#!/usr/bin/env ruby # Requires rubygems #ENV['MAGICK_CONFIGURE_PATH'] = '/gpfs/group/mdr23/usr/tools/etc/ImageMagick' Font_family = 'Verdana' SNPDefaultColor = 'black' DefaultEthnicity = '-' DefaultPhenotype = 'Unknown' $color_column_included = false ScriptDir =File.expand_path(File.dirname(__FILE__)) begin require 'rubygems' rescue LoadError => e puts e puts "Please install rubygems -- http://docs.rubygems.org/read/chapter/3 " exit(1) end # Requires RMagick (http://rmagick.rubyforge.org/) begin require 'rvg/rvg' rescue LoadError => e puts puts e puts "\nPlease install RMagick -- See documentation for pheno_gram or http://rmagick.rubyforge.org/install-faq.html " puts exit(1) end #require '/Users/dudeksm/lab/rails/visualization/lib/file_handling.rb' require 'optparse' require 'ostruct' include Magick Version = '1.2.0' Name = 'pheno_gram.rb' # check for windows and select alternate font based on OS Font_family_style = RUBY_PLATFORM =~ /mswin/ ? "Verdana" : "Times" Font_plot_family = RUBY_PLATFORM =~ /darwin/ ? "Verdana" : "Helvetica" if RUBY_PLATFORM =~ /darwin/ Font_phenotype_names = "Geneva" elsif RUBY_PLATFORM =~ /mswin/ Font_phenotype_names = "Verdana" else Font_phenotype_names = "Helvetica" end ############################################################################# # # Class Arg -- Parses the command-line arguments. # ############################################################################# class Arg def self.parse(args) options = OpenStruct.new options.input = nil options.genome_file = nil options.out_name = 'pheno_gram' options.imageformat = 'png' options.title = " " options.color = 'random' options.pheno_spacing = 'alternative' options.rand_seed = 7 options.chr_only = false options.circle_size = 'medium' options.circle_outline = false options.highres = false options.transparent_lines = false options.thickness_mult = 1 options.thin_lines = false options.color_file = nil options.big_font=false options.shade_inaccessible=false options.cytobandfile = "" options.include_notes=false options.zoomchr = nil options.zoomstart = nil options.zoomend = nil options.restrict_chroms = false options.transverse_lines = true options.group_file = nil options.spec_color_file = nil help_selected = false version_selected = false newargs = Array.new # concatenate any consecutive strings that do not - i=0 new_i=0 while(i < args.length) if(args[i] =~ /^\-/) newargs << args[i] i+=1 else newargs << args[i] i+= 1 new_i = newargs.length-1 while(args[i] !~ /\-/ and i < args.length) newargs[new_i] += " #{args[i]}" i+=1 end end end opts = OptionParser.new do |opts| opts.banner = "Usage: #{Name}.rb [options]" opts.on("-i [input_file]", "Input file") do |input_file| options.input = input_file end opts.on("-g [genome_file]", "Genome definition file"){|genome_file|options.genome_file = genome_file} opts.on("-o [out_name]", "Optional output name for image") do |out_name| options.out_name = out_name end opts.on("-t [title]", "Main title for plot (enclose in quotes)") do |title| title ? options.title = title : options.title=" " end opts.on("-X", "--chrom-only", "Plot only chromosomes with positions") do |chrom_only| options.chr_only = true end opts.on("-S [circle_size]", "Set phenotype circle size (small, medium, large)") do |circle_size| options.circle_size = circle_size end opts.on("-O", "--outline-circle", "Plot circles with black outline") do |outline_circle| options.circle_outline = true end opts.on("-c [color_range]", "Options are random, exhaustive (default), grayscale, web, generator,group or list") do |color_range| options.color = color_range end opts.on("-Z [zoom_location]", "Zoom on chromosome (7) or portion of chromsome (7:10000000-25000000)") do |zoom_location| unless zoom_location =~ /:/ options.zoomchr = Arg::split_nums(zoom_location) else loc = zoom_location.split(/:/) options.zoomchr = Arg::split_nums(loc[0]) positions = loc[1].split(/:|-/) options.zoomstart = positions[0].to_i options.zoomend = positions[1].to_i end end opts.on("-R", "--restrict-chroms", "Include only chromosomes with input data on plot"){|restrict|options.restrict_chroms=true} opts.on("-a", "--include-annotation", "Include any annotation on plot"){|notes|options.include_notes=true} opts.on("-z", "--high-res", "Set resolution to 600 dpi") {|hres| options.highres=true} opts.on("-T", "--trans-lines", "Make lines on chromosome more transparent") {|trans| options.transparent_lines=true} opts.on("-n", "--thin-lines", "Make lines across chromosomes thinner") {|thin| options.thin_lines=true} opts.on("-N", "--no-lines", "Remove position lines across chromosomes"){|nolines|options.transverse_lines=false} opts.on("-B", "--thick-boundary", "Increase thickness of chromosome boundary") {|thick| options.thickness_mult=2} opts.on("-F", "--big-font", "Increase font size of labels") {|big_font| options.big_font=true} opts.on("-x", "--cross-hatch", "Add cross-hatch shading to inaccessible regions of chromosomes"){|cross_hatch|options.shade_inaccessible=true} opts.on("-Y [cytoBand_file]", "Location of file with banding information for use with shading chromatin"){|cytoBand_file|options.cytobandfile=cytoBand_file} opts.on("-C [color_file]", "Color file for generator") do |color_file| options.color_file = color_file end opts.on("-s [spec_color_file]", "File for specifying colors to phenotypes") do |spec_color_file| options.spec_color_file = spec_color_file end opts.on("-G [group_file]", "File for specifying shapes for specific groups") do |group_file| options.group_file = group_file end opts.on("-p [pheno_spacing]", "Options are standard or equal or proximity (default) ") do |pheno_spacing| options.pheno_spacing = pheno_spacing options.pheno_spacing = 'alternative' if options.pheno_spacing == 'proximity' end opts.on("-r [random_seed]", "Random number generator seed (default=7") do |random_seed| options.rand_seed = random_seed.to_i end opts.on("-f [image_type]", "Image format for output (png default). Other options depend on ImageMagick installation.") do |image_type| options.imageformat = image_type end opts.on_tail("-h", "--help", "Show this usage statement") do puts opts help_selected = true end opts.on_tail("-v", "--version", "Show version") do puts "\n\tVersion: #{Version}" version_selected = true end end begin opts.parse!(newargs) rescue => e puts e, "", opts exit(1) end if version_selected puts exit(0) end if help_selected puts exit(0) end if !options.input help_string = opts.help puts "\n",help_string,"\n" puts "\nExamples: #{Name} -i pheno_input.txt -o new_plot -t \"New Image\"\n" puts " #{Name} -i pheno_input.txt -f jpg\n" print "\n" exit(1) end return options end # splits string up to list individual values def self.split_nums(str) values = Array.new pcs = str.split(/,/) pcs.each do |p| nums = p.split(/-/) if nums.length > 1 (nums[0].to_i..nums[1].to_i).each {|n| values << n} else values << nums[0] end end return values end end class Phenotype attr_accessor :name, :color, :sortnumber, :group def initialize(n,s,g) @name = n @sortnumber = s @group = g end end class PhenotypeHolder attr_accessor :phenonames, :maxname, :spec_colors def initialize(params) @pheno_number = 1 @spec_colors = Hash.new if params[:color]=='group' @colormaker = GroupColorMaker.new elsif params[:color]=='exhaustive' or params[:color] == 'optimized' @colormaker = ExhaustiveSearchColorMaker.new elsif params[:color]=='grayscale' @colormaker = GrayScaleColorMaker.new else @colormaker = ExhaustiveSearchColorMaker.new end @maxname = 0 @phenonames = Hash.new @phenocolororder = Array.new end def add_phenotype(name, group) unless @phenonames.has_key?(name) pheno = Phenotype.new(name, @pheno_number, group) @pheno_number += 1 @phenonames[pheno.name] = pheno @colormaker.add_group(group) @maxname = name.length unless @maxname > name.length @phenocolororder << pheno.name end return @phenonames[name] end def get_phenotype(name) return @phenonames[name] end def set_colors @colormaker.set_color_num(@phenonames.length) @phenocolororder.each do |phenoname| pheno = @phenonames[phenoname] if @spec_colors.has_key?(phenoname) pheno.color = @spec_colors[phenoname] else pheno.color = @colormaker.gen_html(pheno.group) end end end def set_color(groupname) if @spec_colors.has_key?(phenoname) return @spec_colors[phenoname] else return @colormaker.gen_html(groupname) end end end class Genome attr_accessor :chromosomes, :ethnicities, :designated_shapes def initialize @chromosomes = Array.new @ethnicities = Hash.new @shapefactory=ShapeFactory.new @max_chr_size=0 @chrNames = Hash.new @designated_shapes = Hash.new end def set_chroms(chroms) @chromosomes = chroms @max_chr_size=0 @chrNames.clear @chromosomes.each do |chr| @max_chr_size=chr.size if chr.size > @max_chr_size @chrNames[chr.display_num.to_s]=chr end end # remove any chromosomes that have no data points def remove_empty newchroms = Array.new newchroms << Chromosome.new(:number=>0, :size=>0) new_chr_names = Hash.new @max_chr_size = 0 @chromosomes.each do |chr| unless chr.snps.empty? @max_chr_size=chr.size if chr.size > @max_chr_size new_chr_names[chr.display_num.to_s]=chr newchroms << chr end end @chromosomes = newchroms @chrNames = new_chr_names end def remove_unwanted(keepers) keep = Hash.new keepers.each{|k|keep[k.to_s]=1} newchroms = Array.new newchroms << Chromosome.new(:number=>0, :size=>0) new_chr_names = Hash.new @max_chr_size = 0 @chromosomes.each do |chr| if keep.has_key?(chr.display_num.to_s) @max_chr_size=chr.size if chr.size > @max_chr_size new_chr_names[chr.display_num.to_s]=chr newchroms << chr end end @chromosomes = newchroms @chrNames = new_chr_names end def add_snp(params) shape = @shapefactory.get_shape(params[:eth],@designated_shapes) params[:chr].add_snp(:name=>params[:name], :pos=>params[:pos], :pheno=>params[:pheno], :chr=>params[:chr], :snpcolor=>params[:snpcolor], :endpos=>params[:endpos], :shape=>shape, :note=>params[:note]) @ethnicities[params[:eth]]=shape unless @ethnicities.has_key?(params[:eth]) end def snps_per_chrom @chromosomes.each do |chrom| puts "chrom #{chrom.display_num} has #{chrom.snps.length} SNPs" end end def pos_good?(pos, chr) return @chromosomes[chr.to_i].pos_good?(pos) end def get_chrom(chrid) if @chrNames.has_key?(chrid.to_s) return @chrNames[chrid.to_s] elsif chrid.to_i >=1 and chrid.to_i < @chromosomes.length return @chromosomes[chrid.to_i] else return nil end end def get_chrom_by_name(name) return @chrNames[name] end def get_eth_shapes return @shapefactory.get_phenotypes_shapes end def max_chrom_size return @max_chr_size end def max_in_range(chrom_nums) max=0 chrom_nums.each{|n| max = @chromosomes[n].size if @chromosomes[n].size > max} return max end def chr_good?(chrnum) return true if @chrNames.has_key?(chrnum) return true if chrnum.to_i >=1 and chrnum.to_i < @chromosomes.length return false end end class CytoBand attr_accessor :start, :finish, :type def initialize(params) @start = params[:start] || 0 @finish = params[:finish] || 0 @type = params[:type] || 0 end end class Chromosome attr_accessor :number, :snps, :snpnames, :centromere, :size, :display_num, :note_length, :cytobands, :maxphenos @@centromeres = Array.new @@centromeres << 0 @@centromeres << [121535434, 124535434] @@centromeres << [92326171, 95326171] @@centromeres << [90504854, 93504854] @@centromeres << [49660117, 52660117] @@centromeres << [46405641, 49405641] @@centromeres << [58830166, 61830166] @@centromeres << [58054331, 61054331] @@centromeres << [43838887, 46838887] @@centromeres << [47367679, 50367679] @@centromeres << [39254935, 42254935] @@centromeres << [51644205, 54644205] @@centromeres << [34856694, 37856694] @@centromeres << [16000000, 19000000] @@centromeres << [16000000, 19000000] @@centromeres << [17000000, 20000000] @@centromeres << [35335801, 38335801] @@centromeres << [22263006, 25263006] @@centromeres << [15460898, 18460898] @@centromeres << [24681782, 27681782] @@centromeres << [26369569, 29369569] @@centromeres << [11288129, 14288129] @@centromeres << [13000000, 16000000] @@centromeres << [58632012, 61632012] @@centromeres << [10104553, 13104553] # sizes taken from ensembl @@chromsize = Array.new @@chromsize << 0 @@chromsize << 249239465 @@chromsize << 243199373 @@chromsize << 199411731 @@chromsize << 191252270 @@chromsize << 180915260 @@chromsize << 171115067 @@chromsize << 159138663 @@chromsize << 146364022 @@chromsize << 141213431 @@chromsize << 135534747 @@chromsize << 135006516 @@chromsize << 133851895 @@chromsize << 115169878 @@chromsize << 107349540 @@chromsize << 102531392 @@chromsize << 90354753 @@chromsize << 81195210 @@chromsize << 78077248 @@chromsize << 64705560 @@chromsize << 63025520 @@chromsize << 48129895 @@chromsize << 51304566 @@chromsize << 155270560 @@chromsize << 59373566 @@display = Array.new def self.chromsize(n) return @@chromsize[n] end def self.create_human_chroms @@display.clear (1..22).each {|i| @@display[i]=i.to_s} @@display[23] = 'X' @@display[24] = 'Y' chroms = Array.new chroms << Chromosome.new(:id=>0, :centromere=>[], :size=>0, :number=>0) (1..24).each do |num| chroms << Chromosome.new(:id=>@@display[num], :centromere=>@@centromeres[num], :size=>@@chromsize[num], :number=>num) end return chroms end def initialize(params) @number = params[:number] @display_num = params[:id] @snps = Hash.new @snpnames = Array.new @centromere = params[:centromere] @size = params[:size] @centromere_triangle=Array.new @note_length=0 @cytobands = Array.new @maxphenos=0 end def add_snp(params) unless snp = @snps[params[:name]] snp = @snps[params[:name]] = SNP.new(params[:chr], params[:pos], params[:endpos]) @snpnames << params[:name] end if params[:note] snp.note = params[:note] @note_length = snp.note.length if snp.note.length > @note_length end snp.phenos << PhenoPoint.new(params[:pheno], params[:shape]) @maxphenos = snp.phenos.length if snp.phenos.length > @maxphenos snp.linecolors[params[:snpcolor]]=1 end def sort_snps! @snpnames.sort!{|x,y| @snps[x].pos.to_i <=> @snps[y].pos.to_i} end def add_cytoband(cyto) @cytobands << cyto end def pos_good?(pos) if pos.to_i <= @size return true else return false end end end class PhenoPoint attr_accessor :pheno, :shape def initialize(p,s) @pheno = p @shape = s end end class SNP attr_accessor :chrom, :pos, :phenos, :linecolors, :endpos, :note def initialize(c,p,e=nil) @chrom = c @pos = p e ? @endpos=e : @endpos = @pos @phenos = Array.new @linecolors = Hash.new end end class ColorMaker def add_group(groupname) end def gen_html(groupname) return "rgb(220,220,220)" end def set_color_num(nColors) @nColors = nColors end end class ColorRange attr_accessor :name, :start, :maxlum def initialize(n, st, maxl=85) @name = n @start = st @l_adjust=0 @maxlum=maxl end def set_intervals(total_colors) @l_adjust = (@maxlum.to_f - @start.luminance) / (total_colors-1) if total_colors > 1 end # vary the luminescence from dark to light def get_color color = @start.clone @start.luminance = @start.luminance + @l_adjust return [color.hue, color.saturation, color.luminance] end end class HSL attr_accessor :hue, :saturation, :luminance def initialize(hue, sat, lum) @hue = hue @saturation = sat @luminance = lum end # def to_color # return ColorSpaceHelper.hsl_to_rgb(@hue, @saturation, @luminance) # end end class GroupColorMaker < ColorMaker def initialize @color_ranges = Array.new # @color_ranges << ColorRange.new('blue', HSL.new(67, 100, 50)) # @color_ranges << ColorRange.new('red', HSL.new(0, 100, 50)) # @color_ranges << ColorRange.new('yellow', HSL.new(17, 100, 50),90) # @color_ranges << ColorRange.new('gray', HSL.new(0, 0, 50),95) # @color_ranges << ColorRange.new('green', HSL.new(33.3, 100, 25)) # @color_ranges << ColorRange.new('orange', HSL.new(6.7, 100, 50)) # @color_ranges << ColorRange.new('purple', HSL.new(83.3, 100, 25)) # @color_ranges << ColorRange.new('brown', HSL.new(7.2, 70, 22),80) # @color_ranges << ColorRange.new('pink-jeep', HSL.new(93.6, 72, 57)) @color_ranges << ColorRange.new('blue', HSL.new(240, 100, 50)) @color_ranges << ColorRange.new('red', HSL.new(0, 100, 50)) @color_ranges << ColorRange.new('yellow', HSL.new(60, 100, 50),90) @color_ranges << ColorRange.new('gray', HSL.new(0, 0, 38),95) @color_ranges << ColorRange.new('green', HSL.new(120, 100, 40)) @color_ranges << ColorRange.new('orange', HSL.new(30, 100, 50)) @color_ranges << ColorRange.new('purple', HSL.new(2700, 100, 40)) @color_ranges << ColorRange.new('brown', HSL.new(30,51,26),80) @color_ranges << ColorRange.new('pink-jeep', HSL.new(330,100,71)) @curr_group=0 @group_totals = Hash.new @groups = Hash.new @intervals_set=false end def add_group(g) unless @groups.has_key?(g) #print "adding group for #{g}\n" @curr_group = 0 if @curr_group == @color_ranges.length @groups[g]=@color_ranges[@curr_group] #print "curr_group is #{@curr_group}\n" @group_totals[g]=0 @curr_group+=1 end @group_totals[g]+=1 end def set_intervals @groups.each_pair{|groupname, color_range| color_range.set_intervals(@group_totals[groupname])} @intervals_set=true end def gen_html(groupname) set_intervals unless @intervals_set hsl = @groups[groupname].get_color #print "gen_html #{@name} hsl(#{hsl[0]}%,#{hsl[1]}%,#{hsl[2]}%)\n" return "hsl(#{hsl[0]},#{hsl[1]}%,#{hsl[2]}%)" end end class ExhaustiveSearchColorMaker < ColorMaker def initialize @index=0 @colors = ['rgb(0,0,255)','rgb(0,255,0)','rgb(255,0,0)','rgb(0,0,52)','rgb(255,0,176)','rgb(0,79,0)','rgb(255,213,0)','rgb(155,147,255)','rgb(12,255,188)','rgb(152,79,63)','rgb(0,124,144)','rgb(62,1,145)','rgb(177,198,112)','rgb(255,150,200)','rgb(254,143,57)','rgb(225,2,255)','rgb(125,0,87)','rgb(29,24,0)','rgb(225,2,82)','rgb(1,172,38)','rgb(37,242,255)','rgb(196,255,70)','rgb(139,108,0)','rgb(126,101,143)','rgb(254,184,152)','rgb(149,199,255)','rgb(8,157,118)','rgb(105,112,80)','rgb(0,98,255)','rgb(238,118,255)','rgb(165,24,0)','rgb(3,66,156)','rgb(180,255,213)','rgb(69,0,20)','rgb(255,204,105)','rgb(254,120,106)','rgb(162,255,142)','rgb(160,0,155)','rgb(180,164,167)','rgb(0,51,71)','rgb(130,172,0)','rgb(0,255,115)','rgb(2,123,192)','rgb(124,48,235)','rgb(180,99,183)','rgb(247,209,255)','rgb(82,54,0)','rgb(251,255,123)','rgb(218,65,137)','rgb(123,189,183)','rgb(0,66,43)','rgb(143,0,50)','rgb(64,8,95)','rgb(255,242,188)','rgb(94,67,69)','rgb(79,151,64)','rgb(139,83,211)','rgb(182,163,1)','rgb(176,91,121)','rgb(171,88,22)','rgb(178,153,96)','rgb(77,33,73)','rgb(94,216,0)','rgb(250,255,0)','rgb(251,92,48)','rgb(90,110,0)','rgb(13,187,224)','rgb(237,170,255)','rgb(112,211,141)','rgb(255,171,0)','rgb(109,15,0)','rgb(230,30,212)','rgb(35,221,192)','rgb(28,1,22)','rgb(255,115,211)','rgb(45,62,113)','rgb(129,169,123)','rgb(0,114,234)','rgb(255,3,59)','rgb(166,154,219)','rgb(237,141,147)','rgb(42,56,0)','rgb(105,115,124)','rgb(182,253,255)','rgb(3,216,116)','rgb(202,211,30)','rgb(106,69,143)','rgb(220,148,83)','rgb(211,79,102)','rgb(51,120,102)','rgb(254,194,202)','rgb(196,208,184)','rgb(196,144,179)','rgb(185,134,115)','rgb(255,0,130)','rgb(197,132,2)','rgb(0,0,181)','rgb(4,59,183)','rgb(199,82,255)','rgb(109,166,255)','rgb(206,255,173)','rgb(106,145,184)','rgb(67,117,63)','rgb(185,209,227)','rgb(142,100,50)','rgb(179,222,96)','rgb(133,0,181)','rgb(101,112,194)','rgb(120,39,70)','rgb(187,70,56)','rgb(155,151,54)','rgb(56,73,68)','rgb(2,92,132)','rgb(196,6,142)','rgb(113,38,147)','rgb(149,110,120)','rgb(61,24,0)','rgb(121,215,74)','rgb(97,93,30)','rgb(0,173,243)','rgb(1,72,255)','rgb(243,232,140)','rgb(0,22,122)','rgb(137,66,120)','rgb(209,120,91)','rgb(166,0,255)','rgb(193,125,239)','rgb(2,128,0)','rgb(0,160,153)','rgb(156,255,0)','rgb(255,112,0)','rgb(0,173,96)','rgb(132,152,137)','rgb(209,36,50)','rgb(77,67,40)','rgb(2,29,99)','rgb(0,36,32)','rgb(238,198,135)','rgb(240,214,75)','rgb(74,75,99)','rgb(253,220,199)','rgb(117,55,0)','rgb(210,1,8)','rgb(133,94,255)','rgb(126,138,74)','rgb(121,120,255)','rgb(255,115,158)','rgb(204,87,0)','rgb(216,72,196)','rgb(152,45,138)','rgb(121,205,169)','rgb(123,199,96)','rgb(183,217,162)','rgb(166,44,96)','rgb(207,101,162)','rgb(129,96,76)','rgb(139,224,255)','rgb(97,91,198)','rgb(180,173,208)','rgb(77,50,202)','rgb(124,255,96)','rgb(190,194,74)','rgb(106,47,46)','rgb(139,206,0)','rgb(36,34,64)','rgb(230,116,67)','rgb(199,158,63)','rgb(86,137,0)','rgb(200,175,146)','rgb(128,255,238)','rgb(5,235,55)','rgb(45,40,45)','rgb(130,255,197)','rgb(150,0,26)','rgb(181,68,209)','rgb(193,0,89)','rgb(45,27,231)','rgb(254,148,255)','rgb(255,84,100)','rgb(44,0,57)','rgb(230,255,219)','rgb(0,90,93)','rgb(252,173,68)','rgb(120,72,98)','rgb(0,130,69)','rgb(8,34,0)','rgb(134,166,179)','rgb(150,112,181)','rgb(82,102,157)','rgb(138,173,63)','rgb(169,0,221)','rgb(255,75,129)','rgb(69,31,45)','rgb(16,127,223)','rgb(162,64,78)','rgb(209,136,200)','rgb(52,198,207)','rgb(236,215,231)','rgb(111,245,157)','rgb(255,255,255)'] @final_color_index = @colors.length-1 end def gen_html(groupname) @index = 0 if @index > @final_color_index colorname = @colors[@index] @index += 1 return colorname end end class GrayScaleColorMaker < ColorMaker def initialize @darkgray = 68 @lightgray= 238 @colors = Array.new @index = 0 end def set_color_num(nColors) interval = (@lightgray-@darkgray)/(nColors-1).to_f if nColors > 1 currcolor = @darkgray @colors << "'rgb(#{currcolor},#{currcolor},#{currcolor})'" for i in 0..nColors-1 currcolor += interval @colors << "'rgb(#{currcolor},#{currcolor},#{currcolor})'" end @final_color_index = nColors-1 end def gen_html(groupname) @index = 0 if @index > @final_color_index colorname = @colors[@index] @index += 1 return colorname end end class FileHandler def close() @file.close end # strips and splits the line # returns the data array that results def strip_and_split(line) line.rstrip! line.split(/\s/) end def strip_and_split_delim(line,delim) line.rstrip! line.split(/#{delim}/) end end class GroupSpecFileReader < FileHandler def open(filename) @file = File.new(filename, "r") end def parse_file(filename) groupShapes = Hash.new firstline = true open(filename) headers = nil while oline=@file.gets oline.each_line("\r") do |line| if firstline headers = read_headers(line) firstline = false next end next unless line =~ /\w/ cols = strip_and_split_delim(line, "\t") groupShapes[cols[@groupcol]]=cols[@shapecol].downcase end end close return groupShapes end def read_headers(oline) oline.each_line("\r") do |line| cols = strip_and_split_delim(line, "\t") cols.each_with_index do |c,i| if c =~ /group|ethnicity|race/i @groupcol = i elsif c =~ /shape/i @shapecol = i end end end end end class ColorSpecReader < FileHandler def open(filename) @file = File.new(filename, "r") end def parse_file(filename) colors = Hash.new firstline = true open(filename) headers = nil while oline=@file.gets oline.each_line("\r") do |line| if firstline headers = read_headers(line) firstline = false next end next unless line =~ /\w/ cols = strip_and_split_delim(line, "\t") colors[cols[@phenocol]]=cols[@colorcol].downcase end end close return colors end def read_headers(oline) oline.each_line("\r") do |line| cols = strip_and_split_delim(line, "\t") cols.each_with_index do |c,i| if c =~ /phenotype/i @phenocol = i elsif c =~ /color/i @colorcol = i end end end end end class ChromosomeFileReader < FileHandler def initialize @idcol = 0 @sizecol = 1 @centcol = nil end def open(filename) @file = File.new(filename, "r") end def parse_file(filename) chroms = Array.new chroms << Chromosome.new(:number=>0, :size=>0) number=1 firstline = true open(filename) headers = nil while oline=@file.gets oline.each_line("\r") do |line| if firstline headers = read_headers(line) firstline = false next end next unless line =~ /\d/ cols = strip_and_split_delim(line, "\t") cent_array = Array.new if !@centcol.nil? if !cols[@centcol].nil? cent_array = cols[@centcol].split(",") end end centromere_info = cent_array.collect{|s| s.to_i} chroms << Chromosome.new(:id=>cols[@idcol], :centromere=>centromere_info, :size=>cols[@sizecol].to_i, :number=>number) number += 1 end end close return chroms end def read_headers(oline) oline.each_line("\r") do |line| cols = strip_and_split_delim(line, "\t") cols.each_with_index do |c,i| if c =~ /id/i @idcol = i elsif c =~ /size/i @sizecol = i elsif c =~ /centro/i @centcol = i end end end end end class CytoBandFileReader < FileHandler def open(filename) @file = File.new(filename, "r") end def parse_file(filename, genome) open(filename) headerline = @file.gets set_columns(headerline) while oline=@file.gets oline.each_line("\r") do |line| next unless line =~ /\w/ cols = strip_and_split_delim(line, "\t") cols[@chromcol] =~ /^chr(\w+)/ if $1 chromstr = $1; else chromstr = cols[@chromcol] end if cols[@endcol].to_f <= cols[@startcol].to_f next elsif cols[@startcol].to_f == 0 cols[@startcol] = 0.05 end cyto = CytoBand.new(:start=>cols[@startcol].to_f, :finish=>cols[@endcol].to_f, :type=>cols[@giecol]) genome.get_chrom(chromstr).add_cytoband(cyto) end end end def set_columns(headerline) @chromcol = @startcol = @endcol = @giecol = nil headers = strip_and_split_delim(headerline, "\t") headers.each_with_index do |header,i| if header =~ /#chrom/i @chromcol = i elsif header =~ /chromStart/i @startcol = i elsif header =~ /chromEnd/i @endcol = i elsif header =~ /gieStain/i @giecol = i end end unless @chromcol and @startcol and @endcol and @giecol error_string = 'Cytoband input file must include #chrom, chromStart, chromEnd, gieStain columns ' + pcs raise error_string end end end class PhenoGramFileReader < FileHandler def open(filename) @file = File.new(filename, "r") @snpcolors = ['black','blue','red','green','orange','purple','pink', 'gold'] end def set_columns(headerline, chr_only) @snpcol = @chromcol = @bpcol = @phenocol = @snpcolorcol = @bpendcol = nil headers = strip_and_split_delim(headerline, "\t") headers.each_with_index do |header, i| if header =~ /^snp$|^snp_id$/i @snpcol = i elsif header =~ /^chrom|^chr$/i @chromcol = i elsif header =~ /poscolor|snpcolor/i @snpcolorcol = i $color_column_included = true elsif header =~ /^bp|^pos|^start/i @bpcol = i elsif header =~ /^end/i @bpendcol = i elsif header =~ /^pheno/i @phenocol = i elsif header =~ /^colorgroup$|^colourgroup$/i @groupcol = i elsif header =~ /^race|^ethnic|^ancestry|^group/i @ethcol = i elsif header =~ /^annotation|^note/i @notecol = i end end unless @chromcol and @bpcol and (@phenocol || chr_only) error_string = 'Input file must include chrom, pos' error_string = error_string + ' and phenotype' unless chr_only error_string = error_string + ' columns' raise error_string end end def parse_file(filename, genome, phenoholder, params) positions_added=0 max_pos_allowed=params[:max_pos_allowed].to_i || 1000000 chr_only = params[:chr_only] || false if(params[:zoomchr]) included_chroms = Hash.new params[:zoomchr].each {|name| included_chroms[name.to_s]=1} end open(filename) lines = Array.new # read in all lines and split to accommodate Mac files while oline=@file.gets oline.each_line("\r") {|line| lines << line} end close set_columns(lines.shift, chr_only) group = 'default' lines.each do |line| next unless line =~ /\w/ data = strip_and_split_delim(line,"\t") # add SNP info next if data[@chromcol] =~ /chrM/ chromosome = genome.get_chrom(data[@chromcol]) raise "Problem in #{filename} with line:\n#{line}\n#{data[@chromcol]} is not a valid chromsome number" unless chromosome raise "Problem in #{filename} with line:\n#{line}\nPosition outside chromosome boundaries" unless chromosome.pos_good?(data[@bpcol]) group = data[@groupcol] if @groupcol @phenocol ? phenotype = data[@phenocol] : phenotype = DefaultPhenotype @snpcol ? name = data[@snpcol] : name = data[@chromcol] + "." + data[@bpcol] @snpcolorcol ? snpcolor = @snpcolors[data[@snpcolorcol].to_i] : snpcolor = SNPDefaultColor @bpendcol ? endbp = data[@bpendcol].to_i : endbp = data[@bpcol].to_i @ethcol ? ethnicity = data[@ethcol] : ethnicity = DefaultEthnicity if @notecol notecol = data[@notecol] if @notecol raise "Problem in #{filename} with line:\n#{line}\nAnnotation may be no longer than 10 characters in length" if notecol and notecol.length > 10 end # if(!params[:zoomchr] or (chromosome.display_num == params[:zoomchr] and # (!params[:zoomstart] or (data[@bpcol].to_i >= params[:zoomstart] and endbp <= params[:zoomend])))) if(!params[:zoomchr] or (included_chroms.has_key?(chromosome.display_num) and (!params[:zoomstart] or (data[@bpcol].to_i >= params[:zoomstart] and endbp <= params[:zoomend])))) pheno = phenoholder.add_phenotype(phenotype, group) genome.add_snp(:name => name, :chr=>chromosome, :pos=>data[@bpcol].to_i, :pheno=>pheno, :snpcolor=>snpcolor, :endpos=>endbp, :eth=>ethnicity, :note=>notecol) positions_added += 1 raise "Input file exceeded maximum allowed data points (#{max_pos_allowed})" if positions_added > max_pos_allowed end end phenoholder.set_colors end end class Plotter @@circle_size=0 @@maxchrom=0 @@drawn_circle_size=0 @@circle_multiplier=1 def self.set_circle(n, params) @@circle_size = n size = params[:size] if size == 'large' @@drawn_circle_size =@@circle_size*2 @@circle_multiplier = 2.0 elsif size == 'small' @@drawn_circle_size =@@circle_size/2 @@circle_multiplier = 0.5 else # medium (default) @@drawn_circle_size = @@circle_size @@circle_multiplier = 1.0 end end def self.get_circle_multiplier return @@circle_multiplier end def self.get_drawn_size return @@drawn_circle_size end def self.set_maxchrom(n) @@maxchrom=n end end class Circle attr_accessor :x, :y, :color def initialize(x,y,col) @x = x @y = y @color = color end end class ShapeFactory def initialize @shapes = Hash.new @shapecounter=1 end def get_shape(name, designated_shapes) if designated_shapes.has_key?(name) @shapes[name] = type_by_name(designated_shapes[name]) else unless @shapes.has_key?(name) @shapes[name] = create_shape(@shapecounter) @shapecounter+=1 end end return @shapes[name] end def get_phenotypes_shapes return @shapes end def type_by_name(shapename) case shapename when "circle" return PhenoCircle.new when "diamond" return PhenoDiamond.new when "triangle" return PhenoTriangle.new when "square" return PhenoSquare.new end end def create_shape(shapenum) case shapenum when 1 return PhenoCircle.new when 2 return PhenoDiamond.new when 3 return PhenoTriangle.new when 4 return PhenoSquare.new else return PhenoCircle.new end end end class PhenoShape def draw(pen,size,x,y,color,circle_outline) # base class end end class PhenoCircle < PhenoShape def draw(pen,size,x,y,color,circle_outline) pen.circle(size.to_f/2, x, y).styles(:fill=>color, :stroke=>circle_outline) end end class PhenoDiamond < PhenoShape def draw(pen,size,x,y,color,circle_outline) offset = size.to_f/2 pts = Array.new pts << x pts << y-offset pts << x+offset pts << y pts << x pts << y+offset pts << x-offset pts << y pen.polygon(pts).styles(:fill=>color, :stroke=>circle_outline) end end class PhenoSquare < PhenoShape def draw(pen,size,x,y,color,circle_outline) offset = size.to_f/2 xpt = x-offset ypt = y-offset height=width=size pen.rect(height,width,xpt,ypt).styles(:fill=>color, :stroke=>circle_outline) end end class PhenoTriangle < PhenoShape def draw(pen,size,x,y,color,circle_outline) offset = size.to_f/2 pts = Array.new pts << x pts << y-offset pts << x+offset pts << y+offset pts << x-offset pts << y+offset pen.polygon(pts).styles(:fill=>color, :stroke=>circle_outline) end end class PhenoBox < Plotter attr_accessor :top_y, :bottom_y, :circles, :phenocolors, :chrom_y, :height, :up, :line_colors, :chrom_end_y, :endpos, :phenoshapes, :note @@circles_per_row = 0 def self.set_circles_per_row(c) @@circles_per_row = c end def initialize @circles = Array.new @phenocolors = Array.new @phenoshapes = Array.new @up = true @line_colors = Array.new end def add_circle(x,y,color) @circles << Circle.new(x,y,color) end def add_phenocolor(p) @phenocolors << p end def add_shape(s) @phenoshapes << s end def add_line_color(color) @line_colors << color end def estimate_height # est = (@phenocolors.length.to_f/@@circles_per_row).ceil * @@drawn_circle_size return (@phenocolors.length.to_f/@@circles_per_row).ceil * @@drawn_circle_size end def set_default_boundaries(center, end_y) @chrom_y = center @chrom_end_y = end_y if @up adjust = -@@drawn_circle_size else adjust = @@drawn_circle_size end @top_y = center+adjust.to_f/4 if @phenocolors.length <= @@circles_per_row @bottom_y = @top_y + @@drawn_circle_size else # each row will overlap by 1/4 of a circle on one above @bottom_y = @top_y + @@drawn_circle_size + @@drawn_circle_size * 0.75 * @phenocolors.length/@@circles_per_row end @height = @bottom_y - @top_y end def set_even_boundaries(chrom_y, y, chrom_end_y) @chrom_y = chrom_y @chrom_end_y = chrom_end_y @top_y = y if @phenocolors.length <= @@circles_per_row @bottom_y = @top_y + @@drawn_circle_size else # each row will overlap by 1/4 of a circle on one above @bottom_y = @top_y + @@drawn_circle_size + @@drawn_circle_size * 0.75 * @phenocolors.length/@@circles_per_row end @height = @bottom_y - @top_y end # set the top and bottom location # top is simply halfway above first row def set_boundaries(center) @chrom_y = center @top_y = center#+adjust.to_f/4 if @phenocolors.length <= @@circles_per_row @bottom_y = @top_y + @@drawn_circle_size else # each row will overlap by 1/4 of a circle on one above @bottom_y = @top_y + @@drawn_circle_size + @@drawn_circle_size * 0.75 * @phenocolors.length/@@circles_per_row end @height = @bottom_y - @top_y end end class PhenoBin attr_accessor :actual_height,:height_needed, :starty, :endy, :boxes, :startbase, :endbase, :boxpos def initialize @actual_height=@height_needed=@starty=@endy=0 @boxes = Array.new @boxpos = Hash.new end def calc_height_needed @height_needed=0 @boxpos.each_value{|box| @height_needed+=box.height} return @height_needed end def estimate_height estimate_total=0 @boxpos.each_value{|box| estimate_total+=box.estimate_height} return estimate_total end def sort_boxes! @boxes.sort!{|x,y| x.to_i <=> y.to_i} end def height_discrepancy return @actual_height-@height_needed end def add_phenotype_snp(pos, endpos, col, shape, note=nil) if @boxpos.has_key?(pos) pbox = @boxpos[pos] else pbox = PhenoBox.new pbox.endpos = endpos @boxpos[pos]=pbox @boxes << pos end pbox.add_phenocolor(col) pbox.add_shape(shape) pbox.note = note if note # linecolors.each {|color| pbox.add_line_color(color)} end def add_linecolors(pos,linecolors) pbox = @boxpos[pos] linecolors.each{|color| pbox.add_line_color(color)} end def bp_from_y(y) return y/@actual_height.to_f * (@endbase-@startbase) + @startbase end def y_from_bp(bp) return (bp.to_f-@startbase)/(@endbase-@starbase) * @actual_height end def set_phenobox_y @height_needed=0 @boxpos.each_pair do |pos, phenobox| ycenter = (pos.to_i-@startbase)/(@endbase-@startbase).to_f * @actual_height @height_needed += phenobox.set_boundaries(ycenter) end end end # contains the phenoboxes class PhenoBinHolder attr_accessor :phenobins, :totalchromy, :totalbases, :totaly, :startbases def initialize @phenobins = Array.new end def set_num_bins(n) n.times do |i| @phenobins << PhenoBin.new @phenobins.last.actual_height = totaly.to_f/n end end # set base intervals for the bins def set_bases height=0 y=0 y_interval = @totaly.to_f/@phenobins.length curr_y = 0 base_interval = @totalbases.to_f/@phenobins.length currbase=0 @phenobins.each do |pb| pb.starty = curr_y pb.startbase = currbase currbase += base_interval curr_y += y_interval pb.endy = curr_y pb.endbase = currbase pb.actual_height = pb.endy-pb.starty end end # rails generate model PhenogramSize name:string description:string def get_box_array(y_from_top, chrom_size, total_chrom_y) final_phenoboxes = Array.new bin_y = y_from_top @phenobins.each do |pbin| phenoboxes = Array.new boxes_total = 0 pbin.boxpos.each_pair do |pos, phenobox| phenobox.top_y = bin_y + phenobox.top_y phenobox.bottom_y = bin_y + phenobox.bottom_y phenobox.chrom_y = pos.to_f / chrom_size * total_chrom_y phenobox.chrom_end_y = phenobox.endpos.to_f / chrom_size * total_chrom_y phenoboxes << phenobox boxes_total +=1 end phenoboxes.sort!{|x,y| x.top_y <=> y.top_y} # spread out phenoboxes throughout the bin if any collisions # if too many boxes for bin just arrange along as spread out as possible # if space and collisions again just spread out # if space and no collisions don't change top_y, bottom_y spread_boxes = false if pbin.height_needed > pbin.actual_height spread_boxes = true else j=phenoboxes.length-1 for i in 1..j if phenoboxes[i].top_y < phenoboxes[i-1].bottom_y spread_boxes=true break end end end if spread_boxes y_spread = pbin.actual_height / boxes_total.to_f phenoboxes.clear y_pos = 0 pbin.boxpos.each_pair do |pos, phenobox| phenobox.top_y = bin_y + y_pos phenobox.bottom_y = bin_y + (phenobox.bottom_y - phenobox.top_y) + y_pos phenobox.chrom_y = pos.to_f / chrom_size * total_chrom_y phenobox.chrom_end_y = phenobox.endpos.to_f / chrom_size * total_chrom_y y_pos += y_spread phenoboxes << phenobox end end bin_y += pbin.actual_height final_phenoboxes.push(*phenoboxes) end return final_phenoboxes end # adds a phenotype to appropriate bin def add_phenotype_snp(position, endpos, color, linecolors, shape, note) @phenobins.each do |pb| if position.to_i >= pb.startbase and position.to_i < pb.endbase pb.add_phenotype_snp(position, endpos, color, shape, note) return pb end end @phenobins.last.add_phenotype_snp(position, endpos, color, shape, note) return @phenobins.last3 end def set_pheno_positions @phenobins.each do |pb| pb.set_phenobox_y end end def show_bin_info @phenobins.each do |pb| puts "bin endy=#{pb.endy} startbase=#{pb.startbase} endbase=#{pb.endbase} actual_height=#{pb.actual_height}" pb.boxpos.each do |pos, box| puts "box pos=#{pos} topy=#{box.top_y} bottomy=#{box.bottom_y}" end puts "---- END BIN ----" end end # for each phenotype adjust its placement # relative to its enclosing bin def adjust_phenos i=0 @phenobins.each do |pb| y_span = pb.endy-pb.starty bp_span = pb.endbase - pb.startbase pb.boxes.each do |pos| box=pb.boxpos[pos] y_center = (pos.to_i-pb.startbase)/bp_span.to_f * y_span box.set_boundaries(y_center) end i+=1 end end # change the bp represented in a bin if it the top # and bottom boxes have additional space and # there isn't enough room to fit all the phenotype boxes # contained in it def adjust_bp @phenobins.each_with_index do |pbin, i| pbin.calc_height_needed pbin.sort_boxes! # do nothing when the bin has enough space for its phenotypes # no need to change the bp spread if pbin.actual_height <= pbin.height_needed or pbin.boxes.empty? next end topbp = pbin.startbase bottombp = pbin.endbase alter_top = alter_bottom = false # first check top y on first box to see if it is within the bin if pbin.boxpos[pbin.boxes.first].top_y > 0 topbp = pbin.bp_from_y(pbin.boxpos[pbin.boxes.first].top_y) alter_top=true end if pbin.boxpos[pbin.boxes.last].bottom_y < pbin.actual_height #bottombp = pbin.boxes.last bottombp = pbin.bp_from_y(pbin.boxpos[pbin.boxes.last].bottom_y) alter_bottom=true end # adjust for change in ratio #fract_adjust = (bottombp-topbp)/(pbin.endbase-pbin.startbase).to_f if alter_top pbin.startbase = topbp end if alter_bottom pbin.endbase = bottombp end # reposition phenotype boxes if any change in top or bottom if alter_top or alter_bottom pbin.set_phenobox_y end end end # place box in appropriate bin based on chromosome y value def add_pheno_box(box) # integer division works here index = box.chromy / @totalchromy @phenobins[index] << box end def estimate_height_needed total_height = 0 @phenobins.each do |b| total_height+=b.estimate_height end return total_height end def calculate_total_height total_height = 0 @phenobins.each do |b| total_height+=b.actual_height end return total_height end def calculate_height_needed total_height_needed = 0 @phenobins.each do |b| total_height_needed+=b.calc_height_needed end return total_height_needed end def total_bins total_height = calculate_total_height small_bins = Array.new large_bins = Array.new total_deficit=total_excess=0 # determine bins with too little height @phenobins.each_with_index do |b,i| if b.height_discrepancy < 0 small_bins << i total_deficit -= b.height_discrepancy else large_bins << i total_excess += b.height_discrepancy end end # when all bins are large enough return or if no bins have extra # space if small_bins.empty? or large_bins.empty? return end if total_deficit > total_excess fraction = 1.0 else fraction = total_deficit/total_excess.to_f end released_height = total_excess * fraction # shrink any bins that are too large large_bins.each do |i| # take all excess size when needed # only take fraction that is needed to make up deficit remove_amount = (@phenobins[i].height_discrepancy.to_f/total_excess) * released_height @phenobins[i].actual_height -= (@phenobins[i].height_discrepancy.to_f/total_excess) * released_height end # add height to the bins that are too small (add it proportionately # based on the size needed) small_bins.each do |i| add_amount = (-@phenobins[i].height_discrepancy.to_f/total_deficit) * released_height @phenobins[i].actual_height += (-@phenobins[i].height_discrepancy.to_f/total_deficit) * released_height end curr_y=0 phenobins.each_with_index do |pb,i| pb.starty = curr_y pb.endy = curr_y + pb.actual_height curr_y = pb.endy end end def add_chrom(chrom) chrom.snpnames.each do |snpname| snp = chrom.snps[snpname] pb=nil snp_pos = snp.pos-@startbases end_pos = snp.endpos-@startbases snp.phenos.each do |phenopt| pb=add_phenotype_snp(snp_pos, end_pos, phenopt.pheno.color, snp.linecolors.keys, phenopt.shape, snp.note) end pb.add_linecolors(snp_pos, snp.linecolors.keys) end end end class Chromline attr_accessor :colors def initialize @colors = Hash.new end def add_line(col) @colors.has_key?(col) ? @colors[col] += 1 : @colors[col] = 1 end end class ChromLineHolder attr_accessor :chromlines, :colors, :opacity def initialize(total_y, chromsize, opacity) @size = chromsize @chromlines = Array.new(total_y.ceil+1){|index| Chromline.new} @colors = Hash.new @opacity = opacity end # position is relative to start of chromosome def add_line(ypos, params) color = params[:stroke] || 'black' @chromlines[ypos.round].add_line(color) @colors[color]=1 end def draw_lines(params) xbase = params[:xstart] ybase = params[:ystart] canvas = params[:canvas] chrom_width = params[:chrom_width] @colors.each_key do |color| start_index = -1 last_value = -1 currvalue = 0 @chromlines.each_with_index do |chromline, i| chromline.colors.has_key?(color) ? currvalue= @opacity + ((chromline.colors[color]-1) * @opacity * 0.15): currvalue = 0 currvalue = 1.0 if currvalue > 1 # have to consider opacity when calculating values of objects if currvalue != last_value # draw last region when needed if last_value != -1 canvas.g.translate(xbase,ybase) do |draw| # draw it (box or line if only previous index) if start_index == i-1 #and start_index < 50 draw.line(0,start_index,chrom_width,start_index).styles(:stroke=>color, :stroke_width=>1, :stroke_opacity=>last_value) else end_index = i-start_index+start_index-1 draw.rect(chrom_width, end_index-start_index,0, start_index).styles(:stroke=>color, :stroke_width=>1, :stroke_opacity=>last_value, :fill_opacity=>last_value, :fill=>color) end end # set last_value = -1 and start_index = -1 to mark no valid object to draw start_index = -1 last_value = -1 end if currvalue > 0 last_value = currvalue start_index = i end end end if currvalue > 0 and start_index != -1 canvas.g.translate(xbase,ybase) do |draw| # draw it (box or line if only previous index) if start_index == @chromlines.length-1 #and start_index < 50 draw.line(0,start_index,chrom_width,start_index).styles(:stroke=>color, :stroke_width=>1, :stroke_opacity=>last_value) else end_index = @chromlines.length-1 draw.rect(chrom_width, end_index-start_index,0, start_index).styles(:stroke=>color, :stroke_width=>1, :stroke_opacity=>last_value, :fill_opacity=>last_value, :fill=>color) end end end end end end class ChromosomePlotter < Plotter @@chrom_width = 0 @@drawn_circles_per_row=@@num_phenos_row = 6 @@circle_outline = 'black' def self.set_chrom_width(w) @@chrom_width = w end def self.set_circle_outline(color) @@circle_outline=color end def self.calc_chr_per_row(total_num_chromosomes) # want fewest rows for the smallest number in a row # then largest value for that number of rows fewest_rows = 100000 min = 6 max = 12 for i in min..max val = total_num_chromosomes.to_f/i fewest_rows = val.to_i if val.to_i < fewest_rows end number_to_use = 0 for i in (min..max).to_a.reverse val = total_num_chromosomes.to_f/i if val == fewest_rows number_to_use = i break end number_to_use = i if val.to_i == fewest_rows end return number_to_use end def self.set_phenos_row(p, params) @@num_phenos_row = p size = params[:size] if size == 'large' @@drawn_circles_per_row = p/2 elsif size == 'small' @@drawn_circles_per_row = p*2-1 else # medium @@drawn_circles_per_row = p end PhenoBox.set_circles_per_row(@@drawn_circles_per_row) end def self.init_phenobinholder(params) binholder = PhenoBinHolder.new binholder.totalchromy = params[:chrom_y] binholder.totaly = params[:available_y] binholder.totalbases = params[:chrom].size binholder.totalbases = params[:chrom_size] binholder.startbases = params[:chrom_start] binholder.set_num_bins(5) binholder.set_bases return binholder end def self.set_cyto_colors @@cytocolors = Hash.new @@cytocolors['gneg'] = 'white' # grays from http://www.j-a-b.net/web/hue/color-grayscale.phtml @@cytocolors['gpos25'] = '#ECECEC' @@cytocolors['gpos33'] = '#E1E1E1' @@cytocolors['gpos50'] = '#C7C7C7' @@cytocolors['gpos66'] = '#AFAFAF' @@cytocolors['gpos75'] = '#9F9F9F' @@cytocolors['gpos100'] = '#787878' #blues @@cytocolors['stalk'] = '#63B8FF' @@cytocolors['gvar'] = '#4F94CD' @@cytocolors['acen'] = '#0000A0' @@cytocolors['gpos'] = '#C7C7C7' @@cytocolors['black'] = '#000000' @@cytocolors['red'] = '#FF0000' end # utilizes new algorithm to place boxes # maintains relative location along chromosome def self.position_phenoboxes(params) absolutey=totaly = params[:available_y] totalchromy = params[:chrom_y] chrom = params[:chrom] chrom.sort_snps! chrom_size = params[:chrom_size] chrom_start = params[:chrom_start] || 0 binholder=init_phenobinholder(params) # add phenotypes to the bins binholder.add_chrom(chrom) # check to see if can shrink the plotting area to the chromosome only orig_phenobox_offset = phenobox_offset = -((totaly-totalchromy.to_f)/2) estimated_tot=binholder.estimate_height_needed if estimated_tot < totalchromy params[:available_y] = params[:chrom_y] binholder=init_phenobinholder(params) totaly = totalchromy binholder.add_chrom(chrom) phenobox_offset = 0 elsif estimated_tot < totaly adjustedy = estimated_tot params[:available_y] = adjustedy binholder=init_phenobinholder(params) totaly = adjustedy binholder.add_chrom(chrom) phenobox_offset = (totalchromy-estimated_tot.to_f)/2 end binholder.set_pheno_positions # adjust size of bins binholder.total_bins # remap the phenotypes to the bins binholder.adjust_phenos # change bp on bins so top of bin in bp matches first pheno/ # and bottom of bin in bp matches last pheno binholder.adjust_bp # place phenoboxes in an array with locations relative to # the absolute base position phenoboxes = binholder.get_box_array(phenobox_offset,chrom_size,totalchromy) return phenoboxes if phenoboxes.empty? return phenoboxes end # move the boxes for collisions def self.adjust_collisions(phenoboxes, available_y, offset) total_boxes = phenoboxes.length last_index = total_boxes-1 notdone = true rounds=0 while(notdone and rounds < 7) notdone = false for i in (0..last_index) for j in (i+1..last_index) if phenoboxes[i].bottom_y > phenoboxes[j].top_y move_boxes(phenoboxes, available_y, i, j, offset) notdone=true end end end rounds += 1 end end def self.shift_boxes(phenoboxes, i, moveup) if moveup if phenoboxes[i+1].top_y > (phenoboxes[i].bottom_y-phenoboxes[i].height) phenoboxes[i].bottom_y = phenoboxes[i+1].top_y phenoboxes[i].top_y = phenoboxes[i].bottom_y - phenoboxes[i].height else phenoboxes[i].top_y -= phenoboxes[i].height phenoboxes[i].bottom_y -= phenoboxes[i].height end else if phenoboxes[i-1].bottom_y < (phenoboxes[i].top_y+phenoboxes[i].height) phenoboxes[i].top_y = phenoboxes[i-1].bottom_y phenoboxes[i].bottom_y = phenoboxes[i].top_y+phenoboxes[i].height else phenoboxes[i].bottom_y += phenoboxes[i].height phenoboxes[i].top_y += phenoboxes[i].height end end end def self.move_boxes(phenoboxes, available_y, i, j, offset) last_index = phenoboxes.length-1 # check for room on top and bottom toproom=bottomroom=false if (i==0 or (phenoboxes[i].top_y - phenoboxes[i].height > phenoboxes[i-1].bottom_y)) and phenoboxes[0].top_y > offset toproom=true end if (j==last_index or (phenoboxes[j].bottom_y+phenoboxes[j].height < phenoboxes[j].top_y)) and phenoboxes.last.top_y < available_y + offset bottomroom=true end # move in direction with more space available # use xor to move in direction when only one available # when both are ok or neither is, move in direction of more available space if (toproom and bottomroom)# or (!toproom and !bottomroom) topdist = (phenoboxes[i].top_y.to_f - offset) / i bottomdist = (available_y.to_f - phenoboxes[j].bottom_y-offset)/(last_index-j) if topdist > bottomdist shift_boxes(phenoboxes,i,true) else shift_boxes(phenoboxes,j,false) end elsif toproom # shift top box up shift_boxes(phenoboxes, i, true) elsif bottomroom # shift lower box down shift_boxes(phenoboxes, j, false) end # when no room do nothing end def self.plot_chrom(params) padding = @@circle_size*4 # leave some space at top and bottom available_y = params[:height]-padding maxchromsize = params[:maxchrom] || @@maxchrom chrom = params[:chrom] chrom_start = params[:zoomstart]|| 0 params[:zoomstart] ? chrom_size = params[:zoomend]-params[:zoomstart] : chrom_size = chrom.size.to_f # determine location of the chromosome -- leave a circle at top and bottom total_chrom_y = chrom_size/ maxchromsize * available_y # create a number of bins to hold information for each possible line unless $color_column_included params[:transparent] ? opacity = 0.05 : opacity = 1.0 else params[:transparent] ? opacity = 0.35 : opacity = 1.0 end line_container = ChromLineHolder.new(total_chrom_y.ceil, chrom_size, opacity) start_chrom_y = padding.to_f/2 + (available_y-total_chrom_y).to_f/2 end_chrom_y = start_chrom_y + total_chrom_y canvas = params[:canvas] xbase = params[:xstart] ybase = params[:ystart] #circle_start_x = @@circle_size*3 circle_start_x = @@chrom_width + @@circle_size*1.5 circle_start_x += @@circle_size * 4 if params[:zoomchr] centromere_pos = chrom.centromere unless(centromere_pos.empty? or (params[:zoomstart] and (centromere_pos[0] < params[:zoomstart] or centromere_pos[1] > params[:zoomend]))) centromere_y = total_chrom_y * ((((centromere_pos[0]+centromere_pos[1])/2)-chrom_start)/chrom_size.to_f) + start_chrom_y centromere_start = total_chrom_y * ((centromere_pos[0]-chrom_start)/chrom_size.to_f) + start_chrom_y centromere_end = total_chrom_y * ((centromere_pos[1]-chrom_start)/chrom_size.to_f) + start_chrom_y end params[:zoomstart] ? startbp = params[:zoomstart] : startbp = 0 params[:zoomend] ? endbp = params[:zoomend] : endbp = chrom.size draw_chr(:canvas=>canvas, :centromere_y=>centromere_y, :start_chrom_y=>start_chrom_y, :end_chrom_y=>end_chrom_y, :xbase=>xbase, :ybase=>ybase, :chromnum=>chrom.display_num, :thickness_mult=>params[:thickness_mult], :chr_only=>params[:chr_only], :bigtext=>params[:bigtext], :cent_start=>centromere_start, :cent_end=>centromere_end, :shade=>params[:shade], :startbp=>startbp, :endbp=>endbp, :chrom_start=>chrom_start, :chrom_bp=>chrom_size, :chrom=>chrom, :increase_cyto_opacity=>!params[:draw_transverse]) if params[:chr_only] or !(params[:alt_spacing]==:alternative or params[:alt_spacing]==:equal) phenoboxes = get_pheno_boxes(total_chrom_y, chrom, chrom_size, chrom_start) phenoboxes.sort!{|x,y| x.top_y <=> y.top_y} phenoboxes.each do |box| draw_phenos(canvas, box, circle_start_x, xbase, ybase + start_chrom_y, line_container, :chr_only=>params[:chr_only], :transparent=>params[:transparent], :include_notes=>params[:include_notes], :bigtext=>params[:bigtext], :draw_transverse=>params[:draw_transverse]) end line_container.draw_lines(:canvas=>canvas, :xstart=>xbase, :ystart=>ybase + start_chrom_y, :chrom_width=>@@chrom_width) elsif params[:alt_spacing]==:alternative phenoboxes = position_phenoboxes(:chrom=>chrom, :available_y=>available_y, :chrom_y=>total_chrom_y, :chrom_size=>chrom_size, :chrom_start=>chrom_start) phenoboxes.sort!{|x,y| x.top_y <=> y.top_y} phenoboxes.each do |box| draw_phenos(canvas, box, circle_start_x, xbase, ybase + start_chrom_y, line_container, :chr_only=>false, :include_notes=>params[:include_notes], :bigtext=>params[:bigtext], :draw_transverse=>params[:draw_transverse]) end line_container.draw_lines(:canvas=>canvas, :xstart=>xbase, :ystart=>ybase + start_chrom_y, :chrom_width=>@@chrom_width) elsif params[:alt_spacing]==:equal orig_circle=@@circle_size phenoboxes = get_pheno_boxes_equal_spacing(available_y, total_chrom_y, chrom, chrom_size, chrom_start) # sort by y location phenoboxes.sort!{|x,y| x.top_y <=> y.top_y} phenoboxes.each do |box| draw_phenos_equal(canvas, box, circle_start_x, xbase, ybase + padding.to_f/2, :chr_only=>params[:chr_only], :include_notes=>params[:include_notes], :bigtext=>params[:bigtext], :draw_transverse=>params[:draw_transverse]) end @@circle_size=orig_circle end if params[:zoomstart] interval_y = end_chrom_y - start_chrom_y mini_start_y = start_chrom_y + interval_y / 3.to_f mini_end_y = end_chrom_y - interval_y / 3.to_f mini_interval_y = mini_end_y - mini_start_y mini_startbp = 0 mini_chromsize = chrom.size if centromere_pos[0] centromere_y = mini_interval_y * (((centromere_pos[0]+centromere_pos[1])/2)/chrom.size.to_f) + mini_start_y centromere_start = mini_interval_y * (centromere_pos[0]/chrom.size.to_f) + mini_start_y centromere_end = mini_interval_y * (centromere_pos[1]/chrom.size.to_f) + mini_start_y end params[:chr_only] ? chrom_width_mult=4 : chrom_width_mult=6 mini_xbase = xbase-@@chrom_width*chrom_width_mult width_adjust=0.5 draw_chr(:canvas=>canvas, :centromere_y=>centromere_y, :start_chrom_y=>mini_start_y, :end_chrom_y=>mini_end_y, :xbase=>mini_xbase, :ybase=>ybase, :chromnum=>chrom.display_num, :thickness_mult=>params[:thickness_mult], :chr_only=>true, :bigtext=>params[:bigtext], :cent_start=>centromere_start, :cent_end=>centromere_end, :shade=>params[:shade], :chrom_start=>mini_startbp, :chrom_bp=>mini_chromsize, :chrom=>chrom, :width_adjust=>width_adjust) # draw lines showing where the zoom occurs mini_z_start_y = mini_interval_y * (chrom_start/chrom.size.to_f) + mini_start_y mini_z_end_y = mini_interval_y * ((chrom_start+chrom_size)/chrom.size.to_f) + mini_start_y connect_start_y = start_chrom_y connect_end_y = end_chrom_y min_x_start = @@chrom_width*width_adjust min_x_ext = @@chrom_width + min_x_start min_x_end = @@chrom_width*(chrom_width_mult-1) line_top= [min_x_start, mini_z_start_y, min_x_ext, mini_z_start_y, min_x_end, connect_start_y] line_bottom=[min_x_start, mini_z_end_y, min_x_ext, mini_z_end_y, min_x_end, connect_end_y] stroke_width = get_stroke_width(params) canvas.g.translate(mini_xbase,ybase) do |draw| draw.polyline(line_top).styles(:stroke=>'darkgray',:stroke_width=>stroke_width, :fill=>'none') draw.polyline(line_bottom).styles(:stroke=>'darkgray',:stroke_width=>stroke_width, :fill=>'none') end end end # ybase is from start of chromosome drawing # need start of chromosome and start of bins def self.draw_phenos(canvas, phenobox, start_x, xbase, ybase, line_container, params) y = phenobox.top_y - @@drawn_circle_size * 0.75 x = start_x unless $color_column_included params[:transparent] ? opacity = 0.05 : opacity = 1.0 else params[:transparent] ? opacity = 0.55 : opacity = 1.0 end annotation_x=annotation_y=0 font_size = get_font_size(params) / 1.35 phenobox.line_colors.each do |linecolor| canvas.g.translate(xbase,ybase) do |draw| if params[:draw_transverse] if phenobox.chrom_end_y - phenobox.chrom_y <= 1.0 line_container.add_line(phenobox.chrom_y, :stroke=>linecolor) else (phenobox.chrom_end_y-phenobox.chrom_y).round.times {|i| line_container.add_line(phenobox.chrom_y+i, :stroke=>linecolor)} end end if params[:chr_only] if params[:include_notes] and phenobox.note annotation_x = start_x-@@circle_size annotation_y = phenobox.chrom_y+@@drawn_circle_size.to_f/2.25 end else draw.line(@@chrom_width,phenobox.chrom_y.round,start_x,phenobox.top_y).styles(:stroke=>linecolor,:stroke_width=>1) unless params[:chr_only] end end end unless params[:chr_only] x = start_x annotation_y = y+@@drawn_circle_size.to_f/2.25 + @@drawn_circle_size * 0.75 phenobox.phenocolors.each_with_index do |color, i| if i % @@drawn_circles_per_row == 0 y += @@drawn_circle_size * 0.75 x = start_x end canvas.g.translate(xbase, ybase) do |draw| phenobox.phenoshapes[i].draw(draw,@@drawn_circle_size,x,y,color,@@circle_outline) end x += @@drawn_circle_size end if params[:include_notes] and phenobox.note phenobox.phenocolors.length >= @@drawn_circles_per_row ? annotation_x = start_x + @@drawn_circles_per_row* @@drawn_circle_size : annotation_x = x end end if params[:include_notes] and phenobox.note canvas.g.translate(xbase, ybase).text(annotation_x,annotation_y) do |write| write.tspan(phenobox.note).styles(:font_size=>font_size, :text_anchor=>'start') end end end # ybase is from start of chromosome drawing def self.draw_phenos_equal(canvas, phenobox, start_x, xbase, ybase, params) y = phenobox.top_y - @@circle_size * 0.75 x = start_x annotation_y = y+@@drawn_circle_size.to_f/2.25 + @@drawn_circle_size * 0.75 phenobox.line_colors.each do |linecolor| canvas.g.translate(xbase,ybase) do |draw| if phenobox.chrom_end_y - phenobox.chrom_y <= 1.0 draw.line(0, phenobox.chrom_y, @@chrom_width, phenobox.chrom_y).styles(:stroke=>linecolor, :stroke_width=>1) else draw.rect(@@chrom_width, phenobox.chrom_end_y-phenobox.chrom_y,0, phenobox.chrom_y).styles(:stroke=>linecolor, :stroke_width=>1, :fill=>linecolor) end draw.line(@@chrom_width,phenobox.chrom_y,start_x,phenobox.top_y).styles(:stroke=>linecolor,:stroke_width=>1) unless params[:chr_only] end end phenobox.phenocolors.each_with_index do |color, i| if i % @@num_phenos_row == 0 y += @@circle_size * 0.75 x = start_x end canvas.g.translate(xbase, ybase) do |draw| # draw.circle(@@circle_size.to_f/2, x, y).styles(:fill=>color, :stroke=>'black') phenobox.phenoshapes[i].draw(draw,@@drawn_circle_size,x,y,color,@@circle_outline) end x += @@circle_size end if params[:include_notes] and phenobox.note font_size = get_font_size(params) x = start_x + @@drawn_circles_per_row* @@drawn_circle_size if phenobox.phenocolors.length >= @@drawn_circles_per_row canvas.g.translate(xbase, ybase).text(x,annotation_y) do |write| write.tspan(phenobox.note).styles(:font_size=>font_size, :text_anchor=>'start') end end end # adds phenotypes to sets matching same SNP def self.get_pheno_boxes(total_chrom_y, chrom, chrom_size, chrom_start=0) pheno_boxes = Array.new chrom.snps.each_value do |snp| # center of first circle that will be pointed at pos_fraction = (snp.pos.to_f-chrom_start)/chrom_size y_offset = pos_fraction * total_chrom_y y_end = (snp.endpos.to_f-chrom_start)/chrom_size * total_chrom_y phenobox = PhenoBox.new if pos_fraction <= 0.5 phenobox.up = true else phenobox.up = false end phenobox.note = snp.note snp.phenos.each do |phenopt| phenobox.add_phenocolor(phenopt.pheno.color) phenobox.add_shape(phenopt.shape) end snp.linecolors.each_key {|col| phenobox.add_line_color(col)} phenobox.set_default_boundaries(y_offset, y_end) pheno_boxes << phenobox end return pheno_boxes end # for this case can spread the snps out along the chromosome and the entire # box dedicated to the chromosomes def self.get_pheno_boxes_equal_spacing(available_y, total_chrom_y, chrom, chrom_size, chrom_start) pheno_boxes = Array.new # determine amount of y dedicated to each snp y_per_snp = available_y/chrom.snpnames.length.to_f y = 0 chrom_offset = (available_y - total_chrom_y.to_f)/2 # change circle size based on number of snps if y_per_snp < 20 if y_per_snp > 10 @@circle_size = y_per_snp else @@circle_size = 10 end end # sort by position chrom.sort_snps! chrom.snpnames.each do |snpname| snp = chrom.snps[snpname] pos_fraction = (snp.pos.to_f-chrom_start)/chrom_size y_offset = pos_fraction * total_chrom_y + chrom_offset y_end = (snp.endpos.to_f-chrom_start)/chrom_size * total_chrom_y + chrom_offset phenobox = PhenoBox.new snp.phenos.each do |phenopt| phenobox.add_phenocolor(phenopt.pheno.color) phenobox.add_shape(phenopt.shape) end phenobox.note = snp.note snp.linecolors.each_key {|col| phenobox.add_line_color(col)} phenobox.set_even_boundaries(y_offset, y, y_end) pheno_boxes << phenobox y += y_per_snp end return pheno_boxes end def self.get_font_size(params) params[:bigtext] ? font_size = @@circle_size * 1.5 : font_size = @@circle_size end def self.get_stroke_width(params) line_thickness = params[:thickness_mult] || 1 stroke_width = @@circle_size / 10 * line_thickness stroke_width = 1 if stroke_width < 1 return stroke_width end def self.draw_chr(params) canvas = params[:canvas] centromere_y = params[:centromere_y] centromere_start = params[:cent_start] centromere_end = params[:cent_end] start_chrom_y = params[:start_chrom_y] end_chrom_y = params[:end_chrom_y] xbase = params[:xbase] ybase = params[:ybase] number = params[:chromnum] chrom = params[:chrom] chrom_start = params[:chrom_start] chrom_bp = params[:chrom_bp] width_adjust = params[:width_adjust] || 1.0 increase_cyto_opacity = params[:increase_cyto_opacity] || false total_chrom_y = end_chrom_y-start_chrom_y chrom_width = @@chrom_width * width_adjust centromere_offset = chrom_width/2 stroke_width = get_stroke_width(params) tpath = "M0,#{start_chrom_y} C0,#{start_chrom_y-@@circle_size/2} #{chrom_width},#{start_chrom_y-@@circle_size/2} #{chrom_width},#{start_chrom_y}" bpath = "M0,#{end_chrom_y} C0,#{end_chrom_y+@@circle_size/2} #{chrom_width},#{end_chrom_y+@@circle_size/2} #{chrom_width},#{end_chrom_y}" if params[:shade] #and centromere_y increase_cyto_opacity ? fill_opacity = 0.95 : fill_opacity = 0.7 chrom.cytobands.each do |band| canvas.g.translate(xbase,ybase) do |draw| band_start = (total_chrom_y * ((band.start-chrom_start)/chrom_bp.to_f) + start_chrom_y).round next if band_start >= end_chrom_y band_end = (total_chrom_y * ((band.finish-chrom_start)/chrom_bp.to_f) + start_chrom_y).round # ensure no overlap on banding band_end = end_chrom_y if band_end > end_chrom_y @@cytocolors[band.type] ? fill_color = @@cytocolors[band.type] : fill_color = band.type draw.rect(chrom_width, band_end-band_start, 0, band_start).styles(:stroke=>'none', :fill=>fill_color, :fill_opacity=>fill_opacity) end end end # if drawing chromosomes only fill in with white the centromere triangle # to overwrite any regions that are over the centromere if centromere_y canvas.g.translate(xbase,ybase) do |draw| # draw triangle and fill it with white 'rgb(255,255,255)' draw.styles(:fill=>'rgb(255,255,255)', :stroke=>'rgb(255,255,255)') xpoints = [0,centromere_offset.to_f/2,0] ypoints = [centromere_start,centromere_y,centromere_end] draw.polygon(xpoints, ypoints).styles(:stroke_width=>2) xpoints = [chrom_width, chrom_width-centromere_offset.to_f/2,chrom_width] ypoints = [centromere_start, centromere_y,centromere_end] draw.polygon(xpoints, ypoints).styles(:stroke_width=>stroke_width) end end chrom_style = {:stroke=>'darkgray',:stroke_width=>stroke_width, :fill=>'none'} if centromere_y line1 = [0,start_chrom_y,0,centromere_start,centromere_offset.to_f/2,centromere_y, 0,centromere_end,0,end_chrom_y] line2 = [chrom_width,start_chrom_y,chrom_width,centromere_start,chrom_width-centromere_offset.to_f/2,centromere_y, chrom_width,centromere_end, chrom_width,end_chrom_y] else line1 = [0,start_chrom_y, 0, end_chrom_y] line2 = [chrom_width, start_chrom_y, chrom_width, end_chrom_y] end canvas.g.translate(xbase,ybase) do |draw| draw.polyline(line1).styles(:stroke=>'darkgray',:stroke_width=>stroke_width, :fill=>'none') draw.path(tpath).styles(chrom_style) if chrom_start == 0 draw.polyline(line2).styles(:stroke=>'darkgray',:stroke_width=>stroke_width, :fill=>'none') draw.path(bpath).styles(chrom_style) if chrom_bp + chrom_start >= chrom.size end font_size = get_font_size(params) # add basepair locations for partial chroms unless chrom_start == 0 canvas.g.translate(xbase,ybase).text(-chrom_width/4,start_chrom_y) do |write| write.tspan(chrom_start.to_i).styles(:font_size=>font_size/1.25, :text_anchor=>'end') end end unless chrom_bp + chrom_start >= chrom.size canvas.g.translate(xbase,ybase).text(-chrom_width/4,end_chrom_y+@@circle_size) do |write| write.tspan(chrom_start.to_i+chrom_bp.to_i).styles(:font_size=>font_size/1.25, :text_anchor=>'end') end end canvas.g.translate(xbase,ybase).text(chrom_width.to_f/2,end_chrom_y+1.6*font_size) do |write| write.tspan(number.to_s).styles(:font_size=>font_size, :text_anchor=>'middle') end end end class Title < Plotter def self.draw(params) xbase = params[:ybase] ybase = params[:xbase] anchor = params[:anchor] || 'middle' end def self.draw_center(params) xtotal = params[:xtotal] xcenter = params[:xpos] || xtotal.to_f/2 title = params[:title] ypos = params[:ypos] canvas = params[:canvas] font_size = @@circle_size * 1.7 canvas.g.translate(xcenter,ypos).text(0,0) do |write| write.tspan(title).styles(:font_size=>font_size, :text_anchor=>'middle') end end end class Ethlabels < Plotter def self.draw(params) canvas=params[:canvas] ystart=params[:ystart] xstart=params[:xstart] xtotal=params[:xtotal] shapes_per_row=params[:shapes_per_row] eth_shapes=params[:eth_shapes] if params[:bigtext] font_size = 33 vert_offset = 2 y_offset = 2.5 else font_size = 22 vert_offset = 2 y_offset = 2 end shape_space = xtotal.to_f/shapes_per_row y = 0 x = 0 shape_size = @@circle_size curr_eth=0 eth_shapes.each_pair do |ethnicity, shape| canvas.g.translate(xstart,ystart) do |pen| shape.draw(pen,shape_size,x,y,'none','black') end canvas.g.translate(xstart,ystart).text(x+@@circle_size*1.5,y+@@circle_size.to_f/vert_offset) do |text| text.tspan(ethnicity).styles(:font_size=>font_size) end x+=shape_space curr_eth+=1 if curr_eth % shapes_per_row==0 y+=@@circle_size*y_offset x=0 end end end end class PhenotypeLabels < Plotter def self.phenotypes_per_row(maxname_length, params) # total number of characters for each type if(params[:big_font]) if params[:zoom] label_size = 33 char_per_row = label_size * 3 else label_size = 32 char_per_row = label_size * 4 end else if params[:zoom] label_size = 40 char_per_row = label_size * 4 else label_size = 38 char_per_row = label_size * 5 end end label_size = maxname_length if maxname_length > label_size phenos_per_row = char_per_row/label_size.to_f phenos_per_row *= params[:chroms_in_row].to_f / 12 return phenos_per_row.round end def self.draw(params) canvas=params[:canvas] ystart=params[:ystart] xstart=params[:xstart] phenoholder=params[:phenoholder] phenos_per_row=params[:pheno_row] xtotal=params[:xtotal] shape=params[:shape] pheno_space = xtotal.to_f/phenos_per_row radius = @@circle_size.to_f/2 y = 0 x = 0 if params[:bigtext] font_size = 33 vert_offset = 2 y_offset = 2.5 else font_size = 22 vert_offset = 2 y_offset = 2 end phenokeys = phenoholder.phenonames.keys.sort{|a,b| phenoholder.phenonames[a].sortnumber <=> phenoholder.phenonames[b].sortnumber} phenos_per_column = phenokeys.length / phenos_per_row phenos_column_rem = phenokeys.length % phenos_per_row curr_pheno = 0 phenos_per_row.times do |col| phenos_to_do = phenos_per_column if phenos_column_rem > 0 phenos_to_do += 1 phenos_column_rem -= 1 end phenos_to_do.times do |row| pheno = phenoholder.phenonames[phenokeys[curr_pheno]] curr_pheno += 1 canvas.g.translate(xstart,ystart) do |draw| # draw.circle(radius, x, y).styles(:fill=>pheno.color, :stroke=>'black') shape.draw(draw,@@circle_size,x,y,pheno.color,'black') end canvas.g.translate(xstart,ystart).text(x+@@circle_size*1.5,y+@@circle_size.to_f/vert_offset) do |text| text.tspan(pheno.name).styles(:font_size=>font_size) end y += @@circle_size * y_offset end x += pheno_space y = 0 end end end def draw_plot(genome, phenoholder, options) if options.pheno_spacing == 'standard' alternative_pheno_spacing = :standard elsif options.pheno_spacing == 'equal' alternative_pheno_spacing = :equal else alternative_pheno_spacing = :alternative end # 6 phenotypes in a row (when more wrap around with some overlap to show they are # linked) -- main problem will be the verical spacing of the dots # will be done in matched pairs (1 & 13, 2 & 14 etc.) # # 1.0 inches at top # 4.5 inches for top row of chromosomes # 2.5 inches for bottom row of chromosomes # 0.5 inches between two rows # 1.0 inches to list below # 8.0 inches to display phenotypes (probably make this dynamic) # so 19.5 inches vertical X 10 inches horizontal # a circle will be 5Y in height # max chrom size (1) will be 40 circles (or 200Y) in height # chromosome will be 2 circles wide options.thin_lines ? circle_size = 20 : circle_size = 20 total_num_chromosomes = genome.chromosomes.length-1 chroms_in_row = ChromosomePlotter.calc_chr_per_row(total_num_chromosomes) num_chr_rows = total_num_chromosomes/chroms_in_row.to_f num_chr_rows = (num_chr_rows + 1).to_i if num_chr_rows.to_i != num_chr_rows if(options.zoomchr) options.chr_only ? num_circles_in_row=2 : num_circles_in_row=20 options.zoomstart=0 if options.zoomstart and options.zoomstart < 0 chr = genome.get_chrom_by_name(options.zoomchr) options.zoomend=chr.size if options.zoomend and options.zoomend > chr.size options.zoomstart ? max_chrom_size=options.zoomend-options.zoomstart : max_chrom_size=chr.size chrom_width = circle_size * 3.5 else options.chr_only ? num_circles_in_row=2 : num_circles_in_row=7 max_chrom_size = genome.max_chrom_size chrom_width = circle_size * 1.5 end Plotter.set_circle(circle_size, :size=>options.circle_size) Plotter.set_maxchrom(max_chrom_size) chrom_circles_width = circle_size * num_circles_in_row chrom_box_width = chrom_circles_width + chrom_width ChromosomePlotter.set_chrom_width(chrom_width) ChromosomePlotter.set_phenos_row(num_circles_in_row-1, :size=>options.circle_size) ChromosomePlotter.set_circle_outline('none') unless options.circle_outline ChromosomePlotter.set_cyto_colors if options.shade_inaccessible title_margin = circle_size * 7 row_starts = Array.new row_starts << title_margin row_box_max = Array.new max_chrom_height = 40 * circle_size max_chrom_box = max_chrom_height + circle_size * 4 row_box_max << max_chrom_box last_max_chrom_box = max_chrom_box # X chromosome will be largest chromosome in second row if(options.zoomchr) last_max_chrom_box *= 1.5 else for i in 1..num_chr_rows-1 second_row_start = last_max_chrom_box + row_starts[i-1] second_row_start -= circle_size*2 if alternative_pheno_spacing == :standard row_starts << second_row_start total_num_chromosomes < (i+1) * chroms_in_row ? lastrange = total_num_chromosomes : lastrange = (i+1) * chroms_in_row last_max_chrom_box = max_chrom_box * genome.max_in_range((chroms_in_row*i)+1..lastrange)/max_chrom_size.to_f row_box_max << last_max_chrom_box end end phenotypes_per_row = PhenotypeLabels.phenotypes_per_row(phenoholder.maxname, :big_font=>options.big_font, :zoom=>options.zoomchr, :chroms_in_row=>chroms_in_row) options.big_font ? label_offset_y = 2.5 : label_offset_y = 2 phenotype_rows = phenoholder.phenonames.length/phenotypes_per_row phenotype_rows += 1 unless phenoholder.phenonames.length % phenotypes_per_row == 0 total_y = row_starts.last + last_max_chrom_box total_y += last_max_chrom_box / 10 if options.chr_only single_chrom_total_y = total_y - row_starts[0] # add row showing shapes/ethnicities when needed eth_shapes = genome.get_eth_shapes if eth_shapes.length > 1 and !options.chr_only eth_label_row_size = circle_size * label_offset_y max_ethlength=0 eth_shapes.each_pair {|ethnicity,shape| max_ethlength = ethnicity.length if ethnicity.length > max_ethlength} ethlabels_per_row = PhenotypeLabels.phenotypes_per_row(max_ethlength, :big_font=>options.big_font, :zoom=>options.zoomchr, :chroms_in_row=>chroms_in_row) ethlabel_rows = eth_shapes.length / ethlabels_per_row ethlabel_rows += 1 unless eth_shapes.length % ethlabels_per_row == 0 eth_label_y_start = eth_label_row_size + total_y + circle_size total_y += eth_label_row_size*ethlabel_rows + circle_size end # each row should be 2 circles high + 2 circle buffer on top phenotype_labels_total = circle_size * label_offset_y * (phenotype_rows+1) phenotype_labels_total += circle_size * 3 phenotype_labels_y_start = total_y + (circle_size * label_offset_y)/2 phenotype_labels_y_start += circle_size * 3 total_y += phenotype_labels_total unless options.chr_only # total y for now # default width is 8 for 12 chromosomes in a row width_in = 8 * chroms_in_row.to_f/12 padded_width = circle_size x_per_chrom = chrom_width + num_circles_in_row * circle_size # total_y is 2 for chromsome width 6 for circles * number of chroms + space on sides options.zoomchr ? total_x = x_per_chrom * 4 + padded_width*2 : total_x = x_per_chrom * chroms_in_row + padded_width * 2 total_x += x_per_chrom * 4 if options.zoomchr and options.zoomstart and options.chr_only # determine how many additional x based on the starting position for each # change to an array that lists the X start for each chromosome # as work way across can add up total of the inches and adjust overall # size - the chromosomes match up as 0 to 12 (which is 1 to 13, etc.) # want to make them align the same along the horizontal grid # first chromosomes start at standard left position x_chr_start = Array.new(chroms_in_row+1){ |i| 0 } maxsize_chr_row = Array.new(num_chr_rows){|i| 0} for i in 0..num_chr_rows-1 for j in 1..chroms_in_row chrIdx = j + chroms_in_row * i next if genome.chromosomes[chrIdx].nil? if genome.chromosomes[chrIdx].size > maxsize_chr_row[i] maxsize_chr_row[i]=genome.chromosomes[chrIdx].size end end end additional_notation_x=0 # for i in 2..13 for i in 2..chroms_in_row+1 if options.include_notes # adjust for maxphenos of previous chromosome # 3 characters per circle? for small text and 2 for big (font size diff is 1.5) # look at num_circles_in_row and then see if maxphenos plus notes will fit options.big_font ? chars_per_circle=1.1 : chars_per_circle=1.6 # compare all the chromosomes that line up and use the one with the greatest circles needed circles_needed=0 zero_notes = true for rownum in 0..num_chr_rows-1 chrom_number = i+rownum*chroms_in_row-1 if chrom_number < genome.chromosomes.length-1 genome.chromosomes[chrom_number].maxphenos > num_circles_in_row-1 ? maxphenos = num_circles_in_row-1 : maxphenos = genome.chromosomes[chrom_number].maxphenos curr_circles_needed = maxphenos * Plotter.get_circle_multiplier + genome.chromosomes[chrom_number].note_length/chars_per_circle.to_f + 1 circles_needed = curr_circles_needed if curr_circles_needed > circles_needed zero_notes = false if genome.chromosomes[chrom_number].note_length > 0 end end if zero_notes if circles_needed < num_circles_in_row circles_needed = circles_needed * Plotter.get_circle_multiplier else circles_needed += 0.5 * Plotter.get_circle_multiplier end end size_needed = circles_needed * circle_size x_chr_start[i] = chrom_width + x_chr_start[i-1] + size_needed # shrinks or expands overall size additional_notation_x += size_needed + chrom_width - x_per_chrom #if i < 13 or size_needed > x_per_chrom else x_chr_start[i] = x_chr_start[i-1]+x_per_chrom end end if additional_notation_x > 0 and options.include_notes width_in = width_in/total_x.to_f * additional_notation_x + width_in total_x += additional_notation_x end # height can now be determined based on a width of 10 and the ratios # of the total x and total y height_in = width_in * total_y / total_x.to_f xmax = total_x ymax = total_y inches_ratio = height_in/width_in.to_f coord_ratio = ymax/xmax.to_f rvg=RVG.new(width_in.in, height_in.in).viewbox(0,0,xmax,ymax) do |canvas| canvas.background_fill = 'rgb(255,255,255)' xstart = padded_width title_x = total_x/2 - x_per_chrom/4 if options.zoomchr Title.draw_center(:canvas=>canvas, :title=>options.title, :ypos=>title_margin-circle_size*3, :xtotal=>xmax, :xpos=>title_x) unless(options.zoomchr) # draw each row of chroms for i in 0..num_chr_rows-1 xstart = padded_width total_num_chromosomes < (i+1) * chroms_in_row ? lastrange = total_num_chromosomes : lastrange = (i+1) * chroms_in_row for chr in i*chroms_in_row+1..lastrange xstart = x_chr_start[chr-i*chroms_in_row] + padded_width ChromosomePlotter.plot_chrom(:canvas=>canvas, :chrom=>genome.chromosomes[chr], :xstart=>xstart, :ystart=>row_starts[i], :height=>row_box_max[i], :alt_spacing=>alternative_pheno_spacing, :chr_only=>options.chr_only, :transparent=>options.transparent_lines, :thickness_mult=>options.thickness_mult, :bigtext=>options.big_font, :shade=>options.shade_inaccessible, :include_notes=>options.include_notes, :draw_transverse=>options.transverse_lines, :maxchrom => maxsize_chr_row[i]) end end else # center single chromosome xstart = total_x/2 - x_per_chrom/2 height = single_chrom_total_y ChromosomePlotter.plot_chrom(:canvas=>canvas, :chrom=>genome.get_chrom(options.zoomchr), :xstart=>xstart, :ystart=>row_starts.first, :height=>single_chrom_total_y, :alt_spacing=>alternative_pheno_spacing, :chr_only=>options.chr_only, :transparent=>options.transparent_lines, :thickness_mult=>options.thickness_mult, :bigtext=>options.big_font, :shade=>options.shade_inaccessible, :include_notes=>options.include_notes, :zoomstart=>options.zoomstart, :zoomend=>options.zoomend, :zoomchr=>options.zoomchr, :draw_transverse=>options.transverse_lines) end # insert a row listing the shapes for the ethnicity shapes when more than one eth_shapes = genome.get_eth_shapes Ethlabels.draw(:canvas=>canvas, :xstart=>padded_width, :bigtext=>options.big_font, :eth_shapes=>eth_shapes, :ystart=>eth_label_y_start, :shapes_per_row=>ethlabels_per_row, :xtotal=>xmax-padded_width) if eth_shapes.length > 1 and !options.chr_only eth_shapes.length > 1 ? label_shape=PhenoSquare.new : label_shape = PhenoCircle.new PhenotypeLabels.draw(:canvas=>canvas, :xstart=>padded_width, :ystart=>phenotype_labels_y_start, :phenoholder=>phenoholder, :pheno_row=>phenotypes_per_row, :xtotal=>xmax-padded_width, :bigtext=>options.big_font, :shape=>label_shape) unless options.chr_only end # produce output file outfile = options.out_name + '.' + options.imageformat STDOUT.flush begin img = rvg.draw img.write(outfile) print "Created file #{outfile}\n" rescue => e STDERR.puts "Error: #{e.to_s}" exit! end end options = Arg.parse(ARGV) options.highres ? RVG::dpi=600 : RVG::dpi=300 srand(options.rand_seed) genome = Genome.new chrom_reader = ChromosomeFileReader.new options.genome_file ? genome.set_chroms(chrom_reader.parse_file(options.genome_file)) : genome.set_chroms(Chromosome.create_human_chroms) # read in group and color specification files if they exist and add maps to genome if options.group_file group_reader = GroupSpecFileReader.new genome.designated_shapes=group_reader.parse_file(options.group_file) end phenoholder = PhenotypeHolder.new(:color=>options.color, :color_file=>options.color_file, :spec_color_file=>options.spec_color_file) if options.spec_color_file color_reader = ColorSpecReader.new phenoholder.spec_colors = color_reader.parse_file(options.spec_color_file) end filereader = PhenoGramFileReader.new begin filereader.parse_file(options.input, genome, phenoholder, :chr_only=>options.chr_only, :zoomchr=>options.zoomchr, :zoomstart=>options.zoomstart, :zoomend=>options.zoomend, :max_pos_allowed=>30320000) if options.shade_inaccessible and File.exists?(options.cytobandfile) cytoreader = CytoBandFileReader.new cytoreader.parse_file(options.cytobandfile, genome) end genome.remove_empty if options.restrict_chroms if options.zoomchr if options.zoomchr.length > 1 genome.remove_unwanted(options.zoomchr) options.zoomchr = nil elsif options.zoomchr.length == 1 options.zoomchr = options.zoomchr[0] end end rescue => e puts "ERROR:" puts e.message exit(1) end draw_plot(genome, phenoholder, options)