egor 0.0.5 → 0.9.0

data/lib/egor.rb

@@ -2,5 +2,5 @@ $:.unshift(File.dirname(__FILE__)) unless
   $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
 
 module Egor
-  VERSION = '0.0.5'
+  VERSION = '0.9.0'
 end

data/lib/egor/cli.rb

@@ -5,16 +5,17 @@ require 'narray'
 require 'bio'
 require 'set'
 require 'facets'
-require 'simple_memoize'
 
+require 'math_extensions'
+require 'string_extensions'
 require 'narray_extensions'
 require 'nmatrix_extensions'
-require 'enumerable_extensions'
-require 'math_extensions'
-require 'environment'
-require 'environment_class_hash'
-require 'environment_feature'
-require 'environment_feature_array'
+
+require 'egor/environment'
+require 'egor/environment_class_hash'
+require 'egor/environment_feature'
+require 'egor/environment_feature_array'
+require 'egor/heatmap_array'
 
 # This is a module for an actual command line interpreter for Egor
 # ---
@@ -25,7 +26,7 @@ module Egor
 
       # :nodoc:
       def print_version
-        puts Egor::VERSION
+        puts VERSION
       end
 
       # Print Egor's Usage on the screen
@@ -62,14 +63,26 @@ Options:
         0 for raw counts (no smoothing performed)
         1 for probabilities
         2 for log-odds (default)
-    --noround: do not round off log odds ratio
+    --noroundoff: do not round off log odds ratio
     --scale INTEGER: log-odds matrices in 1/n bit units (default 3)
     --sigma DOUBLE: change the sigma value for smoothing (default 5.0)
     --autosigma: automatically adjust the sigma value for smoothing
     --add DOUBLE: add this value to raw counts when deriving log-odds without smoothing (default 1/#classes)
-    --penv: use environment-dependent frequencies for log-odds calculation (default false) (NOT implemented yet!!!)
     --pidmin DOUBLE: count substitutions only for pairs with PID equal to or greater than this value (default none)
     --pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
+    --heatmap INTEGER:
+        0 create a heat map file for each substitution table
+        1 create one big file containing all heat maps from substitution tables
+        2 do both 0 and 1
+    --heatmap-format INTEGER:
+        0 for Portable Network Graphics (PNG) Format (default)
+        1 for Graphics Interchange Format (GIF)
+        2 for Joint Photographic Experts Group (JPEG) Format
+        3 for Microsoft Windows bitmap (BMP) Format
+        4 for Portable Document Format (PDF)
+    --heatmap-columns INTEGER: number of tables to print in a row when --heatmap 1 or 2 set (default: sqrt(no. of tables))
+    --heatmap-stem STRING: stem for a file name when --heatmap 1 or 2 set (default: 'heatmap')
+    --heatmap-values: print values in the cells when generating heat maps
     --verbose (-v) INTEGER
         0 for ERROR level
         1 for WARN or above level (default)
@@ -87,12 +100,12 @@ Options:
       #   Egor::CLI::calculate_pid(seq1, seq2) -> Float
       #
       def calculate_pid(seq1, seq2)
-        s1    = seq1.split('')
-        s2    = seq2.split('')
-        cols  = s1.zip(s2)
-        align = 0
-        ident = 0
-        intgp = 0
+        aas1  = seq1.split('')
+        aas2  = seq2.split('')
+        cols  = aas1.zip(aas2)
+        align = 0 # no. of aligned columns
+        ident = 0 # no. of identical columns
+        intgp = 0 # no. of internal gaps
 
         cols.each do |col|
           if (col[0] != '-') && (col[1] != '-')
@@ -100,14 +113,14 @@ Options:
             if col[0] == col[1]
               ident += 1
             end
-          elsif (((col[0] == '-') && (col[1] != '-')) || ((col[0] != '-') && (col[1] == '-')))
+          elsif (((col[0] == '-') && (col[1] != '-')) ||
+                 ((col[0] != '-') && (col[1] == '-')))
             intgp += 1
           end
         end
 
         pid = 100.0 * ident.to_f / (align + intgp)
       end
-      memoize :calculate_pid
 
       # :nodoc:
       def execute(arguments=[])
@@ -121,7 +134,7 @@ Options:
         # aa: weighted amino acid
         # tot: total
         # rel: relative
-        # obs: observation
+        # jnt: joint
         # cnt: count
         # mut: mutation
         # mutb: mutability
@@ -145,31 +158,42 @@ Options:
         $logger.level = Logger::WARN
 
         # default set of 21 amino acids including J (Cysteine, the free thiol form)
-        $amino_acids  = 'ACDEFGHIKLMNPQRSTVWYJ'.split('')
-
-        $tem_list     = nil
-        $tem_file     = nil
-        $classdef     = 'classdef.dat'
-        $outfile      = 'allmat.dat'
-        $outfh        = nil # file hanfle for outfile
-        $output       = 2 # default: log odds matrix
-        $ali_size     = 0
-        $tot_aa       = 0
-        $sigma        = 5.0
-        $autosigma    = false
-        $weight       = 60
-        $noweight     = false
-        $smooth       = :partial
-        $nosmooth     = false
-        $noround      = false
-        $p1smooth     = false
-        $scale        = 3
-        $pidmin       = nil
-        $pidmax       = nil
-        $scale        = 3
-        $add          = nil
-        $cys          = 0
-        $penv         = false
+        $amino_acids    = 'ACDEFGHIKLMNPQRSTVWYJ'.split('')
+        $tem_list       = nil
+        $tem_file       = nil
+        $classdef       = 'classdef.dat'
+        $outfile        = 'allmat.dat'
+        $outfh          = nil # file hanfle for outfile
+        $output         = 2 # default: log odds matrix
+        $ali_size       = 0
+        $tot_aa         = 0
+        $sigma          = 5.0
+        $autosigma      = false
+        $weight         = 60
+        $noweight       = false
+        $smooth         = :partial
+        $nosmooth       = false
+        $noroundoff     = false
+        $p1smooth       = false
+        $scale          = 3
+        $pidmin         = nil
+        $pidmax         = nil
+        $scale          = 3
+        $add            = nil
+        $cys            = 0
+        $targetenv      = false
+        $penv           = false
+        $heatmap        = nil
+        $heatmapcol     = nil
+        $heatmapformat  = 'png'
+        $heatmapstem    = 'heatmaps'
+        $heatmapvalues   = false
+        $rvg_width      = 550
+        $rvg_height     = 650
+        $canvas_width   = 550
+        $canvas_height  = 650
+        $cell_width     = 20
+        $cell_height    = 20
 
         $aa_tot_cnt   = Hash.new(0)
         $aa_mut_cnt   = Hash.new(0)
@@ -184,7 +208,7 @@ Options:
         $tot_smooth_prob = {}
 
         # minimum ratio of amino acid count to sigma value
-        $min_obs_sigma_ratio = 500.0
+        $min_cnt_sigma_ratio = 500.0
 
         #
         # Part 1 END
@@ -205,11 +229,16 @@ Options:
           [ '--p1smooth',       GetoptLong::NO_ARGUMENT ],
           [ '--weight',   '-w', GetoptLong::REQUIRED_ARGUMENT ],
           [ '--noweight',       GetoptLong::NO_ARGUMENT ],
-          [ '--noround',        GetoptLong::NO_ARGUMENT ],
+          [ '--noroundoff',     GetoptLong::NO_ARGUMENT ],
           [ '--sigma',          GetoptLong::REQUIRED_ARGUMENT ],
           [ '--autosigma',      GetoptLong::NO_ARGUMENT ],
-          #[ '--heatmap',        GetoptLong::NO_ARGUMENT ],
+          [ '--heatmap',        GetoptLong::REQUIRED_ARGUMENT ],
+          [ '--heatmap-stem',   GetoptLong::REQUIRED_ARGUMENT ],
+          [ '--heatmap-format', GetoptLong::REQUIRED_ARGUMENT ],
+          [ '--heatmap-columns',GetoptLong::REQUIRED_ARGUMENT ],
+          [ '--heatmap-values', GetoptLong::NO_ARGUMENT ],
           [ '--output',         GetoptLong::REQUIRED_ARGUMENT ],
+          [ '--targetenv','-t', GetoptLong::REQUIRED_ARGUMENT ],
           [ '--cys',      '-y', GetoptLong::REQUIRED_ARGUMENT ],
           [ '--penv',           GetoptLong::NO_ARGUMENT ],
           [ '--outfile',  '-o', GetoptLong::REQUIRED_ARGUMENT ],
@@ -235,6 +264,8 @@ Options:
               $outfile      = arg
             when '--cys'
               $cys          = arg.to_i
+            when '--targetenv'
+              $targetenv    = (arg.to_i == 1) ? true : false
             when '--weight'
               $weight       = arg.to_i
             when '--sigma'
@@ -247,8 +278,8 @@ Options:
               $pidmax       = arg.to_f
             when '--noweight'
               $noweight     = true
-            when '--noround'
-              $noround      = true
+            when '--noroundoff'
+              $noroundoff   = true
             when '--smooth'
               $smooth       = (arg.to_i == 1) ? :full : :partial
             when '--nosmooth'
@@ -260,18 +291,42 @@ Options:
             when '--add'
               $add          = arg.to_f
             when '--penv'
-              warn "--penv option is not supported yet."
+              warn "--penv option is not supported."
               exit 1
               $penv         = true
-#            when '--heatmap'
-#              $heatmap      = true
+            when '--heatmap'
+              $heatmap      = case arg.to_i
+                              when (0..2) then arg.to_i
+                              else
+                                warn "--heatmap #{arg.to_i} is not allowed."
+                                exit1
+                              end
+            when '--heatmap-columns'
+              $heatmapcol   = arg.to_i
+            when '--heatmap-stem'
+              $heatmapstem  = arg.to_s
+            when '--heatmap-format'
+              $heatmapformat   = case arg.to_i
+                              when 0 then 'png'
+                              when 1 then 'gif'
+                              when 2 then 'jpg'
+                              when 3 then 'bmp'
+                              when 4 then 'pdf'
+                              else
+                                warn "--heatmap-format #{arg.to_i} is not supported."
+                                exit 1
+                              end
+            when '--heatmap-values'
+              $heatmapvalues   = true
             when '--verbose'
               $logger.level = case arg.to_i
                               when 0 then Logger::ERROR
                               when 1 then Logger::WARN
                               when 2 then Logger::INFO
                               when 3 then Logger::DEBUG
-                              else Logger::WARN
+                              else
+                                warn "--verbose (-v) #{arg.to_i} is not supported."
+                                exit 1
                               end
             when '--version'
               print_version
@@ -284,7 +339,9 @@ Options:
         end
 
         # when arguments are nonsense, print usage
-        if ((ARGV.length != 0) || (!$tem_list && !$tem_file) || ($tem_list && $tem_file))
+        if ((ARGV.length != 0) ||
+            (!$tem_list && !$tem_file) ||
+            ($tem_list && $tem_file))
           print_usage
           exit 1
         end
@@ -305,7 +362,6 @@ Options:
           exit 1
         end
 
-
         #
         # Part 2 END
         #
@@ -316,23 +372,28 @@ Options:
         # Reading Environment Class Definition File
         #
 
-        $logger.info "Egor START."
-
         # check --cys option and modify amino_acids set if necessary
         if $cys == 2
           $amino_acids = 'ACDEFGHIKLMNPQRSTVWY'.split('')
         end
 
-        # create an EnvironmentFeatureList object for storing all environment features
+        # create an EnvironmentFeatureList object for storing all environment
+        # features
         $env_features = EnvironmentFeatureArray.new
 
         # an array for storing indexes of constrained environment features
         $cst_features = []
 
-        # add substituted amino acid (aa1) in a substitution to the environment feature list
-        $env_features << EnvironmentFeature.new('sequence', $amino_acids, $amino_acids, 'F', 'F')
+        # add substituted amino acid (aa1) in a substitution to the environment
+        # feature list
+        $env_features << EnvironmentFeature.new('sequence',
+                                                $amino_acids,
+                                                $amino_acids,
+                                                'F',
+                                                'F')
 
-        # read environment class definiton file and store them into the hash prepared above
+        # read environment class definiton file and store them into
+        # the hash prepared above
         env_index = 1
 
         IO.foreach($classdef) do |line|
@@ -350,10 +411,15 @@ Options:
               $cst_features << env_index
               $logger.warn "The environment feature, #{line} constrained."
             end
-            $env_features << EnvironmentFeature.new(env_ftr[0], env_ftr[1].split(''), env_ftr[2].split(''), env_ftr[3], env_ftr[4])
+            $env_features << EnvironmentFeature.new(env_ftr[0],
+                                                    env_ftr[1].split(''),
+                                                    env_ftr[2].split(''),
+                                                    env_ftr[3],
+                                                    env_ftr[4])
             env_index += 1
           else
-            $logger.error "\"#{line}\" doesn't seem to be a proper format for a environment class definition."
+            $logger.error "\"#{line}\" doesn't seem to be a proper format for" +
+                          "a environment class definition."
             exit 1
           end
         end
@@ -361,9 +427,13 @@ Options:
         # a hash for storing all environment classes
         $env_classes = EnvironmentClassHash.new
 
-        # generate all possible combinations of environment labels, and store every environment class into the hash prepared above with the label as a key
+        # generate all possible combinations of environment labels, and store
+        # every environment class into the hash prepared above with the label
+        # as a key
         $env_features.label_combinations.each_with_index { |e, i|
-          $env_classes[e.flatten.join] = Environment.new(i, e.flatten.join, $amino_acids)
+          $env_classes[e.flatten.join] = Environment.new(i,
+                                                         e.flatten.join,
+                                                         $amino_acids)
         }
 
         #
@@ -390,19 +460,17 @@ Options:
         $tem_list_io.each_line do |tem_file|
           tem_file.chomp!
 
-          $logger.info "Analysing #{tem_file} ..."
-
           ali = Bio::Alignment::OriginalAlignment.new
           ff  = Bio::FlatFile.auto(tem_file)
 
           ff.each_entry do |pir|
             if (pir.definition == 'sequence') || (pir.definition == 'structure')
-              ali.add_seq(pir.data.gsub("\n", ''), pir.entry_id)
+              ali.add_seq(pir.data.remove_internal_spaces, pir.entry_id)
             end
           end
 
           if ali.size < 2
-            $logger.warn "Skipped #{tem_file}, there is only one unique entry."
+            $logger.warn "Skipped #{tem_file} which has only one unique entry."
             next
           end
 
@@ -414,8 +482,10 @@ Options:
             # check disulphide bond environment first!
             ff.rewind
             ff.each_entry do |pir|
-              if (pir.entry_id == key) && ((pir.definition == "disulphide") || (pir.definition == "disulfide"))
-                disulphide[key] = pir.data.gsub("\n", '').split('')
+              if ((pir.entry_id == key) &&
+                  ((pir.definition == "disulphide") ||
+                   (pir.definition == "disulfide")))
+                disulphide[key] = pir.data.remove_internal_spaces.split('')
               end
             end
 
@@ -425,14 +495,16 @@ Options:
               ff.rewind
               ff.each_entry do |pir|
                 if (pir.entry_id == key) && (pir.definition == ec.name)
-                  labels = pir.data.gsub("\n", '').split('').map_with_index do |sym, pos|
+                  labels = pir.data.remove_internal_spaces.split('').map_with_index do |sym, pos|
                     if sym == '-'
                       '-'
                     elsif sym == 'X' || sym == 'x'
                       'X'
                     else
                       if ei == 0 # Amino Acid Environment Feature
-                        (disulphide.has_key?(key) && (disulphide[key][pos] == 'F') && (sym == 'C')) ? 'J' : sym
+                        (disulphide.has_key?(key) &&
+                         (disulphide[key][pos] == 'F') &&
+                         (sym == 'C')) ? 'J' : sym
                       else
                         ec.labels[ec.symbols.index(sym)]
                       end
@@ -442,7 +514,9 @@ Options:
                   if env_labels[key].empty?
                     env_labels[key] = labels
                   else
-                    env_labels[key].each_with_index { |e, i| env_labels[key][i] = e + labels[i] }
+                    env_labels[key].each_with_index { |e, i|
+                      env_labels[key][i] = e + labels[i]
+                    }
                   end
                 end
               end
@@ -459,13 +533,15 @@ Options:
 
                   # check PID_MIN
                   if $pidmin && (pid < $pidmin)
-                    $logger.info "Skip alignment between #{id1} and #{id2} having PID, #{pid}% less than PID_MIN, #{$pidmin}."
+                    $logger.info  "Skip alignment between #{id1} and #{id2} " +
+                                  "having PID, #{pid}% less than PID_MIN, #{$pidmin}."
                     next
                   end
 
                   # check PID_MAX
                   if $pidmax && (pid > $pidmax)
-                    $logger.info "Skip alignment between #{id1} and #{id2} having PID, #{pid}% greater than PID_MAX, #{$pidmax}."
+                    $logger.info  "Skip alignment between #{id1} and #{id2} " +
+                                  "having PID, #{pid}% greater than PID_MAX, #{$pidmax}."
                     next
                   end
 
@@ -574,7 +650,7 @@ Options:
             end while(continue)
 
             if clusters.size < 2
-              $logger.debug "Skipped #{tem_file} because there is only one cluster at the #{$weight} PID level."
+              $logger.debug "Skipped #{tem_file} which has only one cluster at the #{$weight} PID level."
               next
             end
 
@@ -610,16 +686,16 @@ Options:
 
                     aa1   = (disulphide.has_key?(id1) && (disulphide[id1][pos] == 'F') && (aa1 == 'C')) ? 'J' : aa1
                     aa2   = (disulphide.has_key?(id2) && (disulphide[id2][pos] == 'F') && (aa2 == 'C')) ? 'J' : aa2
-                    obs1  = 1.0 / cluster1.size
-                    obs2  = 1.0 / cluster2.size
-                    obs_cnt = obs1 * obs2
+                    cnt1  = 1.0 / cluster1.size
+                    cnt2  = 1.0 / cluster2.size
+                    jnt_cnt = cnt1 * cnt2
 
                     if $cst_features.empty?
-                      $env_classes[env_labels[id1][pos]].increase_residue_count(aa2, obs_cnt)
-                      $env_classes[env_labels[id2][pos]].increase_residue_count(aa1, obs_cnt)
+                      $env_classes[env_labels[id1][pos]].increase_residue_count(aa2, jnt_cnt)
+                      $env_classes[env_labels[id2][pos]].increase_residue_count(aa1, jnt_cnt)
                     elsif (env_labels[id1][pos].split('').values_at(*$cst_features) == env_labels[id2][pos].split('').values_at(*$cst_features))
-                      $env_classes[env_labels[id1][pos]].increase_residue_count(aa2, obs_cnt)
-                      $env_classes[env_labels[id2][pos]].increase_residue_count(aa1, obs_cnt)
+                      $env_classes[env_labels[id1][pos]].increase_residue_count(aa2, jnt_cnt)
+                      $env_classes[env_labels[id2][pos]].increase_residue_count(aa1, jnt_cnt)
                     else
                       $logger.debug "#{id1}-#{pos}-#{aa1} and #{id2}-#{pos}-#{aa2} have different symbols for constrained environment features each other."
                       next
@@ -630,64 +706,65 @@ Options:
 
                     if $aa_env_cnt.has_key? grp_label1
                       if $aa_env_cnt[grp_label1].has_key? aa1
-                        $aa_env_cnt[grp_label1][aa1] += obs1
+                        $aa_env_cnt[grp_label1][aa1] += cnt1
                       else
-                        $aa_env_cnt[grp_label1][aa1] = obs1
+                        $aa_env_cnt[grp_label1][aa1] = cnt1
                       end
                     else
                       $aa_env_cnt[grp_label1] = Hash.new(0.0)
-                      $aa_env_cnt[grp_label1][aa1] = obs1
+                      $aa_env_cnt[grp_label1][aa1] = cnt1
                     end
 
                     if $aa_env_cnt.has_key? grp_label2
                       if $aa_env_cnt[grp_label2].has_key? aa2
-                        $aa_env_cnt[grp_label2][aa2] += obs2
+                        $aa_env_cnt[grp_label2][aa2] += cnt2
                       else
-                        $aa_env_cnt[grp_label2][aa2] = obs2
+                        $aa_env_cnt[grp_label2][aa2] = cnt2
                       end
                     else
                       $aa_env_cnt[grp_label2] = Hash.new(0.0)
-                      $aa_env_cnt[grp_label2][aa2] = obs2
+                      $aa_env_cnt[grp_label2][aa2] = cnt2
                     end
 
                     if $aa_tot_cnt.has_key? aa1
-                      $aa_tot_cnt[aa1] += obs1
+                      $aa_tot_cnt[aa1] += cnt1
                     else
-                      $aa_tot_cnt[aa1] = obs1
+                      $aa_tot_cnt[aa1] = cnt1
                     end
 
                     if $aa_tot_cnt.has_key? aa2
-                      $aa_tot_cnt[aa2] += obs2
+                      $aa_tot_cnt[aa2] += cnt2
                     else
-                      $aa_tot_cnt[aa2] = obs2
+                      $aa_tot_cnt[aa2] = cnt2
                     end
 
                     if aa1 != aa2
                       if $aa_mut_cnt.has_key? aa1
-                        $aa_mut_cnt[aa1] += obs1
+                        $aa_mut_cnt[aa1] += cnt1
                       else
-                        $aa_mut_cnt[aa1] = obs1
+                        $aa_mut_cnt[aa1] = cnt1
                       end
                       if $aa_mut_cnt.has_key? aa2
-                        $aa_mut_cnt[aa2] += obs2
+                        $aa_mut_cnt[aa2] += cnt2
                       else
-                        $aa_mut_cnt[aa2] = obs2
+                        $aa_mut_cnt[aa2] = cnt2
                       end
                     end
 
-                    $logger.debug "#{id1}-#{pos}-#{aa1} -> #{id2}-#{pos}-#{aa2} substitution count (#{"%.2f" % obs_cnt}) was added to the environments class, #{env_labels[id1][pos]}."
-                    $logger.debug "#{id2}-#{pos}-#{aa2} -> #{id1}-#{pos}-#{aa1} substitution count (#{"%.2f" % obs_cnt}) was added to the environments class, #{env_labels[id2][pos]}."
+                    $logger.debug "#{id1}-#{pos}-#{aa1} -> #{id2}-#{pos}-#{aa2} substitution count (#{"%.2f" % jnt_cnt}) was added to the environments class, #{env_labels[id1][pos]}."
+                    $logger.debug "#{id2}-#{pos}-#{aa2} -> #{id1}-#{pos}-#{aa1} substitution count (#{"%.2f" % jnt_cnt}) was added to the environments class, #{env_labels[id2][pos]}."
                   end
                 end
               end
             end
           end
+          $logger.info "Analysing #{tem_file} done."
         end
 
         # print out default header
         $outfh.puts <<HEADER
 # Environment-specific amino acid substitution matrices
-# Creator: egor version #{Egor::VERSION}
+# Creator: egor version #{VERSION}
 # Creation Date: #{Time.now.strftime("%d/%m/%Y %H:%M")}
 #
 # Definitions for structural environments:
@@ -739,20 +816,20 @@ HEADER
         $outfh.puts "# Total amino acid frequencies:\n"
         $outfh.puts "# %-3s %9s %9s %5s %8s %8s" % %w[RES TOT_OBS MUT_OBS MUTB REL_MUTB REL_FREQ]
 
-        min_obs = -1
+        min_cnt = -1
         min_sigma = nil
 
         $amino_acids.each do |res|
-          if ($aa_tot_cnt[res] / $sigma) < $min_obs_sigma_ratio
-            if min_obs < 0
-              min_obs = $aa_tot_cnt[res]
-              min_sigma = min_obs / $min_obs_sigma_ratio
-            elsif (min_obs > 0) && (min_obs > $aa_tot_cnt[res])
-              min_obs = $aa_tot_cnt[res]
-              min_sigma = min_obs / $min_obs_sigma_ratio
+          if ($aa_tot_cnt[res] / $sigma) < $min_cnt_sigma_ratio
+            if min_cnt < 0
+              min_cnt = $aa_tot_cnt[res]
+              min_sigma = min_cnt / $min_cnt_sigma_ratio
+            elsif (min_cnt > 0) && (min_cnt > $aa_tot_cnt[res])
+              min_cnt = $aa_tot_cnt[res]
+              min_sigma = min_cnt / $min_cnt_sigma_ratio
             end
 
-            $logger.warn "The current sigma value, #{$sigma} seems to be too big for the total observation (#{"%.2f" % $aa_tot_cnt[res]}) of amino acid, #{res}."
+            $logger.warn "The current sigma value, #{$sigma} seems to be too big for the total count (#{"%.2f" % $aa_tot_cnt[res]}) of amino acid, #{res}."
           end
 
           $aa_mutb[res]     = ($aa_tot_cnt[res] == 0) ? 1.0 : ($aa_mut_cnt[res] / $aa_tot_cnt[res].to_f)
@@ -770,7 +847,7 @@ HEADER
           end
         end
 
-        if min_obs > -1
+        if min_cnt > -1
           $logger.warn "We recommend you to use a sigma value equal to or smaller than #{min_sigma}."
           if $autosigma
             $logger.warn "The sigma value has been changed from #{$sigma} to #{min_sigma}."
@@ -780,12 +857,13 @@ HEADER
 
         $outfh.puts '#'
         $outfh.puts '# RES: Amino acid one letter code'
-        $outfh.puts '# TOT_OBS: Total observations of incidence'
-        $outfh.puts '# MUT_OBS: Total observations of mutation'
+        $outfh.puts '# TOT_OBS: Total count of incidence'
+        $outfh.puts '# MUT_OBS: Total count of mutation'
         $outfh.puts '# MUTB: Mutability (MUT_OBS / TOT_OBS)'
-        $outfh.puts '# REL_MUTB: Relative mutability (ALA=100)'
+        $outfh.puts '# REL_MUTB: Relative mutability (ALA = 100)'
         $outfh.puts '# REL_FREQ: Relative frequency'
         $outfh.puts '#'
+
         #
         # Part 4. END
         #
@@ -804,7 +882,8 @@ HEADER
         end
 
         # count raw frequencies
-        $tot_cnt_mat = NMatrix.send($noweight ? 'int' : 'float', $amino_acids.size, $amino_acids.size)
+        $tot_cnt_mat    = NMatrix.send($noweight ? 'int' : 'float', $amino_acids.size, $amino_acids.size)
+        group_matrices  = []
 
         # for each combination of environment features
         $env_classes.groups_sorted_by_residue_labels.each_with_index do |group, group_no|
@@ -816,22 +895,88 @@ HEADER
           end
 
           $tot_cnt_mat += grp_cnt_mat
-
-          if $output == 0
-            $outfh.puts ">#{group[0]} #{group_no}"
-            $outfh.puts grp_cnt_mat.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids)
-          end
+          group_matrices << [group[0], grp_cnt_mat]
         end
 
+        $logger.info "Counting substitutions done."
+
         if $output == 0
+          heatmaps      = HeatmapArray.new if $heatmap == 1 or $heatmap == 2
+          grp_max_val   = group_matrices.map { |l, m, n| m }.map { |m| m.max }.max
+          $heatmapcol ||= Math::sqrt(group_matrices.size).round
+
+          group_matrices.each_with_index do |(grp_label, grp_cnt_mat), grp_no|
+            # for a matrix file
+            stem = "#{grp_no}. #{grp_label}"
+            $outfh.puts ">#{grp_label} #{grp_no}"
+            $outfh.puts grp_cnt_mat.pretty_string(:col_header => $amino_acids,
+                                                  :row_header => $amino_acids)
+
+            # for a heat map
+            if $heatmap == 0 or $heatmap == 2
+              grp_cnt_mat.heatmap(:col_header     => $amino_acids,
+                                  :row_header     => $amino_acids,
+                                  :rvg_width      => $rvg_width,
+                                  :rvg_height     => $rvg_height,
+                                  :canvas_width   => $canvas_width,
+                                  :canvas_height  => $canvas_height,
+                                  :max_val        => grp_max_val.ceil,
+                                  :min_val        => 0,
+                                  :print_value    => $heatmapvalues,
+                                  :title          => stem).write("#{stem}.#{$heatmapformat}")
+
+              $logger.info "Generating a heat map for #{stem} table done."
+            end
+
+            if $heatmap == 1 or $heatmap == 2
+              heatmaps << grp_cnt_mat.heatmap(:col_header       => $amino_acids,
+                                              :row_header       => $amino_acids,
+                                              :rvg_width        => $rvg_width,
+                                              :rvg_height       => $rvg_height - 50,
+                                              :canvas_width     => $canvas_width,
+                                              :canvas_height    => $canvas_height - 50,
+                                              :max_val          => grp_max_val.ceil,
+                                              :min_val          => 0,
+                                              :print_value      => $heatmapvalues,
+                                              :print_gradient   => false,
+                                              :title            => stem,
+                                              :title_font_size  => $rvg_width * $heatmapcol / 100.0)
+            end
+          end
+
+          if $heatmap == 1 or $heatmap == 2
+            file = "#{$heatmapstem}.#{$heatmapformat}"
+            heatmaps.heatmap(:columns   => $heatmapcol,
+                             :rvg_width => $rvg_width,
+                             :max_val   => grp_max_val.ceil,
+                             :min_val   => 0).write(file)
+
+            $logger.info "Generating heat maps in a file, #{file} done."
+          end
+
+          # total
           $outfh.puts '>Total'
-          $outfh.puts $tot_cnt_mat.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids)
-          $logger.info 'Egor END.'
+          $outfh.puts $tot_cnt_mat.pretty_string(:col_header => $amino_acids,
+                                                 :row_header => $amino_acids)
+
+          if $heatmap == 0 or $heatmap == 2
+            stem    = "#{group_matrices.size}. TOTAL"
+            heatmap = $tot_cnt_mat.heatmap(:col_header    => $amino_acids,
+                                           :row_header    => $amino_acids,
+                                           :rvg_width     => $rvg_width,
+                                           :rvg_height    => $rvg_height,
+                                           :canvas_width  => $canvas_width,
+                                           :canvas_height => $canvas_height,
+                                           :max_val       => $tot_cnt_mat.max.ceil,
+                                           :min_val       => 0,
+                                           :print_value   => $heatmapvalues,
+                                           :title         => stem).write("#{stem}.#{$heatmapformat}")
+
+            $logger.info "Generating a heat map for #{stem} table done."
+          end
           exit 0
         end
 
-        $logger.info "Counting substitutions is done."
-
         #
         # Part 5. END
         #
@@ -867,6 +1012,8 @@ HEADER
           # re-calculate probability vector for each environment class
           $env_classes.values.each { |e| e.prob_array = 100.0 * e.freq_array / e.freq_array.sum }
 
+          group_matrices = []
+
           $env_classes.groups_sorted_by_residue_labels.each_with_index do |group, group_no|
             grp_cnt_mat = NMatrix.float($amino_acids.size, $amino_acids.size)
             grp_prob_mat = NMatrix.float($amino_acids.size, $amino_acids.size)
@@ -878,10 +1025,63 @@ HEADER
             end
 
             $tot_cnt_mat += grp_cnt_mat
+            group_matrices << [group[0], grp_prob_mat]
+          end
+
+          if $output == 1
+            heatmaps      = HeatmapArray.new if $heatmap == 1 or $heatmap == 2
+            grp_max_val   = group_matrices.map { |l, m, n| m }.map { |m| m.max }.max || 100
+            $heatmapcol ||= Math::sqrt(group_matrices.size).round
+
+            group_matrices.each_with_index do |(grp_label, grp_prob_mat), grp_no|
+              # for a matrix file
+              stem = "#{grp_no}. #{grp_label}"
+              $outfh.puts ">#{grp_label} #{grp_no}"
+              $outfh.puts grp_prob_mat.pretty_string(:col_header => $amino_acids,
+                                                     :row_header => $amino_acids)
+
+
+              # for a heat map
+              if $heatmap == 0 or $heatmap == 2
+                grp_prob_mat.heatmap(:col_header    => $amino_acids,
+                                     :row_header    => $amino_acids,
+                                     :rvg_width     => $rvg_width,
+                                     :rvg_height    => $rvg_height,
+                                     :canvas_width  => $canvas_width,
+                                     :canvas_height => $canvas_height,
+                                     :max_val       => grp_max_val.ceil,
+                                     :min_val       => 0,
+                                     :print_value   => $heatmapvalues,
+                                     :title         => stem).write("#{stem}.#{$heatmapformat}")
+
+                $logger.info "Generating a heat map for #{stem} table done."
+              end
+
+              if $heatmap == 1 or $heatmap == 2
+                heatmaps << grp_prob_mat.heatmap(:col_header      => $amino_acids,
+                                                 :row_header      => $amino_acids,
+                                                 :rvg_width       => $rvg_width,
+                                                 :rvg_height      => $rvg_height - 50,
+                                                 :canvas_width    => $canvas_width,
+                                                 :canvas_height   => $canvas_height - 50,
+                                                 :max_val         => grp_max_val.ceil,
+                                                 :min_val         => 0,
+                                                 :print_value     => $heatmapvalues,
+                                                 :print_gradient  => false,
+                                                 :title           => stem,
+                                                 :title_font_size => $rvg_width * $heatmapcol / 100.0)
+              end
+            end
 
-            if ($output == 1)
-              $outfh.puts ">#{group[0]} #{group_no}"
-              $outfh.puts grp_prob_mat.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids)
+            # for heat maps in a single file
+            if $heatmap == 1 or $heatmap == 2
+              file = "#{$heatmapstem}.#{$heatmapformat}"
+              heatmaps.heatmap(:columns   => $heatmapcol,
+                               :rvg_width => $rvg_width,
+                               :max_val   => grp_max_val.ceil,
+                               :min_val   => 0).write(file)
+
+              $logger.info "Generating heat maps in a file, #{file} done."
             end
           end
 
@@ -892,15 +1092,32 @@ HEADER
             0.upto($amino_acids.size - 1) { |i| $tot_prob_mat[aj, i] = 100.0 * $tot_cnt_mat[aj, i] / col_sum }
           end
 
-          $logger.info 'Calculating substitution probabilities is done (no smoothing)'
-
-          if ($output == 1)
+          if $output == 1
             $outfh.puts '>Total'
-            $outfh.puts $tot_prob_mat.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids)
+            $outfh.puts $tot_prob_mat.pretty_string(:col_header => $amino_acids,
+                                                    :row_header => $amino_acids)
             $outfh.close
-            $logger.info 'Egor END.'
+
+            # for a heat map
+            if $heatmap == 0 or $heatmap == 2
+              stem = "#{group_matrices.size}. TOTAL"
+              $tot_prob_mat.heatmap(:col_header     => $amino_acids,
+                                    :row_header     => $amino_acids,
+                                    :rvg_width      => $rvg_width,
+                                    :rvg_height     => $rvg_height,
+                                    :canvas_width   => $canvas_width,
+                                    :canvas_height  => $canvas_height,
+                                    :max_val        => $tot_prob_mat.max.ceil,
+                                    :min_val        => 0,
+                                    :print_value    => $heatmapvalues,
+                                    :title          => stem).write("#{stem}.#{$heatmapformat}")
+
+              $logger.info "Generating a heat map for #{stem} table done."
+            end
             exit 0
           end
+
+          $logger.info 'Calculating substitution probabilities (no smoothing) done.'
         end
 
         # when smoothing!!!
@@ -980,7 +1197,7 @@ HEADER
               end
 
               env_labels.combination(ci) do |c1|
-                Enumerable.cart_prod(*c1).each do |labels|
+                c1[0].product(*c1[1..-1]).each do |labels|
                   pattern = '.' * $env_features.size
 
                   labels.each do |label|
@@ -1081,7 +1298,7 @@ HEADER
                 end
               end
             end
-            $logger.info 'Calculating substitution probabilities is done (partial smoothing).'
+            $logger.info 'Calculating substitution probabilities (partial smoothing) done.'
           else
             $outfh.puts <<HEADER
 #
@@ -1116,7 +1333,7 @@ HEADER
             # full smooting
             1.upto($env_features.size) do |ci|
               env_labels.combination(ci) do |c1|
-                Enumerable.cart_prod(*c1).each do |labels|
+                c1[0].product(*c1[1..-1]).each do |labels|
                   pattern = '.' * $env_features.size
                   labels.each do |label|
                     j = label[0].chr.to_i
@@ -1167,7 +1384,7 @@ HEADER
                 end
               end
             end
-            $logger.info 'Calculating substitution probabilities is done (full smoothing).'
+            $logger.info 'Calculating substitution probabilities (full smoothing) done.'
           end
 
           # updating smoothed probability array for each envrionment
@@ -1176,7 +1393,9 @@ HEADER
           end
 
           # sorting environments and build 21X21 substitution matrices
-          $env_classes.groups_sorted_by_residue_labels.each_with_index do |group, group_no|
+          group_matrices = []
+
+          $env_classes.groups_sorted_by_residue_labels.each do |group|
             # calculating 21X21 substitution probability matrix for each envrionment
             grp_prob_mat = NMatrix.float($amino_acids.size, $amino_acids.size)
 
@@ -1185,9 +1404,62 @@ HEADER
               0.upto($amino_acids.size - 1) { |j| grp_prob_mat[ai, j] = smooth_prob_arr[j] }
             end
 
-            if $output == 1
-              $outfh.puts ">#{group[0]} #{group_no}"
-              $outfh.puts grp_prob_mat.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids)
+            group_matrices << [group[0], grp_prob_mat]
+          end
+
+          if $output == 1
+            heatmaps      = HeatmapArray.new if $heatmap == 1 or $heatmap == 2
+            grp_max_val   = group_matrices.map { |l, m, n| m }.map { |m| m.max }.max || 100
+            $heatmapcol ||= Math::sqrt(group_matrices.size).round
+
+            group_matrices.each_with_index do |(grp_label, grp_prob_mat), grp_no|
+              # for a matrix file
+              stem = "#{grp_no}. #{grp_label}"
+              $outfh.puts ">#{grp_label} #{grp_no}"
+              $outfh.puts grp_prob_mat.pretty_string(:col_header => $amino_acids,
+                                                     :row_header => $amino_acids)
+
+              # for heat map generation
+              if $heatmap == 0 or $heatmap == 2
+                grp_prob_mat.heatmap(:col_header    => $amino_acids,
+                                     :row_header    => $amino_acids,
+                                     :rvg_width     => $rvg_width,
+                                     :rvg_height    => $rvg_height,
+                                     :canvas_width  => $canvas_width,
+                                     :canvas_height => $canvas_height,
+                                     :max_val       => grp_max_val.ceil,
+                                     :min_val       => 0,
+                                     :print_value   => $heatmapvalues,
+                                     :title         => stem).write("#{stem}.#{$heatmapformat}")
+
+                $logger.info "Generating a heat map for #{stem} table done."
+              end
+
+              if $heatmap == 1 or $heatmap == 2
+                heatmaps << grp_prob_mat.heatmap(:col_header      => $amino_acids,
+                                                 :row_header      => $amino_acids,
+                                                 :rvg_width       => $rvg_width,
+                                                 :rvg_height      => $rvg_height - 50,
+                                                 :canvas_width    => $canvas_width,
+                                                 :canvas_height   => $canvas_height - 50,
+                                                 :max_val         => grp_max_val.ceil,
+                                                 :min_val         => 0,
+                                                 :print_value     => $heatmapvalues,
+                                                 :print_gradient  => false,
+                                                 :title           => stem,
+                                                 :title_font_size => $rvg_width * $heatmapcol / 100.0)
+              end
+            end
+
+            # for heat maps in a single file
+            if $heatmap == 1 or $heatmap == 2
+              file = "#{$heatmapstem}.#{$heatmapformat}"
+              heatmaps.heatmap(:columns   => $heatmapcol,
+                               :rvg_width => $rvg_width,
+                               :max_val   => grp_max_val.ceil,
+                               :min_val   => 0).write(file)
+
+              $logger.info "Generating heat maps in a file, #{file} done."
             end
           end
 
@@ -1202,9 +1474,26 @@ HEADER
 
           if $output == 1
             $outfh.puts '>Total'
-            $outfh.puts $tot_prob_mat.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids)
+            $outfh.puts $tot_prob_mat.pretty_string(:col_header => $amino_acids,
+                                                    :row_header => $amino_acids)
             $outfh.close
-            $logger.info 'Egor END.'
+
+            # for a heat map
+            if $heatmap == 0 or $heatmap == 2
+              stem = "#{group_matrices.size}. TOTAL"
+              $tot_prob_mat.heatmap(:col_header     => $amino_acids,
+                                    :row_header     => $amino_acids,
+                                    :rvg_width      => $rvg_width,
+                                    :rvg_height     => $rvg_height,
+                                    :canvas_width   => $canvas_width,
+                                    :canvas_height  => $canvas_height,
+                                    :max_val        => $tot_prob_mat.max.ceil,
+                                    :min_val        => 0,
+                                    :print_value    => $heatmapvalues,
+                                    :title          => stem).write("#{stem}.#{$heatmapformat}")
+
+              $logger.info "Generating a heat map for #{stem} table done."
+            end
             exit 0
           end
         end
@@ -1242,16 +1531,18 @@ HEADER
             # calculating substitution probability matrix for each envrionment
             grp_label     = group[0]
             grp_envs      = group[1]
-            grp_logo_mat  = $cys == 0 ? NMatrix.float($amino_acids.size, $amino_acids.size + 1) : NMatrix.float($amino_acids.size, $amino_acids.size)
+            grp_logo_mat  = $cys == 0 ?
+                            NMatrix.float($amino_acids.size, $amino_acids.size + 1) :
+                            NMatrix.float($amino_acids.size, $amino_acids.size)
 
             $amino_acids.each_with_index do |aa, aj|
               env             = grp_envs.detect { |e| e.label.start_with?(aa) }
-              #paj            = env.send($nosmooth ? 'prob_array' : 'smooth_prob_array').sum / $tot_cnt_mat.sum
-              env.logo_array  = $cys == 0 ? NArray.float($amino_acids.size + 1) : NArray.float($amino_acids.size)
+              env.logo_array  = $cys == 0 ?
+                                NArray.float($amino_acids.size + 1) :
+                                NArray.float($amino_acids.size)
 
               env.send($nosmooth ? 'prob_array' : 'smooth_prob_array').to_a.each_with_index do |prob, ai|
                 pai                   = 100.0 * $aa_tot_freq[$amino_acids[ai]]
-                #odds                  = prob == 0.0 ? 0.000001 / pai : prob / pai
                 odds                  = prob / pai
                 env.logo_array[ai]    = factor * Math::log(odds)
                 grp_logo_mat[aj, ai]  = env.logo_array[ai]
@@ -1262,7 +1553,6 @@ HEADER
                 pai                                 = 100.0 * ($aa_tot_freq['C'] + $aa_tot_freq['J'])
                 prob                                = env.send($nosmooth ? 'prob_array' : 'smooth_prob_array')[$amino_acids.index('C')] +
                                                       env.send($nosmooth ? 'prob_array' : 'smooth_prob_array')[$amino_acids.index('J')]
-                #odds                                = prob == 0.0 ? 0.000001 / pai : prob / pai
                 odds                                = prob / pai
                 env.logo_array[$amino_acids.size]   = factor * Math::log(odds)
                 grp_logo_mat[aj, $amino_acids.size] = env.logo_array[$amino_acids.size]
@@ -1272,13 +1562,14 @@ HEADER
             grp_logo_mats << [grp_label, grp_logo_mat]
           end
 
-          $tot_logo_mat = $cys == 0 ? NMatrix.float($amino_acids.size, $amino_acids.size + 1) : NMatrix.float($amino_acids.size, $amino_acids.size)
+          $tot_logo_mat = $cys == 0 ?
+                          NMatrix.float($amino_acids.size, $amino_acids.size + 1) :
+                          NMatrix.float($amino_acids.size, $amino_acids.size)
 
           $amino_acids.each_with_index do |aa1, aj|
             $amino_acids.each_with_index do |aa2, ai|
               prob  = $tot_prob_mat[aj, ai]
               pai   = 100.0 * $aa_tot_freq[$amino_acids[ai]]
-              #odds  = prob == 0.0 ? 0.000001 / pai : prob / pai
               odds  = prob / pai
               $tot_logo_mat[aj, ai] = factor * Math::log(odds)
             end
@@ -1287,7 +1578,6 @@ HEADER
             if $cys == 0
               pai   = 100.0 * ($aa_tot_freq['C'] + $aa_tot_freq['J'])
               prob  = $tot_prob_mat[aj, $amino_acids.index('C')] + $tot_prob_mat[aj, $amino_acids.index('J')]
-              #odds  = prob == 0.0 ? 0.000001 / pai : prob / pai
               odds  = prob / pai
               $tot_logo_mat[aj, $amino_acids.size] = factor * Math::log(odds)
             end
@@ -1315,7 +1605,7 @@ HEADER
 # 
 # Shown here are logarithms of these values multiplied by #{$scale}/log(2) 
 HEADER
-          unless $noround
+          unless $noroundoff
             $outfh.puts <<HEADER
 # rounded to the nearest integer (log-odds scores in 1/#{$scale} bit units).
 HEADER
@@ -1326,43 +1616,120 @@ HEADER
 #
 HEADER
 
+          grp_max_val = grp_logo_mats.map { |l, m| m }.map { |m| m.max }.max
+          grp_min_val = grp_logo_mats.map { |l, m| m }.map { |m| m.min }.min
+          abs_max_val = [grp_max_val.abs, grp_min_val.abs].max
+          row_header  = $cys ? $amino_acids + %w[U] : $amino_acids
+          heatmaps    = HeatmapArray.new if $heatmap == 1 or $heatmap == 2
+          $heatmapcol ||= Math::sqrt(grp_logo_mats.size).round
+
           grp_logo_mats.each_with_index do |arr, grp_no|
             grp_label     = arr[0]
             grp_logo_mat  = arr[1]
+            stem          = "#{grp_no}. #{grp_label}"
 
-            unless $noround
+            unless $noroundoff
               grp_logo_mat = grp_logo_mat.round
             end
 
+            # for a matrix file
             $outfh.puts ">#{grp_label} #{grp_no}"
-            if $cys
-              $outfh.puts grp_logo_mat.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids + %w[U])
-            else
-              $outfh.puts grp_logo_mat.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids)
+            $outfh.puts grp_logo_mat.pretty_string(:col_header => $amino_acids,
+                                                   :row_header => row_header)
+            # for a heat map
+            if $heatmap == 0 or $heatmap == 2
+              grp_logo_mat.heatmap(:col_header          => $amino_acids,
+                                   :row_header          => row_header,
+                                   :rvg_width           => $rvg_width,
+                                   :rvg_height          => $rvg_height,
+                                   :canvas_width        => $canvas_width,
+                                   :canvas_height       => $canvas_height,
+                                   :gradient_beg_color  => '#0000FF',
+                                   :gradient_mid_color  => '#FFFFFF',
+                                   :gradient_end_color  => '#FF0000',
+                                   :max_val             => abs_max_val.ceil,
+                                   :mid_val             => 0,
+                                   :min_val             => -1 * abs_max_val.ceil,
+                                   :print_value         => $heatmapvalues,
+                                   :title               => stem).write("#{stem}.#{$heatmapformat}")
+
+              $logger.info "Generating a heat map for #{stem} table done."
+            end
+
+            if $heatmap == 1 or $heatmap == 2
+              heatmaps << grp_logo_mat.heatmap(:col_header          => $amino_acids,
+                                               :row_header          => row_header,
+                                               :rvg_width           => $rvg_width,
+                                               :rvg_height          => $rvg_height - 50,
+                                               :canvas_width        => $canvas_width,
+                                               :canvas_height       => $canvas_height - 50,
+                                               :gradient_beg_color  => '#0000FF',
+                                               :gradient_mid_color  => '#FFFFFF',
+                                               :gradient_end_color  => '#FF0000',
+                                               :max_val             => abs_max_val.ceil,
+                                               :mid_val             => 0,
+                                               :min_val             => -1 * abs_max_val.ceil,
+                                               :print_value         => $heatmapvalues,
+                                               :print_gradient      => false,
+                                               :title               => stem,
+                                               :title_font_size     => $rvg_width * $heatmapcol / 100.0)
             end
           end
 
-          $outfh.puts ">Total #{grp_logo_mats.size}"
+          # for heat maps in a single file
+          if $heatmap == 1 or $heatmap == 2
+            file = "#{$heatmapstem}.#{$heatmapformat}"
+            heatmaps.heatmap(:columns             => $heatmapcol,
+                             :rvg_width           => $rvg_width,
+                             :gradient_beg_color  => '#0000FF',
+                             :gradient_mid_color  => '#FFFFFF',
+                             :gradient_end_color  => '#FF0000',
+                             :max_val             => abs_max_val.ceil,
+                             :mid_val             => 0,
+                             :min_val             => -1 * abs_max_val.ceil).write(file)
+
+            $logger.info "Generating heat maps in a file, #{file} done."
+          end
 
-          unless $noround
+          # for a matrix file
+          unless $noroundoff
             $tot_logo_mat = $tot_logo_mat.round
           end
 
-          if $cys == 0
-            $outfh.puts $tot_logo_mat.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids + %w[U])
-          else
-            $outfh.puts $tot_logo_mat.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids)
+          $outfh.puts ">Total #{grp_logo_mats.size}"
+          $outfh.puts $tot_logo_mat.pretty_string(:col_header => $amino_acids,
+                                                  :row_header => row_header)
+
+          # for a heat map
+          if $heatmap == 0 or $heatmap == 2
+            stem            = "#{group_matrices.size}. TOTAL"
+            tot_abs_max_val = [$tot_logo_mat.max.abs, $tot_logo_mat.min.abs].max
+            $tot_logo_mat.heatmap(:col_header          => $amino_acids,
+                                  :row_header          => row_header,
+                                  :rvg_width           => $rvg_width,
+                                  :rvg_height          => $rvg_height,
+                                  :canvas_width        => $canvas_width,
+                                  :canvas_height       => $canvas_height,
+                                  :gradient_beg_color  => '#0000FF',
+                                  :gradient_mid_color  => '#FFFFFF',
+                                  :gradient_end_color  => '#FF0000',
+                                  :max_val             => tot_abs_max_val.ceil,
+                                  :mid_val             => 0,
+                                  :min_val             => -1 * tot_abs_max_val.ceil,
+                                  :print_value         => $heatmapvalues,
+                                  :title               => stem).write("#{stem}.#{$heatmapformat}")
+
+            $logger.info "Generating a heat map for #{stem} table done."
           end
 
-          $logger.info "Calculating log odds ratio is done."
-
-          #
-          # Part 7. END
-          #
+          $logger.info "Calculating log odds ratios done."
         end
 
+        #
+        # Part 7. END
+        #
+
         $outfh.close
-        $logger.info "Egor END."
         exit 0
       end
     end