Merge 7264c01b85dccf1d5e4c45c3a4e1bb374f2c7968 into 8b2a83838894dc6d7f903a75e209362137e4d237

src/Plots.jl

@@ -126,7 +126,8 @@ export
     # recipes
     PlotRecipe,
     # EllipseRecipe,
-    spy
+    spy,
+    arcdiagram
     # corrplot
 
 

src/args.jl

@@ -11,7 +11,7 @@ const _3dTypes = [:path3d, :scatter3d, :surface, :wireframe]
 const _allTypes = vcat([
                         :none, :line, :path, :steppre, :steppost, :sticks, :scatter,
                         :heatmap, :hexbin, :hist, :hist2d, :hist3d, :density, :bar, :hline, :vline, :ohlc,
-                        :contour, :pie
+                        :contour, :pie, :shape
                        ], _3dTypes)
 @compat const _typeAliases = Dict(
     :n             => :none,
@@ -35,6 +35,9 @@ const _allTypes = vcat([
     :line3d        => :path3d,
     :surf          => :surface,
     :wire          => :wireframe,
+    :shapes        => :shape,
+    :poly          => :shape,
+    :polygon       => :shape,
   )
 
 ishistlike(lt::Symbol) = lt in (:hist, :density)
@@ -801,5 +804,3 @@ function getSeriesArgs(pkg::AbstractBackend, plotargs::Dict, kw, commandIndex::I
 
   d
 end
-
-

src/backends/gadfly.jl

@@ -34,7 +34,7 @@ end
 function getLineGeom(d::Dict)
     lt = d[:linetype]
     xbins, ybins = maketuple(d[:nbins])
-  if lt == :hexbin
+    if lt == :hexb
         Gadfly.Geom.hexbin(xbincount = xbins, ybincount = ybins)
     elseif lt == :hist2d
         Gadfly.Geom.histogram2d(xbincount = xbins, ybincount = ybins)
@@ -54,6 +54,8 @@ function getLineGeom(d::Dict)
         Gadfly.Geom.vline
     elseif lt == :contour
         Gadfly.Geom.contour(levels = d[:levels])
+    # elseif lt == :shape
+    #     Gadfly.Geom.polygon(fill = true, preserve_order = true)
     else
         nothing
     end
@@ -75,21 +77,8 @@ function get_extra_theme_args(d::Dict, k::Symbol)
 end
 
 function getGadflyLineTheme(d::Dict)
-  
     lc = convertColor(getColor(d[:linecolor]), d[:linealpha])
-  # lc = getColor(d[:linecolor])
-  # α = d[:linealpha]
-  # if α != nothing
-  #   lc = RGBA(lc, α)
-  # end
-
     fc = convertColor(getColor(d[:fillcolor]), d[:fillalpha])
-  # fc = getColor(d[:fillcolor])
-  # α = d[:fillalpha]
-  # if α != nothing
-  #   fc = RGBA(fc, α)
-  # end
-
 
     Gadfly.Theme(;
         default_color = lc,
@@ -105,8 +94,7 @@ end
 # add a line as a new layer
 function addGadflyLine!(plt::Plot, numlayers::Int, d::Dict, geoms...)
     gplt = getGadflyContext(plt)
-  gfargs = vcat(geoms...,
+    gfargs = vcat(geoms..., getGadflyLineTheme(d))
-                getGadflyLineTheme(d))
     kwargs = Dict()
     lt = d[:linetype]
 
@@ -128,7 +116,6 @@ function addGadflyLine!(plt::Plot, numlayers::Int, d::Dict, geoms...)
             kwargs[:xmin] = d[:x] - w
             kwargs[:xmax] = d[:x] + w
         elseif lt == :contour
-      # d[:y] = reverse(d[:y])
             kwargs[:z] = d[:z].surf
             addGadflyContColorScale(plt, d[:linecolor])
         end
@@ -138,30 +125,7 @@ function addGadflyLine!(plt::Plot, numlayers::Int, d::Dict, geoms...)
 
     end
 
-  # # h/vlines
-  # if lt == :hline
-  #   kwargs[:yintercept] = d[:y]
-  # elseif lt == :vline
-  #   kwargs[:xintercept] = d[:y]
-  # elseif lt == :sticks
-  #   w = 0.01 * mean(diff(d[:x]))
-  #   kwargs[:xmin] = d[:x] - w
-  #   kwargs[:xmax] = d[:x] + w
-  # elseif lt == :contour
-  #   d[:y] = reverse(d[:y])
-  #   kwargs[:z] = d[:surface]
-  # end
-
-  # if lt == :hist
-  #   kwargs[:x] = kwargs[:y] = d[:y]
-  # elseif lt != :hline && lt != :vline
-  #   kwargs[:x] = d[:x]
-  #   kwargs[:y] = d[:y]
-  # end
-  
     # # add the layer
-  # x = d[d[:linetype] == :hist ? :y : :x]
-  # Gadfly.layer(gfargs...; x = x, y = d[:y], order=numlayers, kwargs...)
     Gadfly.layer(gfargs...; order=numlayers, kwargs...)
 end
 
@@ -172,13 +136,13 @@ end
 getMarkerGeom(shape::Shape) = gadflyshape(shape)
 getMarkerGeom(shape::Symbol) = gadflyshape(_shapes[shape])
 getMarkerGeom(shapes::AVec) = map(getMarkerGeom, shapes)
-getMarkerGeom(d::Dict) = getMarkerGeom(d[:markershape])
+function getMarkerGeom(d::Dict)
-
+    if d[:linetype] == :shape
-# function getMarkerGeom(d::Dict)
+        Gadfly.Geom.polygon(fill = true, preserve_order = true)
-#   shape = d[:markershape]
+    else
-#   gadflyshape(isa(shape, Shape) ? shape : _shapes[shape])
+        getMarkerGeom(d[:markershape])
-# end
+    end
-
+end
 
 function getGadflyMarkerTheme(d::Dict, plotargs::Dict)
     c = getColor(d[:markercolor])
@@ -195,12 +159,12 @@ function getGadflyMarkerTheme(d::Dict, plotargs::Dict)
         ms * Gadfly.px
     end
 
-  # fg = getColor(plotargs[:foreground_color])
     Gadfly.Theme(;
         default_color = c,
         default_point_size = ms,
         discrete_highlight_color = c -> RGB(getColor(d[:markerstrokecolor])),
         highlight_width = d[:markerstrokewidth] * Gadfly.px,
+        line_width = d[:markerstrokewidth] * Gadfly.px,
         # get_extra_theme_args(d, :markerstrokestyle)...
     )
 end
@@ -214,9 +178,7 @@ function addGadflyContColorScale(plt::Plot{GadflyBackend}, c)
 end
 
 function addGadflyMarker!(plt::Plot, numlayers::Int, d::Dict, plotargs::Dict, geoms...)
-  gfargs = vcat(geoms...,
+    gfargs = vcat(geoms..., getGadflyMarkerTheme(d, plotargs), getMarkerGeom(d))
-                getGadflyMarkerTheme(d, plotargs),
-                getMarkerGeom(d))
     kwargs = Dict()
 
     # handle continuous color scales for the markers
@@ -224,10 +186,6 @@ function addGadflyMarker!(plt::Plot, numlayers::Int, d::Dict, plotargs::Dict, ge
     if zcolor != nothing && typeof(zcolor) <: AVec
         kwargs[:color] = zcolor
         addGadflyContColorScale(plt, d[:markercolor])
-    # if !isa(d[:markercolor], ColorGradient)
-    #   d[:markercolor] = colorscheme(:bluesreds)
-    # end
-    # push!(getGadflyContext(plt).scales, Gadfly.Scale.ContinuousColorScale(p -> RGB(getColorZ(d[:markercolor], p))))
     end
 
     Gadfly.layer(gfargs...; x = d[:x], y = d[:y], order=numlayers, kwargs...)
@@ -237,8 +195,6 @@ end
 # ---------------------------------------------------------------------------
 
 function addToGadflyLegend(plt::Plot, d::Dict)
-
-  # add the legend?
     if plt.plotargs[:legend] != :none && d[:label] != ""
         gplt = getGadflyContext(plt)
 
@@ -272,9 +228,7 @@ function addToGadflyLegend(plt::Plot, d::Dict)
                 end
             end
         end
-
     end
-
 end
 
 getGadflySmoothing(smooth::Bool) = smooth ? [Gadfly.Geom.smooth(method=:lm)] : Any[]
@@ -282,7 +236,6 @@ getGadflySmoothing(smooth::Real) = [Gadfly.Geom.smooth(method=:loess, smoothing=
 
 
 function addGadflySeries!(plt::Plot, d::Dict)
-
     layers = Gadfly.Layer[]
     gplt = getGadflyContext(plt)
 
@@ -294,9 +247,7 @@ function addGadflySeries!(plt::Plot, d::Dict)
     geom = getLineGeom(d)
     if geom != nothing
         prepend!(layers, addGadflyLine!(plt, length(gplt.layers), d, geom, smooth...))
-
+        smooth = Any[] # don't add a regression for markers too
-    # don't add a regression for markers too
-    smooth = Any[]
     end
 
     # special handling for ohlc and scatter
@@ -310,7 +261,7 @@ function addGadflySeries!(plt::Plot, d::Dict)
     end
 
     # markers
-  if d[:markershape] != :none
+    if d[:markershape] != :none || lt == :shape
         prepend!(layers, addGadflyMarker!(plt, length(gplt.layers), d, plt.plotargs, smooth...))
     end
 
@@ -401,8 +352,6 @@ end
 
 
 function addGadflyLimitsScale(gplt, d::Dict, isx::Bool)
-
-  # get the correct scale function
     gfunc, hasScaleKey = getGadflyScaleFunction(d, isx)
 
     # do we want to add min/max limits for the axis?
@@ -411,7 +360,6 @@ function addGadflyLimitsScale(gplt, d::Dict, isx::Bool)
 
     # map :auto to nothing, otherwise add to limargs
     lims = get(d, limsym, :auto)
-  # lims == :auto && return
     if lims == :auto
         lims = nothing
     else
@@ -485,7 +433,6 @@ function updateGadflyGuides(plt::Plot, d::Dict)
     else
         addGadflyTicksGuide(gplt, ticks, false)
     end
-  # haskey(d, :yticks) && addGadflyTicksGuide(gplt, d[:yticks], false)
 
     updateGadflyAxisFlips(gplt, d, xlims, ylims)
 end
@@ -493,14 +440,7 @@ end
 function updateGadflyPlotTheme(plt::Plot, d::Dict)
     kwargs = Dict()
 
-  # # get the full plotargs, overriding any new settings
-  # # TODO: should this be part of the main `plot` command in plot.jl???
-  # d = merge!(plt.plotargs, d)
-
     # # hide the legend?
-  # if !get(d, :legend, true)
-  #   kwargs[:key_position] = :none
-  # end
     leg = d[d[:legend] == :none ? :colorbar : :legend]
     if leg != :best
         kwargs[:key_position] = leg == :inside ? :right : leg
@@ -576,7 +516,6 @@ end
 
 # plot one data series
 function _add_series(::GadflyBackend, plt::Plot; kw...)
-  
     # first clear out the temporary layer
     gplt = getGadflyContext(plt)
     if gplt.layers[1].geom.tag == :remove
@@ -704,12 +643,10 @@ function Base.display(::PlotsDisplay, plt::Plot{GadflyBackend})
 end
 
 
-
 function Base.display(::PlotsDisplay, subplt::Subplot{GadflyBackend})
     setGadflyDisplaySize(getplotargs(subplt,1)[:size]...)
     ctx = buildGadflySubplotContext(subplt)
 
-
     # taken from Gadfly since I couldn't figure out how to do it directly
 
     filename = string(Gadfly.tempname(), ".html")

src/backends/gr.jl

@@ -98,36 +98,36 @@ function gr_display(plt::Plot{GRBackend}, clear=true, update=true,
   mwidth, mheight, width, height = GR.inqdspsize()
   w, h = d[:size]
   viewport = zeros(4)
+  vp = float(subplot)
   if w > h
     ratio = float(h) / w
     msize = mwidth * w / width
     GR.setwsviewport(0, msize, 0, msize * ratio)
     GR.setwswindow(0, 1, 0, ratio)
-    viewport[1] = subplot[1] + 0.125 * (subplot[2] - subplot[1])
+    vp[3] *= ratio
-    viewport[2] = subplot[1] + 0.95  * (subplot[2] - subplot[1])
+    vp[4] *= ratio
-    viewport[3] = ratio * (subplot[3] + 0.125  * (subplot[4] - subplot[3]))
-    viewport[4] = ratio * (subplot[3] + 0.95  * (subplot[4] - subplot[3]))
   else
     ratio = float(w) / h
     msize = mheight * h / height
     GR.setwsviewport(0, msize * ratio, 0, msize)
     GR.setwswindow(0, ratio, 0, 1)
-    viewport[1] = ratio * (subplot[1] + 0.125 * (subplot[2] - subplot[1]))
+    vp[1] *= ratio
-    viewport[2] = ratio * (subplot[1] + 0.95  * (subplot[2] - subplot[1]))
+    vp[2] *= ratio
-    viewport[3] = subplot[3] + 0.125 * (subplot[4] - subplot[3])
-    viewport[4] = subplot[3] + 0.95  * (subplot[4] - subplot[3])
   end
+  viewport[1] = vp[1] + 0.125 * (vp[2] - vp[1])
+  viewport[2] = vp[1] + 0.95  * (vp[2] - vp[1])
+  viewport[3] = vp[3] + 0.125 * (vp[4] - vp[3])
+  if w > h
+    viewport[3] += (1 - (subplot[4] - subplot[3])^2) * 0.02
+  end
+  viewport[4] = vp[3] + 0.95  * (vp[4] - vp[3])
 
   if haskey(d, :background_color)
     GR.savestate()
     GR.selntran(0)
     GR.setfillintstyle(GR.INTSTYLE_SOLID)
     GR.setfillcolorind(gr_getcolorind(d[:background_color]))
-    if w > h
+    GR.fillrect(vp[1], vp[2], vp[3], vp[4])
-      GR.fillrect(subplot[1], subplot[2], ratio*subplot[3], ratio*subplot[4])
-    else
-      GR.fillrect(ratio*subplot[1], ratio*subplot[2], subplot[3], subplot[4])
-    end
     GR.selntran(1)
     GR.restorestate()
     c = getColor(d[:background_color])
@@ -145,6 +145,7 @@ function gr_display(plt::Plot{GRBackend}, clear=true, update=true,
   cmap = false
   axes_2d = true
   grid_flag = get(d, :grid, true)
+  outside_ticks = false
 
   for axis = 1:2
     xmin = ymin = typemax(Float64)
@@ -176,12 +177,15 @@ function gr_display(plt::Plot{GRBackend}, clear=true, update=true,
           xmin, xmax, ymin, ymax = 0, 1, 0, 1
           x, y = p[:x], p[:y]
         else
-          if p[:linetype] in [:contour, :surface]
+          if p[:linetype] in [:contour, :surface, :heatmap]
             cmap = true
           end
           if p[:linetype] in [:surface, :wireframe, :path3d, :scatter3d]
             axes_2d = false
           end
+          if p[:linetype] == :heatmap
+            outside_ticks = true
+          end
           x, y = p[:x], p[:y]
         end
         if p[:linetype] != :pie
@@ -267,6 +271,9 @@ function gr_display(plt::Plot{GRBackend}, clear=true, update=true,
       GR.setlinewidth(1)
       GR.setlinecolorind(fg)
       ticksize = 0.0075 * diag
+      if outside_ticks
+        ticksize = -ticksize
+      end
       if grid_flag && fg == 1
         GR.grid(xtick, ytick, 0, 0, majorx, majory)
       end
@@ -285,14 +292,14 @@ function gr_display(plt::Plot{GRBackend}, clear=true, update=true,
     GR.savestate()
     GR.settextalign(GR.TEXT_HALIGN_CENTER, GR.TEXT_VALIGN_TOP)
     GR.settextcolorind(fg)
-    GR.text(0.5 * (viewport[1] + viewport[2]), min(ratio, 1), d[:title])
+    GR.text(0.5 * (viewport[1] + viewport[2]), vp[4], d[:title])
     GR.restorestate()
   end
   if get(d, :xlabel, "") != ""
     GR.savestate()
     GR.settextalign(GR.TEXT_HALIGN_CENTER, GR.TEXT_VALIGN_BOTTOM)
     GR.settextcolorind(fg)
-    GR.text(0.5 * (viewport[1] + viewport[2]), 0, d[:xlabel])
+    GR.text(0.5 * (viewport[1] + viewport[2]), vp[3], d[:xlabel])
     GR.restorestate()
   end
   if get(d, :ylabel, "") != ""
@@ -300,7 +307,7 @@ function gr_display(plt::Plot{GRBackend}, clear=true, update=true,
     GR.settextalign(GR.TEXT_HALIGN_CENTER, GR.TEXT_VALIGN_TOP)
     GR.setcharup(-1, 0)
     GR.settextcolorind(fg)
-    GR.text(0, 0.5 * (viewport[3] + viewport[4]), d[:ylabel])
+    GR.text(vp[1], 0.5 * (viewport[3] + viewport[4]), d[:ylabel])
     GR.restorestate()
   end
   if get(d, :yrightlabel, "") != ""
@@ -308,7 +315,7 @@ function gr_display(plt::Plot{GRBackend}, clear=true, update=true,
     GR.settextalign(GR.TEXT_HALIGN_CENTER, GR.TEXT_VALIGN_TOP)
     GR.setcharup(1, 0)
     GR.settextcolorind(fg)
-    GR.text(1, 0.5 * (viewport[3] + viewport[4]), d[:yrightlabel])
+    GR.text(vp[2], 0.5 * (viewport[3] + viewport[4]), d[:yrightlabel])
     GR.restorestate()
   end
 
@@ -497,6 +504,18 @@ function gr_display(plt::Plot{GRBackend}, clear=true, update=true,
                        viewport[3], viewport[4])
         GR.colormap()
       end
+    elseif p[:linetype] == :heatmap
+      x, y, z = p[:x], p[:y], p[:z].surf
+      zmin, zmax = GR.adjustrange(minimum(z), maximum(z))
+      GR.setspace(zmin, zmax, 0, 90)
+      GR.setcolormap(GR.COLORMAP_COOLWARM)
+      z = reshape(z, length(x) * length(y))
+      GR.surface(x, y, z, GR.OPTION_CELL_ARRAY)
+      if cmap
+        GR.setviewport(viewport[2] + 0.02, viewport[2] + 0.05,
+                       viewport[3], viewport[4])
+        GR.colormap()
+      end
     elseif p[:linetype] in [:path3d, :scatter3d]
       x, y, z = p[:x], p[:y], p[:z]
       zmin, zmax = GR.adjustrange(minimum(z), maximum(z))

src/backends/plotly.jl

@@ -6,26 +6,30 @@ function _initialize_backend(::PlotlyBackend; kw...)
     import JSON
     JSON._print(io::IO, state::JSON.State, dt::Union{Date,DateTime}) = print(io, '"', dt, '"')
 
-    ############################
+    _js_path = Pkg.dir("Plots", "deps", "plotly-latest.min.js")
-    # borrowed from https://github.com/spencerlyon2/Plotlyjs.jl/blob/master/src/display.jl
+    _js_code = open(readall, _js_path, "r")
-    _js_path = joinpath(Pkg.dir("Plots"), "deps", "plotly-latest.min.js")
+
+    # borrowed from https://github.com/plotly/plotly.py/blob/2594076e29584ede2d09f2aa40a8a195b3f3fc66/plotly/offline/offline.py#L64-L71 c/o @spencerlyon2
+    _js_script = """
+        <script type='text/javascript'>
+            define('plotly', function(require, exports, module) {
+                $(_js_code)
+            });
+            require(['plotly'], function(Plotly) {
+                window.Plotly = Plotly;
+            });
+        </script>
+    """
 
     # if we're in IJulia call setupnotebook to load js and css
     if isijulia()
-        # the first script is some hack I needed to do in order for the notebook
+        display("text/html", _js_script)
-        # to not complain about Plotly being undefined
-        display("text/html", """
-            <script type="text/javascript">
-                require=requirejs=define=undefined;
-            </script>
-            <script type="text/javascript">
-                $(open(readall, _js_path, "r"))
-            </script>
-         """)
-        # display("text/html", "<p>Plotly javascript loaded.</p>")
     end
-    # end borrowing (thanks :)
+
-    ###########################
+    # if isatom()
+    #     import Atom
+    #     Atom.@msg evaljs(_js_code)
+    # end
 
   end
   # TODO: other initialization
@@ -436,15 +440,23 @@ function html_body(plt::Plot{PlotlyBackend}, style = nothing)
     style = "width:$(w)px;height:$(h)px;"
   end
   uuid = Base.Random.uuid4()
-  """
+  html = """
     <div id=\"$(uuid)\" style=\"$(style)\"></div>
     <script>
       PLOT = document.getElementById('$(uuid)');
       Plotly.plot(PLOT, $(get_series_json(plt)), $(get_plot_json(plt)));
     </script>
   """
+  # @show html
+  html
 end
 
+function js_body(plt::Plot{PlotlyBackend}, uuid)
+    js = """
+          PLOT = document.getElementById('$(uuid)');
+          Plotly.plot(PLOT, $(get_series_json(plt)), $(get_plot_json(plt)));
+    """
+end
 
 
 function html_body(subplt::Subplot{PlotlyBackend})
@@ -480,6 +492,7 @@ end
 
 function Base.writemime(io::IO, ::MIME"text/html", plt::AbstractPlot{PlotlyBackend})
     write(io, html_head(plt) * html_body(plt))
+    # write(io, html_body(plt))
 end
 
 function Base.display(::PlotsDisplay, plt::AbstractPlot{PlotlyBackend})

src/backends/plotlyjs.jl

@@ -44,6 +44,7 @@ function _add_series(::PlotlyJSBackend, plt::Plot; kw...)
     typ = pop!(pdict, :type)
     gt = PlotlyJS.GenericTrace(typ; pdict...)
     PlotlyJS.addtraces!(syncplot, gt)
+    # PlotlyJS.addtraces!(syncplot.plot, gt)
 
     push!(plt.seriesargs, d)
     plt
@@ -73,6 +74,7 @@ function _update_plot(plt::Plot{PlotlyJSBackend}, d::Dict)
     syncplot = plt.o
     w,h = d[:size]
     PlotlyJS.relayout!(syncplot, pdict, width = w, height = h)
+    # PlotlyJS.relayout!(syncplot.plot, pdict, width = w, height = h)
 end
 
 
@@ -125,4 +127,3 @@ end
 function Base.display(::PlotsDisplay, plt::Subplot{PlotlyJSBackend})
     error()
 end
-

src/backends/supported.jl

@@ -81,7 +81,7 @@ supportedArgs(::GadflyBackend) = [
 supportedAxes(::GadflyBackend) = [:auto, :left]
 supportedTypes(::GadflyBackend) = [:none, :line, :path, :steppre, :steppost, :sticks,
                                    :scatter, :hist2d, :hexbin, :hist, :bar,
-                                   :hline, :vline, :contour]
+                                   :hline, :vline, :contour, :shape]
 supportedStyles(::GadflyBackend) = [:auto, :solid, :dash, :dot, :dashdot, :dashdotdot]
 supportedMarkers(::GadflyBackend) = vcat(_allMarkers, Shape)
 supportedScales(::GadflyBackend) = [:identity, :ln, :log2, :log10, :asinh, :sqrt]
@@ -241,7 +241,7 @@ supportedArgs(::GRBackend) = [
 supportedAxes(::GRBackend) = _allAxes
 supportedTypes(::GRBackend) = [:none, :line, :path, :steppre, :steppost, :sticks,
                                :scatter, :hist2d, :hexbin, :hist, :density, :bar,
-                               :hline, :vline, :contour, :path3d, :scatter3d, :surface,
+                               :hline, :vline, :contour, :heatmap, :path3d, :scatter3d, :surface,
                                :wireframe, :ohlc, :pie]
 supportedStyles(::GRBackend) = [:auto, :solid, :dash, :dot, :dashdot, :dashdotdot]
 supportedMarkers(::GRBackend) = vcat(_allMarkers, Shape)
@@ -770,4 +770,3 @@ supportedStyles(::PGFPlotsBackend) = [:auto, :solid] #, :dash, :dot, :dashdot, :
 supportedMarkers(::PGFPlotsBackend) = [:none, :auto, :ellipse] #, :rect, :diamond, :utriangle, :dtriangle, :cross, :xcross, :star5] #vcat(_allMarkers, Shape)
 supportedScales(::PGFPlotsBackend) = [:identity] #, :log, :log2, :log10, :asinh, :sqrt]
 subplotSupported(::PGFPlotsBackend) = false
-

src/components.jl

@@ -3,6 +3,9 @@ immutable Shape
   vertices::AVec
 end
 
+get_xs(shape::Shape) = Float64[v[1] for v in shape.vertices]
+get_ys(shape::Shape) = Float64[v[2] for v in shape.vertices]
+
 "get an array of tuples of points on a circle with radius `r`"
 function partialcircle(start_θ, end_θ, n = 20, r=1)
   @compat(Tuple{Float64,Float64})[(r*cos(u),r*sin(u)) for u in linspace(start_θ, end_θ, n)]

src/output.jl

@@ -124,18 +124,23 @@ end
 # ---------------------------------------------------------
 
 function setup_atom()
-    # @require Atom begin
+    @require Atom begin
-    #     @eval begin
+        import Atom, Media
-    #         import Atom
+
-    #
+        # connects the render function
+        Media.media{T <: Union{GadflyBackend,ImmerseBackend,PyPlotBackend,GRBackend}}(Plot{T}, Media.Plot)
+
         # Atom.displaysize(::AbstractPlot) = (535, 379)
-    #         Atom.displaytitle(::AbstractPlot) = "Plots.jl"
+        # Atom.displaytitle(plt::AbstractPlot) = "Plots.jl (backend: $(backend(plt)))"
-    #
+
-    #         Atom.@render Atom.PlotPane p::Plot begin
+        # this is like "display"... sends an html div with the plot to the PlotPane
-    #             x, y = Atom.@rpc Atom.plotsize()
+        function Media.render(pane::Atom.PlotPane, plt::Plot)
-    #             plot!(p, size=(x,y))  # changes the size of the Plots.Plot
+            Media.render(pane, Atom.div(Atom.d(), Atom.HTML(stringmime(MIME("text/html"), plt))))
-    #             Atom.div(Dict(:style=>"background: white"), Atom.HTML(stringmime("text/html", p)))
+        end
-    #         end
+
-    #     end
+
+        # function Media.render(pane::Atom.PlotPane, plt::Plot{PlotlyBackend})
+        #     html = Media.render(pane, Atom.div(Atom.d(), Atom.HTML(stringmime(MIME("text/html"), plt))))
         # end
     end
+end

src/plot.jl

@@ -444,6 +444,37 @@ function createKWargsList{T<:Real}(plt::AbstractPlot, x::AMat{T}, y::AMat{T}, zm
   createKWargsList(plt, Any[x], Any[y]; d...) #kw..., z = surf, linetype = :contour)
 end
 
+# plotting arbitrary shapes/polygons
+function createKWargsList(plt::AbstractPlot, shape::Shape; kw...)
+    x, y = unzip(shape.vertices)
+    createKWargsList(plt, x, y; linetype = :shape, kw...)
+end
+
+function shape_coords(shapes::AVec{Shape})
+    xs = map(get_xs, shapes)
+    ys = map(get_ys, shapes)
+    x, y = unzip(shapes[1].vertices)
+    for shape in shapes[2:end]
+        tmpx, tmpy = unzip(shape.vertices)
+        x = vcat(x, NaN, tmpx)
+        y = vcat(y, NaN, tmpy)
+    end
+    x, y
+end
+
+function createKWargsList(plt::AbstractPlot, shapes::AVec{Shape}; kw...)
+    x, y = shape_coords(shapes)
+    createKWargsList(plt, x, y; linetype = :shape, kw...)
+end
+function createKWargsList(plt::AbstractPlot, shapes::AMat{Shape}; kw...)
+    x, y = [], []
+    for j in 1:size(shapes, 2)
+        tmpx, tmpy = shape_coords(vec(shapes[:,j]))
+        push!(x, tmpx)
+        push!(y, tmpy)
+    end
+    createKWargsList(plt, x, y; linetype = :shape, kw...)
+end
 
 function createKWargsList(plt::AbstractPlot, surf::Surface; kw...)
   createKWargsList(plt, 1:size(surf.surf,1), 1:size(surf.surf,2), convert(Matrix{Float64}, surf.surf); kw...)

src/recipes.jl

@@ -137,3 +137,92 @@ function abline!(plt::Plot, a, b; kw...)
 end
 
 abline!(args...; kw...) = abline!(current(), args...; kw...)
+
+# -------------------------------------------------
+# Arc Diagram
+
+curvecolor(value, min, max, grad) = getColorZ(grad, (value-min)/(max-min))
+
+"Plots a clockwise arc, from source to destiny, colored by weight"
+function arc!(source, destiny, weight, min, max, grad)
+    radius = (destiny - source) / 2
+    arc = Plots.partialcircle(0, π, 30, radius)
+    x, y = Plots.unzip(arc)
+    plot!(x .+ radius .+ source,  y, line = (curvecolor(weight, min, max, grad), 0.5, 2))
+end
+
+"""
+`arcdiagram(source, destiny, weight[, grad])`
+
+Plots an arc diagram, form `source` to `destiny` (clockwise), using `weight` to determine the colors.
+"""
+function arcdiagram(source, destiny, weight, grad=ColorGradient(:bluesreds))
+
+    if length(source) == length(destiny) == length(weight)
+
+        vertices = vcat(source, destiny)
+
+        xmin, xmax = extrema(vertices)
+        plot(xlim=(xmin - 0.5, xmax + 0.5))
+
+        wmin,wmax = extrema(weight)
+
+        for (i, j, value) in zip(source,destiny,weight)
+            arc!(i, j, value, wmin, wmax, grad)
+        end
+
+        scatter!(vertices, zeros(length(vertices)), leg=false)
+
+        else
+
+        throw(ArgumentError("source, destiny and weight should have the same length"))
+
+    end
+end
+
+"""
+`arcdiagram(mat[, grad])`
+
+Plots an arc diagram of a matrix, form rows to columns (clockwise),
+using the values on the matrix as weights to determine the colors.
+Doesn't show edges with value zero if the input is sparse.
+For simmetric matrices, only the upper triangular values are used.
+"""
+function arcdiagram{T}(mat::AbstractArray{T,2}, grad=ColorGradient(:bluesreds))
+    nrow, ncol = size(mat) # rows are sources and columns are destinies
+
+    nosymmetric = !issym(mat) # plots only triu for symmetric matrices
+    nosparse = !issparse(mat) # doesn't plot zeros from a sparse matrix
+
+    L = length(mat)
+
+    source  = Array(Int, L)
+    destiny = Array(Int, L)
+    weight  = Array(T, L)
+
+    idx = 1
+    for i in 1:nrow, j in 1:ncol
+        value = mat[i, j]
+        if !isnan(value) && ( nosparse || value != zero(T) ) # TODO: deal with Nullable
+
+            if i < j
+                source[idx]  = i
+                destiny[idx] = j
+                weight[idx]  = value
+                idx += 1
+            elseif nosymmetric && (i > j)
+                source[idx]  = i
+                destiny[idx] = j
+                weight[idx]  = value
+                idx += 1
+            end
+
+        end
+    end
+
+    resize!(source, idx-1)
+    resize!(destiny, idx-1)
+    resize!(weight, idx-1)
+
+    arcdiagram(source, destiny, weight, grad)
+end

src/utils.jl

@@ -198,6 +198,7 @@ function fakedata(sz...)
 end
 
 isijulia() = isdefined(Main, :IJulia) && Main.IJulia.inited
+isatom() = isdefined(Main, :Atom) && Atom.isconnected()
 
 istuple(::Tuple) = true
 istuple(::Any) = false