// New returns a new plot with some reasonable
// default settings.
func New() (*Plot, error) {
titleFont, err := vg.MakeFont(DefaultFont, 12)
if err != nil {
return nil, err
}
x, err := makeAxis()
if err != nil {
return nil, err
}
y, err := makeAxis()
if err != nil {
return nil, err
}
legend, err := makeLegend()
if err != nil {
return nil, err
}
p := &Plot{
BackgroundColor: color.White,
X: x,
Y: y,
Legend: legend,
}
p.Title.TextStyle = draw.TextStyle{
Color: color.Black,
Font: titleFont,
}
return p, nil
}
// NewLabels returns a new Labels using the DefaultFont and
// the DefaultFontSize.
func NewLabels(d interface {
XYer
Labeller
}) (*Labels, error) {
xys, err := CopyXYs(d)
if err != nil {
return nil, err
}
if d.Len() != len(xys) {
return nil, errors.New("Number of points does not match the number of labels")
}
strs := make([]string, d.Len())
for i := range strs {
strs[i] = d.Label(i)
}
fnt, err := vg.MakeFont(DefaultFont, DefaultFontSize)
if err != nil {
return nil, err
}
return &Labels{
XYs: xys,
Labels: strs,
TextStyle: draw.TextStyle{Font: fnt},
}, nil
}
// makeLegend returns a legend with the default
// parameter settings.
func makeLegend() (Legend, error) {
font, err := vg.MakeFont(DefaultFont, vg.Points(12))
if err != nil {
return Legend{}, err
}
return Legend{
ThumbnailWidth: vg.Points(20),
TextStyle: draw.TextStyle{Font: font},
}, nil
}
func main() {
rna, err := readJSON(in)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
minLength, maxLength, binLength = rna.Min, rna.Max, rna.Bin
p, err := plot.New()
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
mm, lo, hi, err := mouseTracks(rna.Features, highlight, palname, 15*vg.Centimeter, rna.Min-rna.Max)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
p.Add(mm...)
p.HideAxes()
font, err := vg.MakeFont("Helvetica", 14)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
n := rna.Sample[:strings.Index(rna.Sample, filepath.Ext(rna.Sample))]
p.Title.Text = fmt.Sprintf(
`%s
%s
min base quality: %v, minimum mapping score: %d
minimum identity: %d%%
length range: [%d,%d]
heat range: [%f,%f]`,
decorate(n, format, rna.Filter),
rna.Sample,
rna.MinQ, rna.MapQ,
rna.MinID,
rna.Min, rna.Max,
lo, hi)
p.Title.TextStyle = draw.TextStyle{Color: color.Gray{0}, Font: font}
err = p.Save(19*vg.Centimeter, 25*vg.Centimeter,
decorate(filepath.Base(rna.Sample), format, rna.Filter),
)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
}
func (text GrobText) Font() vg.Font {
fname := text.font
if fname == "" {
fname = "Courier-Bold"
}
font, err := vg.MakeFont(fname, vg.Length(text.size))
if err != nil {
panic(err.Error())
}
return font
}
// makeAxis returns a default Axis.
//
// The default range is (∞, ∞), and thus any finite
// value is less than Min and greater than Max.
func makeAxis() (Axis, error) {
labelFont, err := vg.MakeFont(DefaultFont, vg.Points(12))
if err != nil {
return Axis{}, err
}
tickFont, err := vg.MakeFont(DefaultFont, vg.Points(10))
if err != nil {
return Axis{}, err
}
a := Axis{
Min: math.Inf(1),
Max: math.Inf(-1),
LineStyle: draw.LineStyle{
Color: color.Black,
Width: vg.Points(0.5),
},
Padding: vg.Points(5),
Scale: LinearScale{},
}
a.Label.TextStyle = draw.TextStyle{
Color: color.Black,
Font: labelFont,
}
a.Tick.Label = draw.TextStyle{
Color: color.Black,
Font: tickFont,
}
a.Tick.LineStyle = draw.LineStyle{
Color: color.Black,
Width: vg.Points(0.5),
}
a.Tick.Length = vg.Points(8)
a.Tick.Marker = DefaultTicks{}
return a, nil
}
func main() {
bf, err := readBED(in)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
p, err := plot.New()
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
hs, err := tracks(scoreFeatures(bf, binLength, hg19.Chromosomes), 15*vg.Centimeter)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
p.Add(hs...)
p.HideAxes()
font, err := vg.MakeFont("Helvetica", 14)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
p.Title.Text = filepath.Base(in)
p.Title.TextStyle = draw.TextStyle{Color: color.Gray{0}, Font: font}
err = p.Save(19*vg.Centimeter, 25*vg.Centimeter, filepath.Base(in)+"."+format)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
}
// ReplayOn applies the set of Actions recorded by the Recorder onto
// the destination Canvas.
func (c *Canvas) ReplayOn(dst vg.Canvas) error {
if c.fonts == nil {
c.fonts = make(map[fontID]vg.Font)
}
for _, a := range c.Actions {
fa, ok := a.(*FillString)
if !ok {
continue
}
f := fontID{name: fa.Font, size: fa.Size}
if _, exists := c.fonts[f]; !exists {
var err error
c.fonts[f], err = vg.MakeFont(fa.Font, fa.Size)
if err != nil {
return err
}
}
fa.fonts = c.fonts
}
for _, a := range c.Actions {
a.ApplyTo(dst)
}
return nil
}
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 TestLegendAlignment(t *testing.T) {
font, err := vg.MakeFont(plot.DefaultFont, 10.822510822510822) // This font size gives an entry height of 10.
if err != nil {
t.Fatalf("failed to create font: %v", err)
}
l := plot.Legend{
ThumbnailWidth: vg.Points(20),
TextStyle: draw.TextStyle{Font: font},
}
for _, n := range []string{"A", "B", "C", "D"} {
b, err := plotter.NewBarChart(plotter.Values{0}, 1)
if err != nil {
t.Fatalf("failed to create bar chart %q: %v", n, err)
}
l.Add(n, b)
}
r := recorder.New(100)
c := draw.NewCanvas(r, 100, 100)
l.Draw(draw.Canvas{
Canvas: c.Canvas,
Rectangle: draw.Rectangle{
Min: draw.Point{0, 0},
Max: draw.Point{100, 100},
},
})
got := r.Actions
// want is a snapshot of the actions for the code above when the
// graphical output has been visually confirmed to be correct for
// the bar charts example show in gonum/plot#25.
want := []recorder.Action{
&recorder.SetColor{
Color: color.Gray16{},
},
&recorder.Fill{
Path: vg.Path{
{Type: vg.MoveComp, X: 80, Y: 30},
{Type: vg.LineComp, X: 80, Y: 40},
{Type: vg.LineComp, X: 100, Y: 40},
{Type: vg.LineComp, X: 100, Y: 30},
{Type: vg.CloseComp},
},
},
&recorder.SetColor{
Color: color.Gray16{},
},
&recorder.SetLineWidth{
Width: 1,
},
&recorder.SetLineDash{},
&recorder.Stroke{
Path: vg.Path{
{Type: vg.MoveComp, X: 80, Y: 30},
{Type: vg.LineComp, X: 80, Y: 40},
{Type: vg.LineComp, X: 100, Y: 40},
{Type: vg.LineComp, X: 100, Y: 30},
{Type: vg.LineComp, X: 80, Y: 30},
},
},
&recorder.SetColor{},
&recorder.FillString{
Font: string("Times-Roman"),
Size: 10.822510822510822,
X: 69.48051948051948,
Y: 30.82251082251082,
String: "A",
},
&recorder.SetColor{
Color: color.Gray16{},
},
&recorder.Fill{
Path: vg.Path{
{Type: vg.MoveComp, X: 80, Y: 20},
{Type: vg.LineComp, X: 80, Y: 30},
{Type: vg.LineComp, X: 100, Y: 30},
{Type: vg.LineComp, X: 100, Y: 20},
{Type: vg.CloseComp},
},
},
&recorder.SetColor{
Color: color.Gray16{},
},
&recorder.SetLineWidth{
Width: 1,
},
&recorder.SetLineDash{},
&recorder.Stroke{
Path: vg.Path{
{Type: vg.MoveComp, X: 80, Y: 20},
{Type: vg.LineComp, X: 80, Y: 30},
{Type: vg.LineComp, X: 100, Y: 30},
{Type: vg.LineComp, X: 100, Y: 20},
{Type: vg.LineComp, X: 80, Y: 20},
},
},
&recorder.SetColor{},
&recorder.FillString{
Font: string("Times-Roman"),
Size: 10.822510822510822,
X: 70.07575757575758,
Y: 20.82251082251082,
String: "B",
},
&recorder.SetColor{
Color: color.Gray16{
Y: uint16(0),
},
},
&recorder.Fill{
Path: vg.Path{
{Type: vg.MoveComp, X: 80, Y: 10},
{Type: vg.LineComp, X: 80, Y: 20},
{Type: vg.LineComp, X: 100, Y: 20},
{Type: vg.LineComp, X: 100, Y: 10},
{Type: vg.CloseComp},
},
},
&recorder.SetColor{
Color: color.Gray16{},
},
&recorder.SetLineWidth{
Width: 1,
},
&recorder.SetLineDash{},
&recorder.Stroke{
Path: vg.Path{
{Type: vg.MoveComp, X: 80, Y: 10},
{Type: vg.LineComp, X: 80, Y: 20},
{Type: vg.LineComp, X: 100, Y: 20},
{Type: vg.LineComp, X: 100, Y: 10},
{Type: vg.LineComp, X: 80, Y: 10},
},
},
&recorder.SetColor{},
&recorder.FillString{
Font: string("Times-Roman"),
Size: 10.822510822510822,
X: 70.07575757575758,
Y: 10.822510822510822,
String: "C",
},
&recorder.SetColor{
Color: color.Gray16{},
},
&recorder.Fill{
Path: vg.Path{
{Type: vg.MoveComp, X: 80, Y: 0},
{Type: vg.LineComp, X: 80, Y: 10},
{Type: vg.LineComp, X: 100, Y: 10},
{Type: vg.LineComp, X: 100, Y: 0},
{Type: vg.CloseComp},
},
},
&recorder.SetColor{
Color: color.Gray16{},
},
&recorder.SetLineWidth{
Width: 1,
},
&recorder.SetLineDash{},
&recorder.Stroke{
Path: vg.Path{
{Type: vg.MoveComp, X: 80, Y: 0},
{Type: vg.LineComp, X: 80, Y: 10},
{Type: vg.LineComp, X: 100, Y: 10},
{Type: vg.LineComp, X: 100, Y: 0},
{Type: vg.LineComp, X: 80, Y: 0},
},
},
&recorder.SetColor{},
&recorder.FillString{
Font: string("Times-Roman"),
Size: 10.822510822510822,
X: 69.48051948051948,
Y: 0.8225108225108215,
String: "D",
},
}
if !reflect.DeepEqual(got, want) {
t.Errorf("unexpected legend actions:\ngot:\n%s\nwant:\n%s", formatActions(got), formatActions(want))
}
}
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
}
func main() {
rna, err := readJSON(in)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
minLength, maxLength, binLength = rna.Min, rna.Max, rna.Bin
switch normalisation {
case 0:
weightFactors[0], weightFactors[1] = float64(rna.Totals[0]), float64(rna.Totals[1])
case 1:
weightFactors, err = normaliseByBin(rna)
case 2:
weightFactors, err = normaliseByBlock(rna)
default:
err = errors.New("illegal normalisation strategy")
}
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
p, err := plot.New()
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
mm, lo, hi, err := mouseTracks(rna.Features, highlight, palname, 15*vg.Centimeter, rna.Min-rna.Max)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
p.Add(mm...)
p.HideAxes()
font, err := vg.MakeFont("Helvetica", 14)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
for i, n := range rna.Pair {
n = filepath.Base(n)
rna.Pair[i] = n[:strings.Index(n, filepath.Ext(n))]
}
p.Title.Text = fmt.Sprintf(
`%s
%s
%s
min base quality: %v, minimum mapping score: %d
minimum identity: %d%%
length range: [%d,%d]
heat range: [%f,%f]`,
decorate(rna.Pair[1], format, rna.Filter),
rna.Classes,
rna.Pair,
rna.MinQ, rna.MapQ,
rna.MinID,
rna.Min, rna.Max,
lo, hi)
p.Title.TextStyle = draw.TextStyle{Color: color.Gray{0}, Font: font}
for i, class := range rna.Classes {
rna.Classes[i] = class[strings.LastIndex(class, "/")+1:]
}
var classes string
if len(rna.Classes) > 0 {
classes = "-" + strings.Join(rna.Classes, ",")
}
err = p.Save(18*vg.Centimeter, 25*vg.Centimeter,
decorate(filepath.Base(rna.Pair[1])+classes, format, rna.Filter),
)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
}