iroki 0.0.10 → 0.0.11

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -12,3 +12,4 @@
 newicks
 test_files
 sandbox
+.coveralls.yml

data/README.md

@@ -1,3 +1,5 @@
+[![Iroki](https://github.com/mooreryan/iroki/blob/master/assets/images/iroki_logo2.png)](https://github.com/mooreryan/iroki/blob/master/assets/images/iroki_logo2.png)
+
 # Iroki #
 
 [![Gem Version](https://badge.fury.io/rb/iroki.svg)](https://badge.fury.io/rb/iroki) [![Build Status](https://travis-ci.org/mooreryan/iroki.svg?branch=master)](https://travis-ci.org/mooreryan/iroki) [![Coverage Status](https://coveralls.io/repos/github/mooreryan/iroki/badge.svg?branch=master)](https://coveralls.io/github/mooreryan/iroki?branch=master)
@@ -117,3 +119,7 @@ Add `reorder_nodes` script.
 ### 0.0.10 ###
 
 - Fix Jess's bug
+
+### 0.0.11 ###
+
+- Add two color, two group color gradients from biom files

data/assets/images/iroki_logo2.svg

@@ -0,0 +1,70 @@
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+    </g>
+  </g>
+  <g id="since_2015">
+    <g>
+      <text transform="matrix(1, 0, -0, 1, 709, 732.145)">
+        <tspan x="-54.78" y="-5.5" font-family="HelveticaNeue-Thin" font-size="15" fill="#000000">Phylogenetic Tree </tspan>
+        <tspan x="-34.912" y="12.5" font-family="HelveticaNeue-Thin" font-size="15" fill="#000000">Customizer</tspan>
+      </text>
+      <path d="M634,703 L784,703" fill-opacity="0" stroke="#000000" stroke-width="1.5"/>
+      <text transform="matrix(1, 0, 0, 1, 709, 672.5)">
+        <tspan x="-35.52" y="16.5" font-family="HelveticaNeue-UltraLight" font-size="48" fill="#000000">Iroki</tspan>
+      </text>
+    </g>
+  </g>
+</svg>

data/exe/iroki

@@ -44,14 +44,22 @@ opts = Trollop.options do
   opt(:exact,
       "Exact pattern matching")
 
-  opt(:remove_bootstraps_below,
-      "Remove bootstrap values below given value",
-      type: :float)
+  # opt(:remove_bootstraps_below,
+  #     "Remove bootstrap values below given value",
+  #     type: :float)
 
   opt(:color_map,
       "File with color mappings",
       type: :string)
 
+  opt(:biom,
+      "Biom file to make color gradient",
+      type: :string)
+
+  opt(:single_color,
+      "Use single color gradient for single group biom files",
+      type: :string)
+
   opt(:name_map,
       "File with name mappings",
       type: :string)
@@ -78,6 +86,8 @@ Iroki::Main.main(
   exact:                      opts[:exact],
   remove_bootstraps_below:    opts[:remove_bootstraps_below],
   color_map_f:                opts[:color_map],
+  biom_f:                     opts[:biom],
+  single_color:               opts[:single_color],
   name_map_f:                 opts[:name_map],
   auto_color:                 opts[:auto_color],
   display_auto_color_options: opts[:display_auto_color_options],

data/lib/iroki.rb

@@ -25,7 +25,8 @@ require "iroki/const/const"
 
 require "iroki/color/color"
 require "iroki/color/gradient"
-require "iroki/color/single_sample_gradient"
+require "iroki/color/single_group_gradient"
+require "iroki/color/two_group_gradient"
 require "iroki/color/palette/palette"
 
 require "iroki/core_ext/hash/hash"

data/lib/iroki/biom.rb

@@ -18,39 +18,28 @@
 
 module Iroki
   class Biom < File
-    def parse_single_sample
+    attr_accessor :single_group
+
+    def parse
       samples = []
       counts  = []
 
       self.each_line do |line|
         unless line.start_with? "#"
-          sample, count = line.chomp.split "\t"
+          sample, *the_counts = line.chomp.split "\t"
 
           samples << sample
-          counts << count.to_f
-        end
-      end
-
-      [samples, counts]
-    end
-
 
-    def parse_two_sample
-      samples = []
-      counts_group1  = []
-      counts_group2  = []
-
-      self.each_line do |line|
-        unless line.start_with? "#"
-          sample, count1, count2 = line.chomp.split "\t"
-
-          samples << sample
-          counts_group1 << count1.to_f
-          counts_group2 << count2.to_f
+          if the_counts.length == 1
+            counts << the_counts.first.to_f
+            @single_group = true
+          else
+            counts << the_counts.map(&:to_f)
+          end
         end
       end
 
-      [samples, counts_group1, counts_group2]
+      [samples, counts, @single_group]
     end
   end
 end

data/lib/iroki/color/color.rb

@@ -20,61 +20,6 @@ require "color"
 
 module Iroki
   module Color
-    GREEN_HUE = 1 / 3.0
-    BLUE_HUE = 2 / 3.0
-    WHITE_HUE = 1.0
-    FULLY_SATURATED = 1
-    PURE_COLOR = 0.5
-    PURE_LIGHT = 1.0
-
-
-
-    GREEN = Object::Color::HSL.from_fraction GREEN_HUE,
-                                             FULLY_SATURATED,
-                                             PURE_COLOR
-
-    BLUE = Object::Color::HSL.from_fraction BLUE_HUE,
-                                            FULLY_SATURATED,
-                                            PURE_COLOR
-
-    WHITE = Object::Color::HSL.from_fraction WHITE_HUE,
-                                             FULLY_SATURATED,
-                                             PURE_LIGHT
-
-    def self.get_tag str, palette=nil
-      if str.hex?
-        self.tag_from_hex str
-      else
-        self.tag_from_color str, palette
-      end
-    end
-
-    def self.tag_from_hex hex
-      assert hex.hex?, "'#{hex}' was not a valid hex code"
-
-      %Q{[&!color="#{hex.upcase}"]}
-    end
-
-    def self.tag_from_color color, palette=nil
-      col = color.downcase.strip
-
-      if palette
-        hash =
-          Hash[palette.keys.zip palette.map(&:last).map{|h| h[:hex]}]
-        colors = COLORS.merge hash
-      else
-        colors = COLORS
-      end
-
-      if colors.has_key? col
-        hex = colors[col]
-      else
-        # if passed color other than one defined, return black
-        hex = colors["black"]
-      end
-
-      %Q{[&!color="#{hex.upcase}"]}
-    end
 
     COLORS = {
       "white" => "#FFFFFF",
@@ -736,6 +681,58 @@ module Iroki
       "yellowgreen" => "#9ACD32",
     }
 
-    DARK_GREEN = Object::Color::RGB.by_hex(COLORS["darkgreen"])
+    # TOP
+
+    GREEN_HUE = 1 / 3.0
+    BLUE_HUE = 2 / 3.0
+    WHITE_HUE = 1.0
+    FULLY_SATURATED = 1
+    PURE_COLOR = 0.5
+    PURE_LIGHT = 1.0
+
+    HSL = Object::Color::HSL
+    RGB = Object::Color::RGB
+
+    GREEN = HSL.from_fraction GREEN_HUE, FULLY_SATURATED, PURE_COLOR
+    BLUE  = HSL.from_fraction BLUE_HUE,  FULLY_SATURATED, PURE_COLOR
+    WHITE = HSL.from_fraction WHITE_HUE, FULLY_SATURATED, PURE_LIGHT
+
+    DARK_GREEN = RGB.by_hex(COLORS["darkgreen"])
+    GRAY =       RGB.by_hex(COLORS["gray"])
+
+    def self.get_tag str, palette=nil
+      if str.hex?
+        self.tag_from_hex str
+      else
+        self.tag_from_color str, palette
+      end
+    end
+
+    def self.tag_from_hex hex
+      assert hex.hex?, "'#{hex}' was not a valid hex code"
+
+      %Q{[&!color="#{hex.upcase}"]}
+    end
+
+    def self.tag_from_color color, palette=nil
+      col = color.downcase.strip
+
+      if palette
+        hash =
+          Hash[palette.keys.zip palette.map(&:last).map{|h| h[:hex]}]
+        colors = COLORS.merge hash
+      else
+        colors = COLORS
+      end
+
+      if colors.has_key? col
+        hex = colors[col]
+      else
+        # if passed color other than one defined, return black
+        hex = colors["black"]
+      end
+
+      %Q{[&!color="#{hex.upcase}"]}
+    end
   end
 end

data/lib/iroki/color/gradient.rb

@@ -19,15 +19,15 @@
 module Iroki
   module Color
     class Gradient
-      attr_accessor :samples, :color_hex_codes, :lumins
+      attr_accessor :samples, :color_hex_codes, :lumins, :single_color
 
-      # scales [min, max] to [A, B]
-      def self.scale x, new_min=0.05, new_max=0.9, old_min=0.0, old_max=1.0
+      # scales [old_min, old_max] to [new_min, new_max]
+      def scale x, new_min=0.05, new_max=0.9, old_min=0.0, old_max=1.0
         ((((new_max - new_min) * (x - old_min.to_f)) / (old_max - old_min)) + new_min)
       end
 
       # scales [old_min, old_max] to [new_max, new_min]
-      def self.scale_reverse x, new_min=0, new_max=0, old_min=0.0, old_max=1.0
+      def scale_reverse x, new_min=0.0, new_max=0.0, old_min=0.0, old_max=1.0
         (new_max - ((((new_max - new_min) * (x - old_min.to_f)) / (old_max - old_min)) + new_min)) + new_min
       end
 
@@ -40,6 +40,20 @@ module Iroki
 
         hash
       end
+
+      def counts_to_rabunds counts
+        max_count = counts.max.to_f
+
+        counts.map do |count|
+          count / max_count
+        end
+      end
+
+      def rabunds_to_lumins rabunds
+        rabunds.map do |count|
+          scale_reverse count, new_min=50, new_max=97
+        end
+      end
     end
   end
 end

data/lib/iroki/color/{single_sample_gradient.rb → single_group_gradient.rb}

@@ -18,15 +18,15 @@
 
 module Iroki
   module Color
-    class SingleSampleGradient < Gradient
-      attr_accessor :counts, :rel_abunds, :single_color
+    class SingleGroupGradient < Gradient
+      attr_accessor :counts, :rel_abunds
 
       def initialize samples, counts, single_color=false
         @single_color = single_color
         @samples = samples
         @counts = counts
-        @rel_abunds = counts_to_rel_abunds
-        @lumins = rel_abunds_to_lumins
+        @rel_abunds = counts_to_rabunds counts
+        @lumins = rabunds_to_lumins @rel_abunds
 
         if @single_color
           @color_hex_codes = single_color_gradient_hex_codes
@@ -35,22 +35,6 @@ module Iroki
         end
       end
 
-      private
-
-      def counts_to_rel_abunds
-        max_count = @counts.max.to_f
-
-        @counts.map do |count|
-          count / max_count
-        end
-      end
-
-      def rel_abunds_to_lumins
-        @rel_abunds.map do |count|
-          Gradient.scale_reverse count, new_min=50, new_max=97
-        end
-      end
-
       def two_color_gradient_hex_codes
         @rel_abunds.map.with_index do |rel_abund, idx|
           lumin = @lumins[idx]
@@ -67,7 +51,7 @@ module Iroki
       def single_color_gradient_hex_codes
         @rel_abunds.zip(@lumins).map do |rel_abund, lumin|
           amt_of_orig_color =
-            Gradient.scale rel_abund, new_min=10, new_max=95
+            scale rel_abund, new_min=10, new_max=95
 
           col =
             Iroki::Color::DARK_GREEN.lighten_by amt_of_orig_color

data/lib/iroki/color/two_group_gradient.rb

@@ -0,0 +1,81 @@
+# Copyright 2016 Ryan Moore
+# Contact: moorer@udel.edu
+#
+# This file is part of Iroki.
+#
+# Iroki is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Iroki is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Iroki.  If not, see <http://www.gnu.org/licenses/>.
+
+module Iroki
+  module Color
+    class TwoGroupGradient < Gradient
+      attr_accessor :g1_counts, :g2_counts, :g1_rabunds, :g2_rabunds
+
+      def initialize samples, g1_counts, g2_counts
+        assert(samples.count == g1_counts.count &&
+                     g1_counts.count == g2_counts.count,
+                     "Samples and counts are different lengths. " +
+                     "Check your biom file.")
+
+        @samples = samples
+        @g1_counts = g1_counts
+        @g2_counts = g2_counts
+        @g1_rabunds = counts_to_rabunds g1_counts
+        @g2_rabunds = counts_to_rabunds g2_counts
+        @color_hex_codes = calc_hex_codes @g1_rabunds, @g2_rabunds
+      end
+
+      def percent_of_group1_color ra1, ra2
+        if ra1 > ra2
+          1 - scale(ra2 / ra1, new_min=0.0, new_max=0.5, old_min=0.0, old_max=1.0)
+        elsif ra1 < ra2
+          scale(ra1 / ra2, new_min=0.0, new_max=0.5, old_min=0.0, old_max=1.0)
+        else
+          0.5
+        end
+      end
+
+      def mix_percent ra1, ra2
+        1 - percent_of_group1_color(ra1, ra2)
+      end
+
+      def lumin_level ra1, ra2
+        if ra1 > ra2
+          scale_reverse ra1, new_min=50, new_max=90, old_min=0.0, old_max=1.0
+        else
+          scale_reverse ra2, new_min=50, new_max=90, old_min=0.0, old_max=1.0
+        end
+      end
+
+      def hex_code ra1, ra2
+        perc = mix_percent ra1, ra2
+
+        col = Iroki::Color::GREEN.mix_with Iroki::Color::BLUE, perc
+
+        col.luminosity = lumin_level ra1, ra2
+
+        col.html
+      end
+
+      def calc_hex_codes g1_rabunds, g2_rabunds
+        g1_rabunds.zip(g2_rabunds).map do |ra1, ra2|
+          if ra1.zero? && ra2.zero?
+            Iroki::Color::GRAY.html
+          else
+            hex_code ra1, ra2
+          end
+        end
+      end
+    end
+  end
+end

data/lib/iroki/main/main.rb

@@ -77,8 +77,15 @@ module Iroki
                                    exact_matching: exact,
                                    auto_color: auto_color_hash
       else
-        samples, counts = Biom.open(biom_f).parse_single_sample
-        patterns = SingleSampleGradient.new(samples, counts, single_color).patterns
+        samples, counts, is_single_group = Biom.open(biom_f).parse
+
+        if is_single_group
+          patterns = SingleGroupGradient.new(samples, counts, single_color).patterns
+        else
+          g1_counts = counts.map(&:first)
+          g2_counts = counts.map(&:last)
+          patterns = TwoGroupGradient.new(samples, g1_counts, g2_counts).patterns
+        end
       end
 
       treeio = Bio::FlatFile.open(Bio::Newick, newick)

data/lib/iroki/version.rb

@@ -18,7 +18,7 @@
 
 # Library metadata
 module Iroki
-  VERSION = "0.0.10"
+  VERSION = "0.0.11"
   COPYRIGHT = "2015 - 2016 Ryan Moore"
   CONTACT   = "moorer@udel.edu"
   WEBSITE   = "https://github.com/mooreryan/iroki"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: iroki
 version: !ruby/object:Gem::Version
-  version: 0.0.10
+  version: 0.0.11
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-07-28 00:00:00.000000000 Z
+date: 2016-07-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -185,6 +185,9 @@ files:
 - Guardfile
 - README.md
 - Rakefile
+- assets/images/iroki_logo2.idraw
+- assets/images/iroki_logo2.png
+- assets/images/iroki_logo2.svg
 - bin/console
 - bin/iroki_docker
 - bin/setup
@@ -198,7 +201,8 @@ files:
 - lib/iroki/color/color.rb
 - lib/iroki/color/gradient.rb
 - lib/iroki/color/palette/palette.rb
-- lib/iroki/color/single_sample_gradient.rb
+- lib/iroki/color/single_group_gradient.rb
+- lib/iroki/color/two_group_gradient.rb
 - lib/iroki/const/const.rb
 - lib/iroki/core_ext/file/file.rb
 - lib/iroki/core_ext/hash/hash.rb