add a simple -legend option for generated diagrams

README.md

@@ -59,11 +59,12 @@ the area is exponentially proportional to the count indicated. Examples:
 ####Diagram generation options
 
 ```
+  -legend                 draw a legend for colored regions
   -syn-color="#0000ff"    color to use for synonymous mutation markers
   -mut-color="#ff0000"    color to use for non-synonymous mutation markers
   -hide-axis              do not draw the amino position x-axis
-  -hide-disordered        do not draw disordered regions on the backbone
-  -hide-motifs            do not draw simple motif regions
+  -show-disordered        draw disordered regions on the backbone
+  -show-motifs            draw simple motif regions
   -labels                 draw label text above lollipop markers
   -no-patterns            use solid fill instead of patterns (SVG only)
 ```

data/fetch_data.go

@@ -30,6 +30,15 @@ import (
 
 const PfamGraphicURL = "http://pfam.xfam.org/protein/%s/graphic"
 
+// PfamMotifNames has human-readable names from http://pfam.xfam.org/help#tabview=tab9
+var PfamMotifNames = map[string]string{
+	"disorder":       "Disordered region (Pfam/IUPred)",
+	"low_complexity": "Low complexity region (Pfam/SEG)",
+	"sig_p":          "Signal peptide region (Pfam/Phobius)",
+	"coiled_coil":    "Coiled-coil motif (Pfam/ncoils)",
+	"transmembrane":  "Transmembrane region (Pfam/Phobius)",
+}
+
 // PfamGraphicFeature is a generic representation of various Pfam feature responses
 type PfamGraphicFeature struct {
 	Color         string              `json:"colour"`

drawing/draw.go

@@ -112,6 +112,10 @@ func (s *Settings) prepare(changelist []string, g *data.PfamGraphicResponse) *di
 		s.GraphicHeight += s.AxisPadding + s.AxisHeight
 	}
 
+	if s.ShowLegend {
+		s.legendInfo = make(map[string]string)
+	}
+
 	d.startY = startY
 	d.ticks = append(d.ticks,
 		Tick{Pos: 0, Pri: 0},           // start isn't very important (0 is implied)
@@ -154,12 +158,16 @@ func (s *Settings) prepare(changelist []string, g *data.PfamGraphicResponse) *di
 			if r.Type == "pfamb" {
 				continue
 			}
+			if r.Type == "disorder" && s.HideDisordered {
+				continue
+			}
 			if r.Type != "disorder" {
 				tstart, _ := r.Start.Int64()
 				tend, _ := r.End.Int64()
 				d.ticks = append(d.ticks, Tick{Pos: int(tstart), Pri: 1})
 				d.ticks = append(d.ticks, Tick{Pos: int(tend), Pri: 1})
 			}
+			s.legendInfo[r.Type] = BlendColorStrings(r.Color, "#FFFFFF")
 		}
 	}
 
@@ -224,9 +232,22 @@ func (s *Settings) prepare(changelist []string, g *data.PfamGraphicResponse) *di
 			}
 		}
 
+		if label != r.Metadata.Description {
+			s.legendInfo[r.Metadata.Description] = r.Color
+		}
 		d.domainLabels = append(d.domainLabels, label)
 	}
 
+	if s.legendInfo != nil {
+		s.GraphicHeight += float64(1+len(s.legendInfo)) * 14.0
+		for key, color := range s.legendInfo {
+			if rename, found := data.PfamMotifNames[key]; found {
+				delete(s.legendInfo, key)
+				s.legendInfo[rename] = color
+			}
+		}
+	}
+
 	sort.Sort(d.ticks)
 	return d
 }

drawing/png.go

@@ -211,6 +211,23 @@ func (s *diagram) png(w io.Writer) {
 			}
 			blackFontDrawer.DrawString(spos)
 		}
+		startY += s.AxisHeight
+	}
+
+	for key, colorstring := range s.legendInfo {
+		startY += 14.0
+		// 15% darker than backbone (i.e. disordered color)
+		clr := color.RGBA{0x9E, 0xA0, 0x9A, 0xFF}
+		if key != data.PfamMotifNames["disorder"] {
+			clr = colorFromHex(BlendColorStrings(colorstring, "#FFFFFF"))
+		}
+		drawRectWHShadow(img, 4, startY, 12, 12, clr, 2*s.dpi/72.0)
+
+		blackFontDrawer.Dot = fixed.Point26_6{
+			X: fixed.I(20),
+			Y: fixed.I(int(startY + 12)), // 12=font height-baseline
+		}
+		blackFontDrawer.DrawString(key)
 	}
 
 	png.Encode(w, img)

drawing/settings.go

@@ -19,6 +19,8 @@ package drawing
 
 // Settings contains all the configurable options for lollipop diagram generation.
 type Settings struct {
+	// ShowLegend adds a color-coding legend above the diagram.
+	ShowLegend bool
 	// ShowLabels adds mutation label text above lollipops markers.
 	ShowLabels bool
 	// HideDisordered hides disordered regions on the backbone even if motifs are shown.
@@ -68,11 +70,14 @@ type Settings struct {
 	GraphicHeight float64
 
 	dpi float64
+
+	legendInfo map[string]string
 }
 
 // DefaultSettings contains the "standard" diagram output config and is used by
 // the package-level Draw invocations.
 var DefaultSettings = Settings{
+	ShowLegend:     false,
 	ShowLabels:     false,
 	HideDisordered: false,
 	HideMotifs:     false,

drawing/svg.go

@@ -173,6 +173,17 @@ func (s *diagram) svg(w io.Writer) {
 		}
 
 		fmt.Fprintln(w, "</g>")
+		startY += s.AxisHeight
+	}
+
+	for key, color := range s.legendInfo {
+		startY += 14.0
+		if key == data.PfamMotifNames["disorder"] {
+			color = disFill
+		}
+		fmt.Fprintf(w, `<rect fill="%s" x="4" y="%f" width="12" height="12" filter="url(#ds)"/>`, color, startY)
+		fmt.Fprintf(w, `<text style="font-size:12px;%sfill:#000000;" text-anchor="start" x="20" y="%f">%s</text>`,
+			fontSpec, startY+12, key) // 12=font height-baseline
 	}
 
 	fmt.Fprintln(w, svgFooter)

main.go

@@ -39,6 +39,7 @@ var (
 	width   = flag.Int("w", 0, "output width (default automatic fit labels)")
 	dpi     = flag.Float64("dpi", 72, "output DPI for PNG rasterization")
 
+	showLegend     = flag.Bool("legend", false, "draw a legend for colored regions")
 	showLabels     = flag.Bool("labels", false, "draw mutation labels above lollipops")
 	showDisordered = flag.Bool("show-disordered", false, "draw disordered regions on the backbone")
 	showMotifs     = flag.Bool("show-motifs", false, "draw simple motif regions")
@@ -91,6 +92,7 @@ Protein changes:
   (N.B. color must come before count in tags)
 
 Diagram generation options:
+  -legend                 draw a legend for colored regions
   -syn-color="#0000ff"    color to use for synonymous mutation markers
   -mut-color="#ff0000"    color to use for non-synonymous mutation markers
   -hide-axis              do not draw the amino position x-axis
@@ -110,6 +112,7 @@ Output options:
 	}
 
 	flag.Parse()
+	drawing.DefaultSettings.ShowLegend = *showLegend
 	drawing.DefaultSettings.ShowLabels = *showLabels
 	drawing.DefaultSettings.HideDisordered = !*showDisordered
 	drawing.DefaultSettings.HideMotifs = !*showMotifs
@@ -208,5 +211,4 @@ Press Enter/Ctrl-C to quit.`)
 	} else {
 		drawing.DrawSVG(f, flag.Args()[varStart:], data)
 	}
-
 }