iroki 0.0.31 → 0.0.32

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: b751c71c6569e45169248b4590d971589f6b0547
-  data.tar.gz: f484b255f98acf4608afd6193ea201de8841039d
+  metadata.gz: 571e5fc652dc40cb60edcb05f06a2a7665b63174
+  data.tar.gz: 814c6974bead105ac50b176706af90360ed236b7
 SHA512:
-  metadata.gz: 6075a849a8b9af0c9faab51b47e7661116376171699dd143560659b9eb52bfd0b130c3cb48573bdc79a6075d311333447235796a9b06718db65c2b393897d89a
-  data.tar.gz: be579ec3a076408d1aaad3ae2edff537f1019ef72ebfed5db601cbe3c5badab93d6214fafc42daf37faf645b8bf09f079051c414387ec7ccb2a76406337e6070
+  metadata.gz: d8ef3ec139f50d020f063d9f226661a4684c5310a4997e223c45d771b330ea3d1e8131ca452f9aa0ffff9861d49f6c1dfc7e6b419bd41eaf9b2c4672cdc2f3bf
+  data.tar.gz: 57e478c4e164883104019233a5ec179f8e2c58df6890a03d95cb0e8120edef80ad3c4aa5a136da156bbe4f3579761243a9dcd12ffce5655fb47d62e1fba3fadc

data/exe/iroki

@@ -59,8 +59,7 @@ opts = Trollop.options do
       type: :string)
 
   opt(:single_color,
-      "Use single color gradient for single group biom files",
-      type: :string)
+      "Use single color gradient for single group biom files")
 
   opt(:name_map,
       "File with name mappings",
@@ -85,6 +84,17 @@ opts = Trollop.options do
       "Default color",
       type: :string,
       default: "black")
+
+    opt(:min_lumin,
+      "Min luminosity (only used for gradients)",
+      type: :int,
+      default: 35)
+
+    opt(:max_lumin,
+      "Max luminosity (only used for gradients)",
+      type: :int,
+      default: 70)
+
 end
 
 Iroki::Main.main(
@@ -100,5 +110,7 @@ Iroki::Main.main(
   display_auto_color_options: opts[:display_auto_color_options],
   newick_f:                   opts[:infile],
   out_f:                      opts[:outfile],
-  default_color:              opts[:default_color]
+  default_color:              opts[:default_color],
+  min_lumin:                  opts[:min_lumin],
+  max_lumin:                  opts[:max_lumin]
 )

data/lib/iroki/color/gradient.rb

@@ -19,16 +19,43 @@
 module Iroki
   module Color
     class Gradient
-      attr_accessor :samples, :color_hex_codes, :lumins, :single_color
+      attr_accessor :samples,
+                    :color_hex_codes,
+                    :lumins,
+                    :single_color,
+                    :min_lumin,
+                    :max_lumin
 
       # 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
+      def scale x,
+                new_min=0.05,
+                new_max=0.9,
+                old_min=0.0,
+                old_max=1.0
+
+        x = x.to_f
+        new_min = new_min.to_f
+        new_max = new_max.to_f
+        old_min = old_min.to_f
+        old_max = old_max.to_f
+
         ((((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 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
+      def scale_reverse x,
+                        new_min=0.0,
+                        new_max=0.0,
+                        old_min=0.0,
+                        old_max=1.0
+
+        x = x.to_f
+        new_min = new_min.to_f
+        new_max = new_max.to_f
+        old_min = old_min.to_f
+        old_max = old_max.to_f
+
+(new_max - ((((new_max - new_min) * (x - old_min.to_f)) / (old_max - old_min)) + new_min)) + new_min
       end
 
       def patterns
@@ -51,7 +78,10 @@ module Iroki
 
       def rabunds_to_lumins rabunds
         rabunds.map do |count|
-          scale_reverse count, new_min=50, new_max=97
+          # scale_reverse count, new_min=50, new_max=97
+          # scale_reverse count, new_min=35, new_max=85
+          scale_reverse count, new_min=@min_lumin, new_max=@max_lumin
+          # scale_reverse count, 0.0, 50.0
         end
       end
     end

data/lib/iroki/color/single_group_gradient.rb

@@ -21,11 +21,19 @@ module Iroki
     class SingleGroupGradient < Gradient
       attr_accessor :counts, :rel_abunds
 
-      def initialize samples, counts, single_color=false
+      def initialize samples,
+                     counts,
+                     single_color=false,
+                     min_lumin,
+                     max_lumin
+
         abort_unless samples.count == counts.count,
                      "Samples (#{samples.count}) and counts " +
                      "#{counts.count} are different size."
 
+        @min_lumin = min_lumin
+        @max_lumin = max_lumin
+
         @single_color = single_color
         @samples = samples
         @counts = counts
@@ -45,6 +53,8 @@ module Iroki
 
           col =
             Iroki::Color::GREEN.mix_with Iroki::Color::BLUE, rel_abund
+          # col =
+          #   Iroki::Color::BLUE.mix_with Iroki::Color::GREEN, rel_abund
 
           col.luminosity = lumin
 
@@ -55,7 +65,8 @@ module Iroki
       def single_color_gradient_hex_codes
         @rel_abunds.zip(@lumins).map do |rel_abund, lumin|
           amt_of_orig_color =
-            scale rel_abund, new_min=10, new_max=95
+            # scale rel_abund, new_min=10, new_max=95
+            scale rel_abund, new_min=@min_lumin, new_max=@max_lumin
 
           col =
             Iroki::Color::DARK_GREEN.lighten_by amt_of_orig_color

data/lib/iroki/color/two_group_gradient.rb

@@ -21,12 +21,20 @@ module Iroki
     class TwoGroupGradient < Gradient
       attr_accessor :g1_counts, :g2_counts, :g1_rabunds, :g2_rabunds
 
-      def initialize samples, g1_counts, g2_counts
+      def initialize samples,
+                     g1_counts,
+                     g2_counts,
+                     min_lumin,
+                     max_lumin
+
         assert(samples.count == g1_counts.count &&
                      g1_counts.count == g2_counts.count,
                      "Samples and counts are different lengths. " +
                      "Check your biom file.")
 
+        @min_lumin = min_lumin
+        @max_lumin = max_lumin
+
         @samples = samples
         @g1_counts = g1_counts
         @g2_counts = g2_counts
@@ -37,9 +45,17 @@ module Iroki
 
       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)
+          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)
+          scale(ra1 / ra2,
+                new_min=0.0,
+                new_max=0.5,
+                old_min=0.0,
+                old_max=1.0)
         else
           0.5
         end
@@ -51,9 +67,17 @@ module Iroki
 
       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
+          scale_reverse ra1,
+                        new_min=@min_lumin,
+                        new_max=@max_lumin,
+                        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
+          scale_reverse ra2,
+                        new_min=@min_lumin,
+                        new_max=@max_lumin,
+                        old_min=0.0,
+                        old_max=1.0
         end
       end
 

data/lib/iroki/main/main.rb

@@ -184,7 +184,9 @@ module Iroki
                   display_auto_color_options: nil,
                   newick_f: nil,
                   out_f: nil,
-                  default_color: "black")
+                  default_color: "black",
+                  min_lumin: 35,
+                  max_lumin: 70)
 
       args = method(__method__).parameters.map { |arg| arg[1] }
       AbortIf::logger.info "Args " + args.map { |arg| "#{arg} = #{eval(arg.to_s).inspect}" }.join(', ')
@@ -287,11 +289,19 @@ module Iroki
         samples, counts, is_single_group = Biom.open(biom_f, "rt").parse
 
         if is_single_group
-          biom_patterns = SingleGroupGradient.new(samples, counts, single_color).patterns
+          biom_patterns = SingleGroupGradient.new(samples,
+                                                  counts,
+                                                  single_color,
+                                                  min_lumin,
+                                                  max_lumin).patterns
         else
           g1_counts = counts.map(&:first)
           g2_counts = counts.map(&:last)
-          biom_patterns = TwoGroupGradient.new(samples, g1_counts, g2_counts).patterns
+          biom_patterns = TwoGroupGradient.new(samples,
+                                               g1_counts,
+                                               g2_counts,
+                                               min_lumin,
+                                               max_lumin).patterns
         end
 
         # these patterns have the original name for the key, so change
@@ -326,11 +336,19 @@ module Iroki
         samples, counts, is_single_group = Biom.open(biom_f, "rt").parse
 
         if is_single_group
-          patterns = SingleGroupGradient.new(samples, counts, single_color).patterns
+          patterns = SingleGroupGradient.new(samples,
+                                             counts,
+                                             single_color,
+                                             min_lumin,
+                                             max_lumin).patterns
         else
           g1_counts = counts.map(&:first)
           g2_counts = counts.map(&:last)
-          patterns = TwoGroupGradient.new(samples, g1_counts, g2_counts).patterns
+          patterns = TwoGroupGradient.new(samples,
+                                          g1_counts,
+                                          g2_counts,
+                                          min_lumin,
+                                          max_lumin).patterns
         end
 
         # these patterns have the original name for the key, so change

data/lib/iroki/version.rb

@@ -18,7 +18,7 @@
 
 # Library metadata
 module Iroki
-  VERSION = "0.0.31"
+  VERSION = "0.0.32"
   COPYRIGHT = "2015 - 2017 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: 0.0.31
+  version: 0.0.32
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-03-16 00:00:00.000000000 Z
+date: 2017-04-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler