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Added command gotree ltt : write lineage through time data, and draw …
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,108 @@ | ||
| package cmd | ||
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| import ( | ||
| "fmt" | ||
| goio "io" | ||
| "os" | ||
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| "image/color" | ||
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| "github.com/evolbioinfo/gotree/io" | ||
| "github.com/evolbioinfo/gotree/tree" | ||
| "github.com/spf13/cobra" | ||
| "gonum.org/v1/plot" | ||
| "gonum.org/v1/plot/font" | ||
| "gonum.org/v1/plot/plotter" | ||
| "gonum.org/v1/plot/vg" | ||
| "gonum.org/v1/plot/vg/draw" | ||
| ) | ||
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| var lttoutimagefile string | ||
| var lttoutimagewidth int | ||
| var lttoutimageheight int | ||
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| // resolveCmd represents the resolve command | ||
| var lttCmd = &cobra.Command{ | ||
| Use: "ltt", | ||
| Short: "Lineage Through Time data", | ||
| Long: `Compute Lineage Through Time data. | ||
| Will output data visualizable in statistal packages (R, python, etc.). | ||
| Set of x,y coordinates pairs: x: time (or mutations) and y: number of lineages. | ||
| `, | ||
| RunE: func(cmd *cobra.Command, args []string) (err error) { | ||
| var f *os.File | ||
| var treefile goio.Closer | ||
| var treechan <-chan tree.Trees | ||
| var p *plot.Plot | ||
| var point *plotter.Scatter | ||
| var line *plotter.Line | ||
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| if f, err = openWriteFile(outtreefile); err != nil { | ||
| io.LogError(err) | ||
| return | ||
| } | ||
| defer closeWriteFile(f, outtreefile) | ||
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| if treefile, treechan, err = readTrees(intreefile); err != nil { | ||
| io.LogError(err) | ||
| return | ||
| } | ||
| defer treefile.Close() | ||
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| if lttoutimagefile != "none" { | ||
| p = plot.New() | ||
| p.Title.Text = "Lineage through time plot" | ||
| p.X.Label.Text = "Time" | ||
| p.Y.Label.Text = "Number of lineages" | ||
| } | ||
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| for tr := range treechan { | ||
| if tr.Err != nil { | ||
| io.LogError(tr.Err) | ||
| return tr.Err | ||
| } | ||
| ltt := tr.Tree.LTT() | ||
| for _, l := range ltt { | ||
| f.WriteString(fmt.Sprintf("%d\t%f\t%d\n", tr.Id, l.X, l.Y)) | ||
| } | ||
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| if lttoutimagefile != "none" { | ||
| pts := make(plotter.XYs, len(ltt)) | ||
| for i, l := range ltt { | ||
| pts[i].X = float64(l.X) | ||
| pts[i].Y = float64(l.Y) | ||
| } | ||
| line, point, err = plotter.NewLinePoints(pts) | ||
| point.Shape = draw.CircleGlyph{} | ||
| point.Radius = 1 | ||
| point.Color = color.RGBA{R: 0, G: 0, B: 255, A: 255} | ||
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| //plotutil.AddLinePoints(p, fmt.Sprintf("LTT_%d", tr.Id), pts, draw.CircleGlyph{}) | ||
| p.Add(line, point) | ||
| p.Legend.Add(fmt.Sprintf("LTT_%d", tr.Id)) | ||
| } | ||
| } | ||
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| if lttoutimagefile != "none" { | ||
| // Save the plot to a PNG file. | ||
| fmt.Println(font.Length(float64(lttoutimagewidth)) * vg.Inch) | ||
| fmt.Println(font.Length(float64(lttoutimageheight)) * vg.Inch) | ||
| if err = p.Save(font.Length(lttoutimagewidth)*vg.Inch, font.Length(lttoutimageheight)*vg.Inch, lttoutimagefile); err != nil { | ||
| io.LogError(err) | ||
| return | ||
| } | ||
| } | ||
| return | ||
| }, | ||
| } | ||
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| func init() { | ||
| RootCmd.AddCommand(lttCmd) | ||
| lttCmd.PersistentFlags().StringVarP(&intreefile, "input", "i", "stdin", "Input tree(s) file") | ||
| lttCmd.PersistentFlags().StringVarP(&outtreefile, "output", "o", "stdout", "LTT output file") | ||
| lttCmd.PersistentFlags().StringVar(<toutimagefile, "image", "none", "LTT plot image image output file") | ||
| lttCmd.PersistentFlags().IntVar(<toutimagewidth, "image-width", 4, "LTT plot image image output width") | ||
| lttCmd.PersistentFlags().IntVar(<toutimageheight, "image-height", 4, "LTT plot image output heigh") | ||
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| } |
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