// DrawFontExtents draws some text and denotes the
// various extents and width with lines. Expects
// about a 4x4 inch canvas.
func DrawFontExtents(c vg.Canvas) {
x, y := vg.Inches(1), vg.Inches(2)
str := "Eloquent"
font, err := vg.MakeFont("Times-Roman", 18)
if err != nil {
panic(err)
}
width := font.Width(str)
ext := font.Extents()
des := ext.Descent
asc := ext.Ascent
c.FillString(font, x, y, str)
// baseline
path := vg.Path{}
path.Move(x, y)
path.Line(x+width, y)
c.Stroke(path)
// descent
c.SetColor(color.RGBA{G: 255, A: 255})
path = vg.Path{}
path.Move(x, y+des)
path.Line(x+width, y+des)
c.Stroke(path)
// ascent
c.SetColor(color.RGBA{B: 255, A: 255})
path = vg.Path{}
path.Move(x, y+asc)
path.Line(x+width, y+asc)
c.Stroke(path)
}
// 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: plot.TextStyle{Font: fnt},
}, nil
}
// 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 = TextStyle{
Color: color.Black,
Font: titleFont,
}
return p, nil
}
func init() {
var err error
plot.DefaultFont = "Helvetica"
defaultFont, err = vg.MakeFont("Helvetica", 6)
if err != nil {
fmt.Println(err.Error())
}
}
// 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: TextStyle{Font: font},
}, nil
}
// 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: LineStyle{
Color: color.Black,
Width: vg.Points(0.5),
},
Padding: vg.Points(5),
Scale: LinearScale,
}
a.Label.TextStyle = TextStyle{
Color: color.Black,
Font: labelFont,
}
a.Tick.Label = TextStyle{
Color: color.Black,
Font: tickFont,
}
a.Tick.LineStyle = LineStyle{
Color: color.Black,
Width: vg.Points(0.5),
}
a.Tick.Length = vg.Points(8)
a.Tick.Marker = DefaultTicks
return a, nil
}
func main() {
ps[0].plot = linesPlot()
ps[1].plot = histPlot()
var err error
font, err = vg.MakeFont("Times-Roman", vg.Points(12))
if err != nil {
panic(err)
}
win, err := x11.NewWindow()
if err != nil {
panic(err)
}
drawPlots(win.Screen())
win.FlushImage()
if cpuProfile != "" {
f, err := os.Create(cpuProfile)
if err != nil {
panic(err)
}
pprof.StartCPUProfile(f)
defer pprof.StopCPUProfile()
}
if memProfile != "" {
f, err := os.Create(memProfile)
if err != nil {
panic(err)
}
pprof.WriteHeapProfile(f)
f.Close()
}
events := win.EventChan()
for ev := range events {
if m, ok := ev.(ui.MouseEvent); ok && m.Buttons == 1 {
winHeight := 600 // hard-coded for ui/x11…
p, x, y := dataCoord(m.Loc.X, winHeight-m.Loc.Y)
if p >= 0 {
str := fmt.Sprintf("plot: %d, coord: %g, %g\n", p, x, y)
crosshair(win.Screen(), m.Loc.X, winHeight-m.Loc.Y, str)
win.FlushImage()
}
}
}
}
// NewLabels returns a new Labels using
// the DefaultFont and the DefaultFontSize.
// An error may be returned if there is an
// error loading the default font.
func NewLabels(d interface {
XYer
Labeller
}) (*Labels, error) {
fnt, err := vg.MakeFont(DefaultFont, DefaultFontSize)
if err != nil {
return nil, err
}
strs := make([]string, d.Len())
for i := range strs {
strs[i] = d.Label(i)
}
return &Labels{
XYs: CopyXYs(d),
Labels: strs,
TextStyle: plot.TextStyle{Font: fnt},
}, nil
}
// DrawFonts draws some text in all of the various
// fonts along with a box to make sure that their
// sizes are computed correctly.
func DrawFonts(c vg.Canvas) {
y := vg.Points(0)
var fonts []string
for fname := range vg.FontMap {
fonts = append(fonts, fname)
}
sort.Strings(fonts)
for _, fname := range fonts {
font, err := vg.MakeFont(fname, 20)
if err != nil {
panic(err)
}
w := font.Width(fname + "Xqg")
h := font.Extents().Ascent
c.FillString(font, 0, y-font.Extents().Descent, fname+"Xqg")
fmt.Println(fname)
var path vg.Path
path.Move(0, y+h)
path.Line(w, y+h)
path.Line(w, y)
path.Line(0, y)
path.Close()
c.Stroke(path)
path = vg.Path{}
c.SetColor(color.RGBA{B: 255, A: 255})
c.SetLineDash([]vg.Length{vg.Points(5), vg.Points(3)}, 0)
path.Move(0, y-font.Extents().Descent)
path.Line(w, y-font.Extents().Descent)
c.Stroke(path)
c.SetColor(color.Black)
c.SetLineDash([]vg.Length{}, 0)
y += h
}
}
func mouseTracks(scores []rings.Scorer, diameter vg.Length, lenRange int) ([]plot.Plotter, error) {
var p []plot.Plotter
radius := diameter / 2
// Relative sizes.
const (
label = 117. / 110.
karyotypeInner = 100. / 110.
karyotypeOuter = 1.
heatInner = 30. / 110.
heatOuter = 75. / 110.
traceInner = 80. / 110.
traceOuter = 95. / 110.
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, 0.005,
)
if err != nil {
return nil, err
}
mm.LineStyle = sty
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, fmt.Errorf("bands: %v", err)
}
p = append(p, b)
c, err := rings.NewBlocks(cens, mm, 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(mm, radius*label, rings.NameLabels(mm.Set)...)
if err != nil {
return nil, err
}
lb.TextStyle = plot.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, err
}
p = append(p, s)
traces := make([]rings.Scorer, len(scores))
for i, s := range scores {
traces[i] = &tfs{s.(*fs)}
}
smallFont, err := vg.MakeFont("Helvetica", radius*small)
if err != nil {
return nil, err
}
t, err := rings.NewScores(traces, mm, radius*traceInner, radius*traceOuter,
&rings.Trace{
LineStyles: func() []plot.LineStyle {
ls := []plot.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: plot.TextStyle{Color: color.Gray16{0}, Font: smallFont},
},
},
},
)
if err != nil {
return nil, err
}
p = append(p, t)
return p, nil
}
func boxplot(path string, sets []set) error {
var (
fiveEnds = make([]plotter.Values, len(sets))
threeEnds = make([]plotter.Values, len(sets))
err error
ln int
)
for i := range sets {
fiveEnds[i], err = plotter.CopyValues(&normalised{vals: sets[i].fiveEnd})
if err != nil {
return err
}
threeEnds[i], err = plotter.CopyValues(&normalised{vals: sets[i].threeEnd})
if err != nil {
return err
}
if i == 0 {
ln = fiveEnds[i].Len()
}
if fiveEnds[i].Len() != threeEnds[i].Len() || fiveEnds[i].Len() != ln {
return errors.New("missing values")
}
}
font, err := vg.MakeFont("Helvetica", 10)
if err != nil {
return err
}
titleFont, err := vg.MakeFont("Helvetica", 12)
if err != nil {
return err
}
style := plot.TextStyle{Color: color.Gray{0}, Font: font}
p, err := plot.New()
if err != nil {
return err
}
p.Title.Text = titles[filter]
p.Title.TextStyle = plot.TextStyle{Color: color.Gray{0}, Font: titleFont}
p.X.Label.Text = "Length Offset"
p.Y.Label.Text = "Relative Frequency"
p.X.Label.TextStyle = style
p.Y.Label.TextStyle = style
p.X.Tick.Label = style
p.Y.Tick.Label = style
p.Legend.TextStyle = style
type boxPair struct{ five, three *plotter.BoxPlot }
var boxes []boxPair
for i := 0; i < ln; i++ {
fiveEnd := make(plotter.Values, len(sets))
threeEnd := make(plotter.Values, len(sets))
for j := range sets {
fiveEnd[j] = fiveEnds[j][i]
threeEnd[j] = threeEnds[j][i]
}
boxFivePrime, err := plotter.NewBoxPlot(1, float64(i), fiveEnd) // A non-zero width is required to prevent the creation failing.
if err != nil {
return err
}
boxFivePrime.MedianStyle.Width = 0.5
boxFivePrime.BoxStyle.Width = 0.75
boxFivePrime.BoxStyle.Color = plotutil.Color(0)
boxThreePrime, err := plotter.NewBoxPlot(1, float64(i), threeEnd) // A non-zero width is required to prevent the creation failing.
if err != nil {
return err
}
boxThreePrime.MedianStyle.Width = 0.5
boxThreePrime.BoxStyle.Width = 0.75
boxThreePrime.BoxStyle.Color = plotutil.Color(1)
boxes = append(boxes, boxPair{boxFivePrime, boxThreePrime})
p.Add(boxFivePrime, boxThreePrime)
}
p.Legend.Add("5'-end", &plotter.BarChart{Color: plotutil.Color(0)})
p.Legend.Add("3'-end", &plotter.BarChart{Color: plotutil.Color(1)})
p.Legend.Top = true
p.NominalX(func() []string {
n := make([]string, ln)
for i := 0; i < ln; i++ {
if v := i - maxLength; v%5 == 0 {
n[i] = fmt.Sprint(v)
}
}
return n
}()...)
p.X.Width = 0.5
p.X.Tick.Width = 0.5
p.X.Tick.Length = 8
p.Add(&plotter.Grid{Vertical: plotter.DefaultGridLineStyle})
c := vgsvg.New(vg.Centimeters(19), vg.Centimeters(10))
da := plot.MakeDrawArea(c)
trX, _ := p.Transforms(&da)
w := ((trX(float64(2*maxLength)) - trX(float64(0))) / vg.Length(2*maxLength)) / 3
for _, b := range boxes {
b.five.Width = w
b.five.Offset = -w / 2
b.three.Width = w
b.three.Offset = w / 2
}
p.Draw(da)
f, err := os.Create(decorate(path, "boxplot.svg", filter))
if err != nil {
return err
}
defer f.Close()
_, err = c.WriteTo(f)
return err
}
func barchart(path string, data set) error {
font, err := vg.MakeFont("Helvetica", 10)
if err != nil {
return err
}
titleFont, err := vg.MakeFont("Helvetica", 12)
if err != nil {
return err
}
style := plot.TextStyle{Color: color.Gray{0}, Font: font}
p, err := plot.New()
if err != nil {
return err
}
p.Title.Text = titles[filter]
p.Title.TextStyle = plot.TextStyle{Color: color.Gray{0}, Font: titleFont}
p.X.Label.Text = "Length Offset"
p.Y.Label.Text = "Relative Frequency"
p.X.Label.TextStyle = style
p.Y.Label.TextStyle = style
p.X.Tick.Label = style
p.Y.Tick.Label = style
p.Legend.TextStyle = style
barsFivePrime, err := plotter.NewBarChart(&normalised{vals: data.fiveEnd}, 1) // A non-zero width is required to prevent the creation failing.
if err != nil {
return err
}
barsFivePrime.LineStyle.Width = vg.Length(0)
barsFivePrime.Color = plotutil.Color(0)
barsThreePrime, err := plotter.NewBarChart(&normalised{vals: data.threeEnd}, 1) // A non-zero width is required to prevent the creation failing.
if err != nil {
return err
}
barsThreePrime.LineStyle.Width = vg.Length(0)
barsThreePrime.Color = plotutil.Color(1)
p.Add(barsFivePrime, barsThreePrime)
p.Legend.Add("5'-end", barsFivePrime)
p.Legend.Add("3'-end", barsThreePrime)
p.Legend.Top = true
p.NominalX(func() []string {
n := make([]string, len(data.fiveEnd))
for i := range data.fiveEnd {
if v := i - maxLength; v%5 == 0 {
n[i] = fmt.Sprint(v)
}
}
return n
}()...)
c := vgsvg.New(vg.Centimeters(19), vg.Centimeters(10))
da := plot.MakeDrawArea(c)
trX, _ := p.Transforms(&da)
w := ((trX(float64(2*maxLength)) - trX(float64(0))) / vg.Length(2*maxLength)) / 3
barsFivePrime.Width = w
barsFivePrime.Offset = -w / 2
barsThreePrime.Width = w
barsThreePrime.Offset = w / 2
p.Draw(da)
f, err := os.Create(decorate(path, "barchart.svg", filter))
if err != nil {
return err
}
defer f.Close()
_, err = c.WriteTo(f)
return err
}