nyaplot 0.1.0 → 0.1.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -52,6 +52,8 @@ Mapnya is an extension library for map visualization.
 See [this notebook](http://nbviewer.ipython.org/github/domitry/nyaplot/blob/master/examples/notebook/Mapnya.ipynb) to learn more.
 
 ## Installation
+### Install nyaplot
+<!--
 ### Build and install nyaplot
 This gem is still under development and is not registered to RubyGems.org. Therefore clone this repository and build gem by yourself to try it.
 
@@ -64,9 +66,8 @@ And then build and install using gem command:
     cd nyaplot
     gem build nyaplot.gemspec
     gem install nyaplot-0.0.1.gem
+-->
 
-
-<!--
 Add this line to your application's Gemfile:
 
     gem 'nyaplot'
@@ -78,16 +79,31 @@ And then execute:
 Or install it yourself as:
 
     $ gem install nyaplot
--->
+
 
 ### Install IRuby notebook
 Nyaplot do not have any dependency, but we strongly recommend to install [IRuby](https://github.com/minad/iruby) by @minad at the same time.
 IRuby is a web-based interactive Ruby environment and Nyaplot is totally designed to work with it.
 You can install the gem itself by running `gem install` command, but it has some dependent libraries outside of Ruby-ecosystem.
 
-#### Ubuntu 14.04
+#### Ubuntu 14.10
+
+There are various ways to install Python and IPython notebook, but [Anaconda](https://store.continuum.io/cshop/anaconda/) is highly recommended.
+
+IRuby requires IPython >= 1.1 and libzmq >= 3.2, so update IPython and install libzmq3 before installing IRuby.
 
-Coming soon.
+```shell
+conda update ipython
+sudo apt-get install libzmq3-dev
+```
+And then try to run `gem install iruby`.
+
+If the code above does not work, try below.
+
+```shell
+conda update zeromq
+conda update pyzmq
+```
 
 #### Mac OS X
 
@@ -102,7 +118,18 @@ brew install zeromq
 
 #### Windows
 
-We have not try that yet. Please send pull-request if you can install it to Windows.
+First, install IPython and its dependencies using [Enthought Canopy](https://www.enthought.com/). There are various ways to install IPython, but Canopy may be the most useful to Windows users.
+
+Then install IRuby by running `gem install iruby`.
+
+After that, install ZeroMQ from [here](http://zeromq.org/area:download). Be sure to install stable release of the version **3.2.?**.  
+**Attention: install 32bit version of Zeromq even if your Windows is built for 64-bit.**
+
+Add the path to the directory of ZeroMQ binaries (Maybe the path is `Program Files (x86)/ZeroMQ 3.2.4/bin`) to environment variables `PATH`.
+
+Then rename `libzmq-v100-mt-3_2_4.dll` to `libzmq.dll`. It maybe in `Program Files (x86)/ZeroMQ 3.2.4/bin`.
+
+At last, pure IRuby do not work on Windows, so please apply [patches I sent before](https://github.com/minad/iruby/pull/30) to IRuby.
 
 ## Acknowledgments
 

data/examples/rb/3d.rb

@@ -0,0 +1,73 @@
+require 'nyaplot'
+require 'nyaplot3d'
+
+# Wireframe
+x=[];y=[];z=[]
+-10.step(10, 0.5) do |i|
+  -10.step(10, 0.5) do |j|
+    x.push(i)
+    y.push(j)
+    z.push(Math.sin(Math.sqrt(i*i+j*j))/Math.sqrt(i*i+j*j))
+  end
+end
+z.map!{|val| next (val.nan? ? 0 : val)} #(0,0) will be -inf
+
+plot = Nyaplot::Plot3D.new
+plot.add(:wireframe, x, y, z)
+plot.export_html("wireframe.html")
+
+# Surface
+plot = Nyaplot::Plot3D.new
+plot.add(:surface, x, y, z)
+plot.export_html("surface.html")
+
+# Line
+step_num = 10000;
+p = 10; r = 28; b = 8/3; dt = 0.01
+
+fx = Proc.new{|x,y,z| ((-1)*p*x + p*y)};
+fy = Proc.new{|x,y,z| ((-1)*x*z + r*x - y)};
+fz = Proc.new{|x,y,z| (x*y - b*z)};
+
+x_arr=[]; y_arr=[]; z_arr=[]
+x = 1; y = 1; z = 1
+step_num.times do |i|
+  x += dt * fx.call(x,y,z);
+  y += dt * fy.call(x,y,z);
+  z += dt * fz.call(x,y,z);
+  x_arr.push(x);
+  y_arr.push(y);
+  z_arr.push(z);
+end
+
+plot = Nyaplot::Plot3D.new
+plot.add(:line, x_arr, y_arr, z_arr)
+plot.export_html("3dline.html")
+
+# Scatter
+plot = Nyaplot::Plot3D.new
+colors = ['#8dd3c7', '#ffffb3', '#bebada', '#fb8072']
+['circle', 'rect', 'rect', 'diamond'].each do |shape|
+  x, y, z = [0,0,0].map{|d| next Array.new(20, rand*5).map{|v| next v+rand}}
+  sc = plot.add(:scatter, x, y, z)
+  sc.shape(shape)
+  sc.fill_color(colors.pop)
+end
+plot.export_html("3dscatter.html")
+
+# Particles
+plot = Nyaplot::Plot3D.new
+['#ff7f00','#1f78b4','#a6cee3'].each_with_index do |color, index|
+  x=[];y=[];z=[];dz = 5*rand
+  0.step(1, 0.2) do |i|
+    0.step(1, 0.2) do |j|
+      x.push(i+rand)
+      y.push(j+rand)
+      z.push(Math.sin(i)*Math.sin(j)+dz+rand)
+    end
+  end
+  p = plot.add(:particles, x, y, z)
+  p.color(color)
+  p.name('molecules')
+end
+plot.export_html("particles.html")

data/examples/rb/basic.rb

@@ -0,0 +1,74 @@
+require 'nyaplot'
+
+# Bar chart
+plot = Nyaplot::Plot.new
+plot.add(:bar, ['Persian', 'Maine Coon', 'American Shorthair'], [10,20,30])
+plot.x_label("Species")
+plot.y_label("Number")
+plot.export_html("bar.html")
+
+# Line chart
+x = []; y = []; theta = 0.6; a=1
+while theta < 14*Math::PI do
+  x.push(a*Math::cos(theta)/theta)
+  y.push(a*Math::sin(theta)/theta)
+  theta += 0.1
+end
+plot1 = Nyaplot::Plot.new
+plot1.add(:line, x, y)
+plot1.export_html("line.html")
+
+# Scatter + Line
+sc_y=[]; line_x=sc_x=[]; line_y=[]; a=0.5; b=3; noise=1.5; x=0
+rnd = Random.new
+while x<10
+  line_x.push(x)
+  line_y.push(a*x+b)
+  sc_y.push(a*x+b+noise*(rnd.rand-0.5))
+  x=(x+0.5).round(1)
+end
+plot2 = Nyaplot::Plot.new
+sc = plot2.add(:scatter, sc_x, sc_y)
+line = plot2.add(:line, line_x, line_y)
+sc.color('#000')
+sc.title('point')
+line.title('line')
+plot2.legend(true)
+plot2.export_html("scatter_line.html")
+
+# Histogram
+arr=[]
+1000.times {|i| arr.push((Float(i-500)/1000)**2)}
+print arr.to_s
+plot3 = Nyaplot::Plot.new
+plot3.add(:histogram, arr)
+plot3.yrange([0,250])
+plot3.export_html("histogram.html")
+
+# Box plot
+arr2 = arr.map{|val| val/0.8-2}
+arr3 = arr.map{|val| val*1.1+0.3}
+arr4 = arr.map{|val| val*1.3+0.3}
+plot4 = Nyaplot::Plot.new
+plot4.add(:box, arr, arr2, arr3, arr4)
+plot4.export_html("box.html")
+
+# 2D- Histogram
+x=[]; y=[]; fill=[]
+-5.step(5, 0.2) do |i|
+  -5.step(5, 0.2) do |j|
+    x.push(i)
+    y.push(j)
+    val = Math.sin(Math.sqrt(i*i+j*j))/Math.sqrt(i*i+j*j)
+    fill.push((val.nan? ? 0 : val))
+  end
+end
+
+plot5 = Nyaplot::Plot.new
+hm = plot5.add(:heatmap, x, y, fill)
+hm.stroke_color("#fff")
+hm.stroke_width("0")
+hm.width(0.2)
+hm.height(0.2)
+plot5.legend(true)
+plot5.export_html("heatmap.html")

data/examples/rb/bio.rb

@@ -0,0 +1,59 @@
+require 'nyaplot'
+require 'bionya'
+
+arr = []
+10.times do |i|
+  arr.push({group: 'group' + i.to_s ,df: Nyaplot::DataFrame.new({axis: ['a', 'b', 'c'], val: [2, 3, 4]})})
+end
+df = Nyaplot::DataFrame.new(arr)
+
+plot = Nyaplot::CircularPlot.new(df, :group, :df)
+plot.add(1, :arc, :axis, :val)
+plot.export_html("example_bionya.html")
+
+df = Nyaplot::DataFrame.from_csv(File.expand_path('../../notebook/data/circular/category.csv',__FILE__))
+df2 = Nyaplot::DataFrame.from_csv(File.expand_path('../../notebook/data/circular/hgmd.tsv', __FILE__), {col_sep: "\t"})
+df3 = Nyaplot::DataFrame.from_csv(File.expand_path('../../notebook/data/circular/genes_hgmd.tsv', __FILE__), {col_sep: "\t"})
+
+hash2 = {}
+df3.each_row do |row|
+  chr_name = "chr" + row[:gene_name].match(/hs(.+)/)[1]
+  hash2[chr_name] ||= []
+  hash2[chr_name].push({locale: row[:start], name: row[:name]})
+end
+
+hash = {}
+df2.each_row do |row|
+  chr_name = "chr" + row[:gene_name].match(/hs(.+)/)[1]
+  hash[chr_name] ||= []
+  hash[chr_name].push({start: row[:start], val: row[:num2]})
+end
+
+bin_size = df.size.max/50
+chr_name = df.column(:name).to_a
+nested = df.column(:size).to_a.map.with_index do |size, i|
+  vals = hash[chr_name[i]]
+  names = hash2[chr_name[i]]
+  vals = [] if vals.nil?
+  names = [] if names.nil?
+  raw = Array.new(size/bin_size, 0).map.with_index {|val, i|
+    val = vals.reduce(0){|memo, v| next memo + v[:val] if v[:start] > i*bin_size && v[:start] < (i+1)*bin_size; memo}
+    name = names.select {|name| name[:locale] > i*bin_size && name[:locale] < (i+1)*bin_size}
+    {axis: i*bin_size, val: val, name: (name.length==0 ? '' : name[0][:name])}
+  }
+  Nyaplot::DataFrame.new(raw)
+end
+df.df = nested
+
+df.name = df.column(:name).to_a.map{|name| name.match(/chr(.+)/)[1]}
+color = Nyaplot::Colors.qual
+
+plot2 = Nyaplot::CircularPlot.new(df, :name, :df)
+arc = plot2.add(1, :arc, :axis, :val)
+arc.color(["rgb(56,108,176)"])
+labels = plot2.add(2, :labels, :axis, :name)
+labels.text_size("0.3em")
+plot2.color(color)
+plot2.text_size("0.5em")
+plot2.text_color("#000")
+plot2.export_html("mutations.html")

data/examples/rb/maps.rb

@@ -0,0 +1,29 @@
+require 'nyaplot'
+require 'mapnya'
+
+raw_df = Nyaplot::Countries.df
+
+hash = [:name, :lat, :lng, :area, :capital].map{|label| {label => raw_df.column(label).to_a}}.reduce({}){|memo, hash| memo.merge(hash)}
+df = Nyaplot::DataFrame.new(hash)
+
+color = Nyaplot::Colors.Reds
+
+plot = Nyaplot::MapPlot.new
+sc = plot.add_with_df(df, :scatter, :lng, :lat) # x->:lng, y->lat
+sc.configure do
+  tooltip_contents([:capital, :name, :area])
+  color(color)
+  size([10, 100000])
+  size_by(:area)
+  fill_by(:area)
+end
+plot.export_html("scatter_on_the_map.html")
+
+plot = Nyaplot::MapPlot.new
+plot.add_map("AUS")
+plot.scale(800)
+plot.export_html("australia.html")
+
+plot.add_map("JPN")
+plot.export_html("japan.html")
+

data/examples/rb/multiple.rb

@@ -0,0 +1,29 @@
+require 'nyaplot'
+
+path = File.expand_path("../../notebook/data/first.tab", __FILE__)
+df = Nyaplot::DataFrame.from_csv(path, sep="\t")
+df.filter! {|row| row[:set1] != 0.0}
+
+plot4=Nyaplot::Plot.new
+plot4.add_with_df(df, :histogram, :set1)
+plot4.configure do
+  height(400)
+  x_label('PNR')
+  y_label('Frequency')
+  filter({target:'x'})
+  yrange([0,130])
+end
+
+plot5=Nyaplot::Plot.new
+plot5.add_with_df(df, :bar, :mutation)
+plot5.configure do
+  height(400)
+  x_label('Mutation types')
+  y_label('Frequency')
+  yrange([0,100])
+end
+
+frame = Nyaplot::Frame.new
+frame.add(plot4)
+frame.add(plot5)
+frame.export_html("multiple_pane.html")

data/examples/rb/scatter.rb

@@ -0,0 +1,26 @@
+require 'nyaplot'
+
+samples = Array.new(10).map.with_index{|d,i| 'cat'+i.to_s}
+address = ['London', 'Kyoto', 'Los Angeles', 'Puretoria']
+x=[];y=[];home=[]
+
+10.times do
+  x.push(5*rand)
+  y.push(5*rand)
+  home.push(address.clone.sample)
+end
+df = Nyaplot::DataFrame.new({x: x,y: y,name: samples, home: home})
+
+plot = Nyaplot::Plot.new
+plot.x_label("weight [kg]")
+plot.y_label("height [m]")
+
+color = Nyaplot::Colors.qual
+
+sc = plot.add_with_df(df, :scatter, :x, :y)
+sc.tooltip_contents([:name, :home])
+sc.fill_by(:home)
+sc.shape_by(:home)
+sc.color(color)
+
+plot.export_html("scatter.html")

data/examples/rb/wind.rb

@@ -0,0 +1,20 @@
+require 'nyaplot'
+require 'mapnya'
+
+path = File.expand_path("../../notebook/data/wind.csv", __FILE__)
+abs = []
+df = Nyaplot::DataFrame.from_csv(path)
+df.filter!{|row| !(row[:lon] < 200 && row[:lon] > 175)}
+df.each_row{|row| row[:uwnd] = row[:uwnd]/3; row[:vwnd] = row[:vwnd]/3}
+df.each_row{|row| abs.push(Math.sqrt(row[:uwnd]*row[:uwnd]+row[:vwnd]*row[:vwnd]))}
+df.abs = abs
+
+plot = Nyaplot::MapPlot.new
+vectors = plot.add_with_df(df, :vectors, :lon, :lat)
+vectors.dx(:uwnd)
+vectors.dy(:vwnd)
+vectors.fill_by(:abs)
+
+color = Nyaplot::Colors.OrRd(3)
+vectors.color(color)
+plot.export_html("wind_vectors.html")

data/lib/nyaplot/core.rb

@@ -26,13 +26,19 @@ module Nyaplot
     @@additional_libraries[name]=url
   end
 
-  # Enable to show plots on IRuby notebook
-  def self.init_iruby
+  # generate initializing code
+  def self.generate_init_code
     path = File.expand_path("../templates/init.js.erb", __FILE__)
     template = File.read(path)
     dep_libraries = @@dep_libraries
     additional_libraries = @@additional_libraries
     js = ERB.new(template).result(binding)
+    js
+  end
+
+  # Enable to show plots on IRuby notebook
+  def self.init_iruby
+    js = self.generate_init_code
     IRuby.display(IRuby.javascript(js))
   end
 

data/lib/nyaplot/data.rb

@@ -135,9 +135,13 @@ module Nyaplot
     end
 
     def to_html(threshold = 15)
-      html = '<table><tr>'
-      @rows[0].each {|key, val| html.concat('<th>' + key.to_s + '</th>')}
-      html += '</tr>'
+      html = '<table>'
+
+      unless @rows[0].nil?
+        html += '<tr>'
+        @rows[0].each {|key, val| html.concat('<th>' + key.to_s + '</th>')}
+        html += '</tr>'
+      end
 
       @rows.each_with_index do |row, i|
         next if i > threshold && i < @rows.length-1

data/lib/nyaplot/frame.rb

@@ -26,23 +26,36 @@ module Nyaplot
       panes.push(plot)
     end
 
-    # export static html file
+    # generate html code for <body> tag
+    def generate_body
+      path = File.expand_path("../templates/iruby.erb", __FILE__)
+      template = File.read(path)
+      id = SecureRandom.uuid()
+      model = self.to_json
+      ERB.new(template).result(binding)
+    end
+
+    # generate static html file
     # @return [String] generated html
-    def export_html
+    def generate_html
+      body = generate_body
+      init = Nyaplot.generate_init_code
       path = File.expand_path("../templates/static_html.erb", __FILE__)
       template = File.read(path)
-      model = self.to_json
-      html = ERB.new(template).result(binding)
-      html
+      ERB.new(template).result(binding)
+    end
+
+    # export static html file
+    def export_html(path="./plot.html")
+      path = File.expand_path(path, Dir::pwd)
+      str = generate_html
+      File.write(path, str)
     end
 
     # show plot automatically on IRuby notebook
     def to_iruby
-      path = File.expand_path("../templates/iruby.erb", __FILE__)
-      template = File.read(path)
-      id = SecureRandom.uuid()
-      model = self.to_json
-      ['text/html', ERB.new(template).result(binding)]
+      html = generate_body
+      ['text/html', html]
     end
 
     # show plot on IRuby notebook

data/lib/nyaplot/plot.rb

@@ -82,6 +82,13 @@ module Nyaplot
       Frame.new.tap {|f| f.add(self) }.show
     end
 
+    # export html file
+    def export_html(path=nil)
+      require 'securerandom'
+      path = "./plot-" + SecureRandom.uuid().to_s + ".html" if path.nil?
+      Frame.new.tap {|f| f.add(self) }.export_html(path)
+    end
+
     # @return [Array<String>] names of dataframe used by diagrams belog to this plot
     def df_list
       arr=[]
@@ -92,6 +99,7 @@ module Nyaplot
 
     def before_to_json
       diagrams = get_property(:diagrams)
+      return if diagrams.length == 0
 
       # set default values when not specified by users
       zoom(true) if diagrams.all?{|d| d.zoom?}

data/lib/nyaplot/templates/static_html.erb

@@ -1,14 +1,8 @@
 <html lang='en'>
 <head>
   <title>Nyaplot</title>
-  <script src='http://d3js.org/d3.v3.min.js'></script>
-  <script src='https://rawgit.com/domitry/Nyaplotjs/master/release/nyaplot.js'></script>
+  <script src="http://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.14/require.min.js"></script>
+  <script><%= init %></script>
 </head>
-<body>
-<div id='vis'></div>
-<script>
-model = <%= model %>
-window.onload = function(){Nyaplot.core.parse(model, '#vis');};
-</script>
-</body>
+<body><%= body %></body>
 </html>

data/lib/nyaplot/version.rb

@@ -1,3 +1,3 @@
 module Nyaplot
-  VERSION = "0.1.0"
+  VERSION = "0.1.1"
 end

data/lib/nyaplot3d/plot3d.rb

@@ -43,9 +43,19 @@ module Nyaplot
 
     # Show plot on IRuby notebook
     def show
-      frame = Frame.new
-      frame.add(self)
-      frame.show
+      Frame.new.tap {|f| f.add(self) }.show
+    end
+
+    # Show plot automatically on IRuby notebook
+    def to_iruby
+      Frame.new.tap {|f| f.add(self) }.to_iruby
+    end
+
+    # export html file
+    def export_html(path=nil)
+      require 'securerandom'
+      path = "./plot-" + SecureRandom.uuid().to_s + ".html" if path.nil?
+      Frame.new.tap {|f| f.add(self) }.export_html(path)
     end
 
     # @return [Array<String>] names of dataframe used by diagrams belog to this plot

data/nyaplot.gemspec

@@ -9,7 +9,7 @@ Gem::Specification.new do |spec|
   spec.authors       = ["Naoki Nishida"]
   spec.email         = ["domitry@gmail.com"]
   spec.summary       = %q{interactive plots generator for Ruby users}
-  spec.description   = %q{To get information about Nyaplot, visit the website or mailing-list of SciRuby, or ask me on GitHub.}
+  spec.description   = %q{interactive plots generator for Ruby users. Visit the GitHub repository to get more information.}
   spec.homepage      = "https://www.github.com/domitry/nyaplot"
   spec.license       = "MIT"
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: nyaplot
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
 platform: ruby
 authors:
 - Naoki Nishida
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-19 00:00:00.000000000 Z
+date: 2014-08-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -66,8 +66,8 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description: To get information about Nyaplot, visit the website or mailing-list of
-  SciRuby, or ask me on GitHub.
+description: interactive plots generator for Ruby users. Visit the GitHub repository
+  to get more information.
 email:
 - domitry@gmail.com
 executables: []
@@ -104,6 +104,13 @@ files:
 - examples/notebook/data/operon.csv
 - examples/notebook/data/ttest.csv
 - examples/notebook/data/wind.csv
+- examples/rb/3d.rb
+- examples/rb/basic.rb
+- examples/rb/bio.rb
+- examples/rb/maps.rb
+- examples/rb/multiple.rb
+- examples/rb/scatter.rb
+- examples/rb/wind.rb
 - lib/bionya.rb
 - lib/bionya/README.md
 - lib/bionya/core.rb