func tracks(scores []rings.Scorer, diameter vg.Length) ([]plot.Plotter, error) {
var p []plot.Plotter
radius := diameter / 2
// Relative sizes.
const (
gap = 0.005
label = 117. / 110.
countsInner = 97. / 110.
countsOuter = 70. / 110.
karyotypeInner = 100. / 110.
karyotypeOuter = 1.
large = 6. / 110.
small = 2. / 110.
)
sty := plotter.DefaultLineStyle
sty.Width /= 2
chr := make([]feat.Feature, len(hg19.Chromosomes))
for i, c := range hg19.Chromosomes {
chr[i] = c
}
hs, err := rings.NewGappedBlocks(
chr,
rings.Arc{rings.Complete / 4 * rings.CounterClockwise, rings.Complete * rings.Clockwise},
radius*karyotypeInner, radius*karyotypeOuter, gap,
)
if err != nil {
return nil, err
}
hs.LineStyle = sty
p = append(p, hs)
bands := make([]feat.Feature, len(hg19.Bands))
cens := make([]feat.Feature, 0, len(hg19.Chromosomes))
for i, b := range hg19.Bands {
bands[i] = colorBand{b}
s := b.Start()
// This condition depends on p -> q sort order in the $karyotype.Bands variable.
// All standard genome packages follow this, though here the test is more general than
// actually required since hs is telocentric.
if b.Band[0] == 'q' && (s == 0 || hg19.Bands[i-1].Band[0] == 'p') {
cens = append(cens, colorBand{&genome.Band{Band: "cen", Desc: "Band", StartPos: s, EndPos: s, Giemsa: "acen", Chr: b.Location()}})
}
}
b, err := rings.NewBlocks(bands, hs, radius*karyotypeInner, radius*karyotypeOuter)
if err != nil {
return nil, fmt.Errorf("bands: %v", err)
}
p = append(p, b)
c, err := rings.NewBlocks(cens, hs, radius*karyotypeInner, radius*karyotypeOuter)
if err != nil {
return nil, fmt.Errorf("centromeres: %v", err)
}
p = append(p, c)
font, err := vg.MakeFont("Helvetica", radius*large)
if err != nil {
return nil, err
}
lb, err := rings.NewLabels(hs, radius*label, rings.NameLabels(hs.Set)...)
if err != nil {
return nil, err
}
lb.TextStyle = draw.TextStyle{Color: color.Gray16{0}, Font: font}
p = append(p, lb)
smallFont, err := vg.MakeFont("Helvetica", radius*small)
if err != nil {
return nil, err
}
counts := make([]rings.Scorer, len(scores))
for i, s := range scores {
counts[i] = s.(*feature)
}
ct, err := rings.NewScores(counts, hs, radius*countsInner, radius*countsOuter,
&rings.Trace{
LineStyles: func() []draw.LineStyle {
ls := []draw.LineStyle{sty}
ls[0].Color = color.Gray16{0}
return ls
}(),
Join: true,
Axis: &rings.Axis{
Angle: rings.Complete / 4,
Grid: plotter.DefaultGridLineStyle,
LineStyle: sty,
Tick: rings.TickConfig{
Marker: plot.DefaultTicks{},
LineStyle: sty,
Length: 2,
Label: draw.TextStyle{Color: color.Gray16{0}, Font: smallFont},
},
},
},
)
if err != nil {
return nil, err
}
p = append(p, ct)
return p, nil
}
func mouseTracks(scores []rings.Scorer, highlight []string, palname string, diameter vg.Length, lenRange int) (pp []plot.Plotter, lo, hi float64, err error) {
var p []plot.Plotter
radius := diameter / 2
// Relative sizes.
const (
gap = 0.005
label = 117. / 110.
countsInner = 25. / 110.
countsOuter = 40. / 110.
heatInner = 45. / 110.
heatOuter = 75. / 110.
traceInner = 80. / 110.
traceOuter = 95. / 110.
karyotypeInner = 100. / 110.
karyotypeOuter = 1.
large = 7. / 110.
small = 2. / 110.
)
sty := plotter.DefaultLineStyle
sty.Width /= 2
chr := make([]feat.Feature, len(mm10.Chromosomes))
for i, c := range mm10.Chromosomes {
chr[i] = c
}
mm, err := rings.NewGappedBlocks(
chr,
rings.Arc{rings.Complete / 4 * rings.CounterClockwise, rings.Complete * rings.Clockwise},
radius*karyotypeInner, radius*karyotypeOuter, gap,
)
if err != nil {
return nil, 0, 0, err
}
mm.LineStyle = sty
pal, err := brewer.GetPalette(brewer.TypeQualitative, palname, len(highlight))
if err == nil {
for i, hn := range highlight {
for _, c := range mm.Set {
if hn == strings.ToLower(c.Name()) {
arc, err := mm.Base.ArcOf(c, nil)
arc.Theta += rings.Complete * gap / 2
arc.Phi -= rings.Complete * gap
if err != nil {
fmt.Printf("could not find: %s\n", hn)
break
}
col := pal.Colors()[i]
nc := color.NRGBAModel.Convert(col).(color.NRGBA)
nc.A = 0x40
h := rings.NewHighlight(
nc,
arc,
radius*(traceInner-2.5/110.),
radius*(label+5./110.),
)
h.LineStyle = sty
h.LineStyle.Width /= 4
p = append(p, h)
break
}
}
}
} else if len(highlight) > 0 {
fmt.Println("no palette")
}
p = append(p, mm)
bands := make([]feat.Feature, len(mm10.Bands))
cens := make([]feat.Feature, 0, len(mm10.Chromosomes))
for i, b := range mm10.Bands {
bands[i] = colorBand{b}
s := b.Start()
// This condition depends on p -> q sort order in the $karyotype.Bands variable.
// All standard genome packages follow this, though here the test is more general than
// actually required since mm is telocentric.
if b.Band[0] == 'q' && (s == 0 || mm10.Bands[i-1].Band[0] == 'p') {
cens = append(cens, colorBand{&genome.Band{Band: "cen", Desc: "Band", StartPos: s, EndPos: s, Giemsa: "acen", Chr: b.Location()}})
}
}
b, err := rings.NewBlocks(bands, mm, radius*karyotypeInner, radius*karyotypeOuter)
if err != nil {
return nil, 0, 0, fmt.Errorf("bands: %v", err)
}
p = append(p, b)
c, err := rings.NewBlocks(cens, mm, radius*karyotypeInner, radius*karyotypeOuter)
if err != nil {
return nil, 0, 0, fmt.Errorf("centromeres: %v", err)
}
p = append(p, c)
font, err := vg.MakeFont("Helvetica", radius*large)
if err != nil {
return nil, 0, 0, err
}
lb, err := rings.NewLabels(mm, radius*label, rings.NameLabels(mm.Set)...)
if err != nil {
return nil, 0, 0, err
}
lb.TextStyle = draw.TextStyle{Color: color.Gray16{0}, Font: font}
p = append(p, lb)
s, err := rings.NewScores(scores, mm, radius*heatInner, radius*heatOuter,
&rings.Heat{Palette: palette.Heat(10, 1).Colors()},
)
if err != nil {
return nil, 0, 0, err
}
p = append(p, s)
smallFont, err := vg.MakeFont("Helvetica", radius*small)
if err != nil {
return nil, 0, 0, err
}
traces := make([]rings.Scorer, len(scores))
for i, s := range scores {
traces[i] = &tfs{s.(*feature)}
}
t, err := rings.NewScores(traces, mm, radius*traceInner, radius*traceOuter,
&rings.Trace{
LineStyles: func() []draw.LineStyle {
ls := []draw.LineStyle{sty, sty}
for i, c := range brewer.Set1[3].Colors()[:len(ls)] {
nc := color.NRGBAModel.Convert(c).(color.NRGBA)
nc.A = 0x80
ls[i].Color = nc
}
return ls
}(),
Join: true,
Axis: &rings.Axis{
Angle: rings.Complete / 4,
Grid: plotter.DefaultGridLineStyle,
LineStyle: sty,
Tick: rings.TickConfig{
Marker: plot.DefaultTicks{},
LineStyle: sty,
Length: 2,
Label: draw.TextStyle{Color: color.Gray16{0}, Font: smallFont},
},
},
},
)
if err != nil {
return nil, 0, 0, err
}
if maxTrace != 0 {
t.Max = maxTrace
if t.Min > t.Max {
return nil, 0, 0, fmt.Errorf("maximum trace out of range: min=%f", t.Min)
}
}
if !math.IsInf(t.Max-t.Min, 0) {
p = append(p, t)
}
counts := make([]rings.Scorer, len(scores))
for i, s := range scores {
counts[i] = ctfs{s.(*feature)}
}
ct, err := rings.NewScores(counts, mm, radius*countsInner, radius*countsOuter,
&rings.Trace{
LineStyles: func() []draw.LineStyle {
ls := []draw.LineStyle{sty}
ls[0].Color = color.Gray16{0}
return ls
}(),
Join: true,
Axis: &rings.Axis{
Angle: rings.Complete / 4,
Grid: plotter.DefaultGridLineStyle,
LineStyle: sty,
Tick: rings.TickConfig{
Marker: plot.DefaultTicks{},
LineStyle: sty,
Length: 2,
Label: draw.TextStyle{Color: color.Gray16{0}, Font: smallFont},
},
},
},
)
if err != nil {
return nil, 0, 0, err
}
if maxCounts != 0 {
ct.Max = maxCounts
if ct.Min > ct.Max {
return nil, 0, 0, fmt.Errorf("maximum counts out of range: min=%f", ct.Min)
}
}
p = append(p, ct)
return p, s.Min, s.Max, nil
}