func main() {
p, err := plot.New()
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
classFilt, err := filterFeats(annot, classes, in)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
rna, err := rnaFeats(in, classFilt, minLength, maxLength, minId, minQ, mapQb, minAvQ)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
mm, err := mouseTracks(rna, vg.Centimeters(15), maxLength-minLength)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
p.Add(mm...)
p.HideAxes()
var name string
switch filter {
case all:
name = fmt.Sprintf("%s.%s", out, format)
case primary:
name = fmt.Sprintf("%s-U1.%s", out, format)
case secondary:
name = fmt.Sprintf("%s-A10.%s", out, format)
}
err = p.Save(vg.Centimeters(19).Inches(), vg.Centimeters(25).Inches(), name)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
}
// Report builds up a plot of the response times of the requests
// in SVG format and writes it to out
func (r *TimingsPlotReporter) Report(out io.Writer) error {
timestamps := make([]time.Time, 0)
timings := make([]time.Duration, 0)
for e := r.responses.Front(); e != nil; e = e.Next() {
r := e.Value.(*result)
timestamps = append(timestamps, r.timestamp)
timings = append(timings, r.timing)
}
p, err := plot.New()
if err != nil {
return err
}
pts := make(plotter.XYs, len(timestamps))
for i := 0; i < len(pts); i++ {
pts[i].X = timestamps[i].Sub(timestamps[0]).Seconds()
pts[i].Y = timings[i].Seconds() * 1000
}
line, err := plotter.NewLine(pts)
if err != nil {
return err
}
line.Color = plotutil.Color(1)
p.Add(line)
p.X.Padding = vg.Length(3.0)
p.X.Label.Text = "Time elapsed"
p.Y.Padding = vg.Length(3.0)
p.Y.Label.Text = "Latency (ms)"
w, h := vg.Millimeters(float64(len(timestamps))), vg.Centimeters(12.0)
canvas := vgsvg.New(w, h)
p.Draw(plot.MakeDrawArea(canvas))
_, err = canvas.WriteTo(out)
return err
}
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
}
