iroki 0.0.8 → 0.0.9

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 1d1d3db465f5741256f6937a8884f0d4e95a6b56
+  metadata.gz: 4e8e1eeaa50a23a42dd81714d8d5301c3acc1fd5
+  data.tar.gz: 150d12ff4ba7d6a6b34643fba5da48b48535ae0e
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+  data.tar.gz: 2877db8a1435c34ad939cda11130858445ba012ed235c0a61e1c9b413a133b7f78890c72c573704a1119fb945590aa59a04c3985069d50e939916d963fb880cc

data/README.md

@@ -104,3 +104,12 @@ Add branch length and bootstraps to `newick_to_phyloxml`.
 ### 0.0.7 ###
 
 Add `reorder_nodes` script.
+
+### 0.0.8 ###
+
+- Add auto coloring with Kelly theme
+- Add ability to color branches and labels separately
+
+### 0.0.9 ###
+
+- Add single sample color gradients (one and two color)

data/lib/iroki.rb

@@ -18,9 +18,16 @@
 
 require "abort_if"
 
+require "iroki/biom"
 require "iroki/version"
+
 require "iroki/const/const"
+
 require "iroki/color/color"
+require "iroki/color/gradient"
+require "iroki/color/single_sample_gradient"
+require "iroki/color/palette/palette"
+
 require "iroki/core_ext/hash/hash"
 require "iroki/core_ext/string/string"
 require "iroki/core_ext/file/file"

data/lib/iroki/biom.rb

@@ -0,0 +1,56 @@
+# 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
+  class Biom < File
+    def parse_single_sample
+      samples = []
+      counts  = []
+
+      self.each_line do |line|
+        unless line.start_with? "#"
+          sample, count = 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
+        end
+      end
+
+      [samples, counts_group1, counts_group2]
+    end
+  end
+end

data/lib/iroki/color/color.rb

@@ -16,67 +16,30 @@
 # You should have received a copy of the GNU General Public License
 # along with Iroki.  If not, see <http://www.gnu.org/licenses/>.
 
+require "color"
+
 module Iroki
   module Color
-    module Palette
-      # BASIC =
-      #   { "1" => "#FF3814",   # red
-      #     "2" => "#712BFF",   # blue
-      #     "3" => "#FFDF14",   # yellow
-      #     "4" => "#14FF63", } # green
-
-      # BASIC_LIGHT =
-      #   { "1" => "#FF8872",
-      #     "2" => "#A97FFE",
-      #     "3" => "#FFEC72",
-      #     "4" => "#71FEA1", }
+    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
 
-      # BASIC_DARK =
-      #   { "1" => "#FF2800",
-      #     "2" => "#4901DD",
-      #     "3" => "#FFDD00",
-      #     "4" => "#00E24D", }
 
-      # FUNKY =
-      #   { "1" => "#FF7314",
-      #     "2" => "#9F23FF",
-      #     "3" => "#FFF814",
-      #     "4" => "#14FFD8", }
 
-      # FUNKY_LIGHT =
-      #   { "1" => "#FFAB72",
-      #     "2" => "#C57AFE",
-      #     "3" => "#FFFB72",
-      #     "4" => "#71FEE6", }
+    GREEN = Object::Color::HSL.from_fraction GREEN_HUE,
+                                             FULLY_SATURATED,
+                                             PURE_COLOR
 
-      # FUNKY_DARK =
-      #   { "1" => "#FF6700",
-      #     "2" => "#7C01DC",
-      #     "3" => "#FFF700",
-      #     "4" => "#00D7B3", }
+    BLUE = Object::Color::HSL.from_fraction BLUE_HUE,
+                                            FULLY_SATURATED,
+                                            PURE_COLOR
 
-      KELLY = {
-        "1"  => { name: "purple",          hex: "#875692" },
-        "2"  => { name: "orange",          hex: "#F38400" },
-        "3"  => { name: "light_blue",      hex: "#A1CAF1" },
-        "4"  => { name: "red",             hex: "#BE0032" },
-        "5"  => { name: "buff",            hex: "#C2B280" },
-        "6"  => { name: "grey",            hex: "#848482" },
-        "7"  => { name: "green",           hex: "#008856" },
-        "8"  => { name: "purplish_pink",   hex: "#E68FAC" },
-        "9"  => { name: "blue",            hex: "#0067A5" },
-        "10" => { name: "yellowish_pink",  hex: "#F99379" },
-        "11" => { name: "violet",          hex: "#604E97" },
-        "12" => { name: "orange_yellow",   hex: "#F6A600" },
-        "13" => { name: "purplish_red",    hex: "#B3446C" },
-        "14" => { name: "reddish_brown",   hex: "#882D17" },
-        "15" => { name: "yellow_green",    hex: "#8DB600" },
-        "16" => { name: "yellowish_brown", hex: "#654522" },
-        "17" => { name: "reddish_orange",  hex: "#E25822" },
-        "18" => { name: "olive_green",     hex: "#2B3D26" },
-        "19" => { name: "yellow",          hex: "#F3C300" },
-      }
-    end
+    WHITE = Object::Color::HSL.from_fraction WHITE_HUE,
+                                             FULLY_SATURATED,
+                                             PURE_LIGHT
 
     def self.get_tag str, palette=nil
       if str.hex?
@@ -89,7 +52,7 @@ module Iroki
     def self.tag_from_hex hex
       assert hex.hex?, "'#{hex}' was not a valid hex code"
 
-      %Q{[&!color="#{hex}"]}
+      %Q{[&!color="#{hex.upcase}"]}
     end
 
     def self.tag_from_color color, palette=nil
@@ -110,7 +73,7 @@ module Iroki
         hex = colors["black"]
       end
 
-      %Q{[&!color="#{hex}"]}
+      %Q{[&!color="#{hex.upcase}"]}
     end
 
     COLORS = {
@@ -773,6 +736,6 @@ module Iroki
       "yellowgreen" => "#9ACD32",
     }
 
-
+    DARK_GREEN = Object::Color::RGB.by_hex(COLORS["darkgreen"])
   end
 end

data/lib/iroki/color/gradient.rb

@@ -0,0 +1,45 @@
+# 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 Gradient
+      attr_accessor :samples, :color_hex_codes, :lumins
+
+      # 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
+        ((((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
+        (new_max - ((((new_max - new_min) * (x - old_min.to_f)) / (old_max - old_min)) + new_min)) + new_min
+      end
+
+      def patterns
+        hash = {}
+        @samples.zip(@color_hex_codes).each do |(sample, hexcode)|
+          tag = Iroki::Color.get_tag hexcode
+          hash[sample] = { label: tag, branch: tag }
+        end
+
+        hash
+      end
+    end
+  end
+end

data/lib/iroki/color/palette/palette.rb

@@ -0,0 +1,39 @@
+module Iroki
+  module Color
+    module Palette
+      # BASIC =
+      #   { "1" => "#FF3814",   # red
+      #     "2" => "#712BFF",   # blue
+      #     "3" => "#FFDF14",   # yellow
+      #     "4" => "#14FF63", } # green
+
+      # FUNKY =
+      #   { "1" => "#FF7314",
+      #     "2" => "#9F23FF",
+      #     "3" => "#FFF814",
+      #     "4" => "#14FFD8", }
+
+      KELLY = {
+        "1"  => { name: "purple",          hex: "#875692" },
+        "2"  => { name: "orange",          hex: "#F38400" },
+        "3"  => { name: "light_blue",      hex: "#A1CAF1" },
+        "4"  => { name: "red",             hex: "#BE0032" },
+        "5"  => { name: "buff",            hex: "#C2B280" },
+        "6"  => { name: "grey",            hex: "#848482" },
+        "7"  => { name: "green",           hex: "#008856" },
+        "8"  => { name: "purplish_pink",   hex: "#E68FAC" },
+        "9"  => { name: "blue",            hex: "#0067A5" },
+        "10" => { name: "yellowish_pink",  hex: "#F99379" },
+        "11" => { name: "violet",          hex: "#604E97" },
+        "12" => { name: "orange_yellow",   hex: "#F6A600" },
+        "13" => { name: "purplish_red",    hex: "#B3446C" },
+        "14" => { name: "reddish_brown",   hex: "#882D17" },
+        "15" => { name: "yellow_green",    hex: "#8DB600" },
+        "16" => { name: "yellowish_brown", hex: "#654522" },
+        "17" => { name: "reddish_orange",  hex: "#E25822" },
+        "18" => { name: "olive_green",     hex: "#2B3D26" },
+        "19" => { name: "yellow",          hex: "#F3C300" },
+      }
+    end
+  end
+end

data/lib/iroki/color/single_sample_gradient.rb

@@ -0,0 +1,80 @@
+# 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 SingleSampleGradient < Gradient
+      attr_accessor :counts, :rel_abunds, :single_color
+
+      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
+
+        if @single_color
+          @color_hex_codes = single_color_gradient_hex_codes
+        else
+          @color_hex_codes = two_color_gradient_hex_codes
+        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]
+
+          col =
+            Iroki::Color::GREEN.mix_with Iroki::Color::BLUE, rel_abund
+
+          col.luminosity = lumin
+
+          col.html
+        end
+      end
+
+      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
+
+          col =
+            Iroki::Color::DARK_GREEN.lighten_by amt_of_orig_color
+
+          col.html
+        end
+      end
+    end
+  end
+end

data/lib/iroki/main/main.rb

@@ -18,6 +18,7 @@
 
 require "bio"
 require "set"
+require "trollop"
 
 module Iroki
   module Main
@@ -26,6 +27,8 @@ module Iroki
                   exact: nil,
                   remove_bootstraps_below: nil,
                   color_map_f: nil,
+                  biom_f: nil,
+                  single_color: nil,
                   name_map_f: nil,
                   auto_color: nil,
                   display_auto_color_options: nil,
@@ -33,19 +36,15 @@ module Iroki
                   out_f: nil)
 
       if display_auto_color_options
-        puts "\n  Choices for --auto-color ..."
-        print "    - kelly: up to 19 high contrast colors (purple, orange, light blue, red, ...)\n\n"
+        STDERR.puts "\n  Choices for --auto-color ..."
+        STDERR.print "    - kelly: up to 19 high contrast colors (purple, orange, light blue, red, ...)\n\n"
         exit
       end
 
       auto_color_options = ["kelly"]
 
-      if !auto_color.nil? && !auto_color_options.include?(auto_color)
-        puts "\n  Choices for --auto-color ..."
-        print "    - kelly: up to 19 high contrast colors (purple, orange, light blue, red, ...)\n\n"
-
-        Trollop.die :auto_color, "#{auto_color} is not a valid option"
-      end
+      abort_if !auto_color.nil? && !auto_color_options.include?(auto_color),
+               "'#{auto_color}' is not a valid option. Try iroki --help for help."
 
       case auto_color
       when nil
@@ -54,10 +53,13 @@ module Iroki
         auto_color_hash = Iroki::Color::Palette::KELLY
       end
 
+      abort_if biom_f && color_map_f,
+               "--color-map and --biom-file cannot both be specified. Try iroki --help for help."
+
       newick = check_file newick_f, :newick
 
       color_f = nil
-      if color_taxa_names || color_branches
+      if !biom_f && (color_taxa_names || color_branches)
         color_f = check_file color_map_f, :color_map_f
       end
 
@@ -74,6 +76,9 @@ module Iroki
         patterns = parse_color_map color_f,
                                    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
       end
 
       treeio = Bio::FlatFile.open(Bio::Newick, newick)

data/lib/iroki/version.rb

@@ -18,7 +18,7 @@
 
 # Library metadata
 module Iroki
-  VERSION = "0.0.8"
+  VERSION = "0.0.9"
   COPYRIGHT = "2015 - 2016 Ryan Moore"
   CONTACT   = "moorer@udel.edu"
   WEBSITE   = "https://github.com/mooreryan/iroki"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: iroki
 version: !ruby/object:Gem::Version
-  version: 0.0.8
+  version: 0.0.9
 platform: ruby
 authors:
 - Ryan Moore
@@ -194,7 +194,11 @@ files:
 - exe/reorder_nodes
 - iroki.gemspec
 - lib/iroki.rb
+- lib/iroki/biom.rb
 - 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/const/const.rb
 - lib/iroki/core_ext/file/file.rb
 - lib/iroki/core_ext/hash/hash.rb