class Bio::KEGG::EXPRESSION

   # File lib/bio/db/kegg/expression.rb
19 def initialize(entry)
20   @orf2val   = Hash.new('')
21   @orf2rgb   = Hash.new('')
22   @orf2ratio = Hash.new('')
23   @max_intensity = 10000
24   entry.split("\n").each do |line|
25     unless /^#/ =~ line
26       ary = line.split("\t")
27       orf = ary.shift
28       val = ary[2, 4].collect {|x| x.to_f}
29       @orf2val[orf] = val 
30     end
31   end
32 end

   # File lib/bio/db/kegg/expression.rb
38 def control_avg
39   sum = 0.0
40   @orf2val.values.each do |v|
41     sum += v[0] - v[1]
42   end
43   sum/orf2val.size
44 end

   # File lib/bio/db/kegg/expression.rb
74 def control_sd
75   var = self.control_var
76   Math.sqrt(var)
77 end

   # File lib/bio/db/kegg/expression.rb
54 def control_var
55   sum = 0.0
56   avg = self.control_avg
57   @orf2val.values.each do |v|
58     tmp = v[0] - v[1]
59     sum += (tmp - avg)*(tmp - avg)
60   end
61   sum/orf2val.size
62 end

    # File lib/bio/db/kegg/expression.rb
 98 def down_regulated(num=20, threshold=nil)
 99   logy_minus_logx
100   ary = @orf2ratio.to_a.sort{|a, b| a[1] <=> b[1]}
101   if threshold != nil
102     i = 0
103     while ary[i][1] < threshold
104       i += 1
105     end
106     return ary[0..i]
107   else
108     return ary[0..num-1]
109   end
110 end

    # File lib/bio/db/kegg/expression.rb
126 def logy_minus_logx
127   @orf2val.each do |k, v|
128     @orf2ratio[k] = (1.0/Math.log10(2))*(Math.log10(v[2]-v[3]) - Math.log10(v[0]-v[1]))
129   end
130 end

    # File lib/bio/db/kegg/expression.rb
112 def regulated(num=20, threshold=nil)
113   logy_minus_logx
114   ary = @orf2ratio.to_a.sort{|a, b| b[1].abs <=> a[1].abs}
115   if threshold != nil
116     i = 0
117     while ary[i][1].abs > threshold
118       i += 1
119     end
120     return ary[0..i]
121   else
122     return ary[0..num-1]
123   end
124 end

   # File lib/bio/db/kegg/expression.rb
46 def target_avg
47   sum = 0.0
48   @orf2val.values.each do |v|
49     sum += v[2] - v[3]
50   end
51   sum/orf2val.size
52 end

   # File lib/bio/db/kegg/expression.rb
79 def target_sd
80   var = self.target_var
81   Math.sqrt(var)
82 end

   # File lib/bio/db/kegg/expression.rb
64 def target_var
65   sum = 0.0
66   avg = self.target_avg
67   @orf2val.values.each do |v|
68     tmp = v[2] - v[3]
69     sum += (tmp - avg)*(tmp - avg)
70   end
71   sum/orf2val.size
72 end

   # File lib/bio/db/kegg/expression.rb
84 def up_regulated(num=20, threshold=nil)
85   logy_minus_logx
86   ary = @orf2ratio.to_a.sort{|a, b| b[1] <=> a[1]}
87   if threshold != nil
88     i = 0
89     while ary[i][1] > threshold
90       i += 1
91     end
92     return ary[0..i]
93   else
94     return ary[0..num-1]
95   end
96 end

    # File lib/bio/db/kegg/expression.rb
132 def val2rgb
133   col_unit = @max_intensity/255
134   @orf2val.each do |k, v|
135     tmp_val = ((v[0] - v[1])/col_unit).to_i
136     if tmp_val > 255
137       g = "ff" 
138     else
139       g = format("%02x", tmp_val)
140     end
141     tmp_val = ((v[2] - v[3])/col_unit).to_i
142     if tmp_val > 255
143       r = "ff" 
144     else
145       r = format("%02x", tmp_val)
146     end
147     @orf2rgb[k] = r + g + "00"
148   end
149 
150 end