1866,12 +1877,12 @@ namespace Drawing {
fonts, gap,
f, any_text, rgn, rect, path, path2, padX, padY_track, stepX, step_track,
y, h, h2, h4, gap2,
xScaling, nLevels, fLevelEnd, text, add_line, faceColour, shadedFaceColour, pointSlop, strand, monitorScale);
xScaling, nLevels, fLevelEnd, text, faceColour, shadedFaceColour, pointSlop, strand, monitorScale);

} else {
drawTrackBlock(f.start, f.end, f.name, rgn, rect, path, padX, padY_track, y, h, stepX, stepY,
gap, gap2,
xScaling, opts, canvas, fonts, any_text, true, add_line, false, fLevelEnd, f.vartype, monitorScale,
xScaling, opts, canvas, fonts, any_text, true, false, fLevelEnd, f.vartype, monitorScale,
text, opts.sv_arcs, trk.kind == HGW::FType::ROI, faceColour, pointSlop, strand);
}
}
Expand Down
24 changes: 11 additions & 13 deletions src/hts_funcs.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1229,8 +1229,10 @@ namespace HGW {

void GwTrack::setPaint(SkPaint &faceColour) {
this->faceColour = faceColour;
this->faceColour.setAntiAlias(true);
this->shadedFaceColour.setAntiAlias(true);
int c = faceColour.getColor();
this->shadedFaceColour.setARGB(faceColour.getAlpha(), SkColorGetR(c)/2, SkColorGetG(c)/2, SkColorGetB(c)/2);
this->shadedFaceColour.setARGB(faceColour.getAlpha() * 0.5, SkColorGetR(c), SkColorGetG(c), SkColorGetB(c));
}

void GwTrack::open(const std::string &p, bool add_to_dict=true) {
Expand Down Expand Up @@ -1459,7 +1461,7 @@ namespace HGW {
b.line = tp;
b.chrom = b.parts[0];
b.vartype = b.parts[2];
b.start = std::stoi(b.parts[3]);
b.start = std::stoi(b.parts[3]) - 1;
b.end = std::stoi(b.parts[4]);
if (b.parts[6] == "+") {
b.strand = 1;
Expand Down Expand Up @@ -1839,7 +1841,7 @@ namespace HGW {
parts = Utils::split(str.s, '\t');
chrom = parts[0];
chrom2 = chrom;
start = std::stoi(parts[3]);
start = std::stoi(parts[3]) - 1;
stop = std::stoi(parts[4]);
if (parts[6] == "+") {
strand = 1;
Expand Down Expand Up @@ -2343,23 +2345,19 @@ namespace HGW {
track.s.push_back(g->start);
track.e.push_back(g->end);

if (g->vartype == "exon" || g->vartype == "CDS") {
if (!track.anyToDraw) { track.anyToDraw = true; }
if (between_codons) {
track.drawThickness.push_back(2); // fat line
} else {
track.drawThickness.push_back(1); // thin line
}
} else if (g->vartype == "mRNA" || g->vartype == "gene") {
if (g->vartype == "CDS") { // g->vartype == "exon" ||
track.anyToDraw = true;
track.drawThickness.push_back(2); // fat line
} else if (g->vartype == "mRNA" || g->vartype == "gene" || g->vartype == "exon") {
track.drawThickness.push_back(0); // no line
} else if (g->vartype == "start_codon") {
between_codons = !between_codons;
track.coding_start = g->start;
track.drawThickness.push_back(2);
track.drawThickness.push_back(0);
} else if (g->vartype == "stop_codon") {
between_codons = !between_codons;
track.coding_end = g->end;
track.drawThickness.push_back(2);
track.drawThickness.push_back(0);
} else {
track.drawThickness.push_back(1);
if (!track.anyToDraw) { track.anyToDraw = true; }
Expand Down
4 changes: 4 additions & 0 deletions src/plot_commands.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -668,6 +668,9 @@ namespace Commands {
} else {
return Err::OPTION_NOT_UNDERSTOOD;
}
for (auto &t: p->tracks) {
t.setPaint(p->opts.theme.fcTrack);
}
p->processed = false;
return Err::NONE;
}
Expand Down Expand Up @@ -1341,6 +1344,7 @@ namespace Commands {
else if (c == "lcJoins") { e = Themes::GwPaint::lcJoins; }
else if (c == "lcCoverage") { e = Themes::GwPaint::lcCoverage; }
else if (c == "lcLightJoins") { e = Themes::GwPaint::lcLightJoins; }
else if (c == "lcGTFJoins") { e = Themes::GwPaint::lcGTFJoins; }
else if (c == "lcLabel") { e = Themes::GwPaint::lcLabel; }
else if (c == "lcBright") { e = Themes::GwPaint::lcBright; }
else if (c == "tcDel") { e = Themes::GwPaint::tcDel; }
Expand Down
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