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draw-diagram.defunct.rb
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#! /usr/bin/env ruby
# Copyright (c) 2007-2008 Michael Specht
#
# This file is part of Proteomatic.
#
# Proteomatic is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Proteomatic is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Proteomatic. If not, see <http://www.gnu.org/licenses/>.
require './include/ruby/proteomatic'
require './include/ruby/evaluate-omssa-helper'
require './include/ruby/ext/fastercsv'
require './include/ruby/misc'
require 'set'
require 'yaml'
class DrawDiagram < ProteomaticScript
def scalex(ai_X)
return (ai_X + 1).to_f / ($gi_ItemCount + 1) * $gi_Width + $gi_Left
end
def scaley(af_Y)
#y = af_Y + 1.0
#y = -1.0 / af_Y + 3.0 if (af_Y < 1.0)
$gf_MinYLog ||= Math::log($gf_MinY)
$gf_MaxYLog ||= Math::log($gf_MaxY)
y = Math::log(af_Y)
return (y - $gf_MinYLog) / ($gf_MaxYLog - $gf_MinYLog) * $gi_Height + $gi_Top
end
def run()
lk_GroupColorsFG = ['#3465a4', '#888a85']
lk_GroupColorsBG = ['#729fcf', '#eeeeec']
lk_OriginalLines = Hash.new
lk_Items = Array.new
File.open(@input[:csvFile].first, 'r') do |lk_File|
lk_Header = mapCsvHeader(lk_File.readline, :col_sep => ',')
lk_File.each_line do |ls_Line|
lk_Line = ls_Line.parse_csv(:col_sep => ',')
lk_Item = Hash.new
lk_Header.each_key do |x|
lk_Item[x] = lk_Line[lk_Header[x]]
lk_Item[x] ||= ''
end
proteinLabel = lk_Item['protein'].dup
items = []
if proteinLabel[0, 9] == '__group__'
items = proteinLabel[9, proteinLabel.size - 9].split("\1")
else
items = [proteinLabel]
end
items.collect! do |x|
x.upcase!
if x.match(/\{.+\}/)
x = $~.to_a.first
x = x[1, x.size - 2].strip
end
if x.index('JGI|CHLRE3|') == 0
x = 'JGI v3.1: ' + x.split('|')[2]
elsif x.index('NCBI|BK000554.2|') == 0
x = 'NCBI vBK000554.2: ' + x.split('|')[3]
elsif x.include?('LHCBM3')
x = 'LhcbM3'.upcase
elsif x.include?('LI818R-1')
x = 'LhcSR1'.upcase
elsif x.include?('LIL,')
x = 'LIL'
end
x
end
lk_Item['label'] = items.sort.uniq.join("/")
lk_Items << lk_Item
lk_OriginalLines[lk_Item['protein']] = ls_Line
end
end
lk_Items.collect! do |x|
x['mean'] = '10000.0' if x['mean'] == 'Infinity'
x
end
lk_Items.sort! do |a, b|
a['pbccount'].to_i != b['pbccount'].to_i ?
(a['pbccount'].to_i == 1 || b['pbccount'].to_i == 1) ?
b['pbccount'].to_i <=> a['pbccount'].to_i :
a['ratiomean'].to_f <=> b['ratiomean'].to_f:
a['ratiomean'].to_f <=> b['ratiomean'].to_f
end
# max rel std dev is 0.6
relstddevcutoff = 0.3
# puts lk_Items.size
lk_Items.reject! { |x| x['rsd'].to_f > relstddevcutoff }
# puts lk_Items.size
# min scan count is 2
lk_Items.reject! { |x| x['scancount'].to_i < 5 }
# min scan count is 2
lk_Items.reject! { |x| x['pbccount'].to_i < 2 }
# puts lk_Items.size
# File.open(@output[:diagram] + '.csv', 'w') do |lk_Out|
# lk_Out.puts "Protein,scan count,peptide/band/charge count,mean,stddev"
# lk_Items.each do |x|
# lk_Out.puts "\"#{x['protein']}\",#{x['scancount']},#{x['peptidebandcount']},#{x['mean']},#{x['stddev']}"
# end
# end
# lk_Groups = lk_Items.collect { |x| x['localization'] }.uniq.sort
# lk_GroupKeys = Hash.new
# (0...lk_Groups.size).each { |i| lk_GroupKeys[lk_Groups[i]] = i }
#
# lk_GroupStart = Array.new(lk_Groups.size)
# lk_GroupEnd = Array.new(lk_Groups.size)
#
# (0...lk_Items.size).each do |i|
# lk_GroupStart[lk_GroupKeys[lk_Items[i]['localization']]] ||= i
# lk_GroupEnd[lk_GroupKeys[lk_Items[i]['localization']]] = i
# end
# this is for PBC 1 / PBC 2 or more
lk_Items.reject! { |x| x['pbccount'].to_i < 2 }
# lk_Items.each do |lk_Item|
# puts lk_OriginalLines[lk_Item['protein']]
# end
File.open(@output[:diagram], 'w') do |lk_Out|
$gi_ItemCount = lk_Items.size
$gi_Border = 16
$gi_LeftBorder = 50
$gi_ImageWidth = 1200
$gi_ImageHeight = 540
$gf_MinY = 4.0
$gf_MaxY = 0.5
$gi_TickWidth = 3.0
# $gi_ImageWidth = 420
# $gi_ImageHeight = 220
# $gf_MinY = 6.0
# $gf_MaxY = 0.0
$gi_Left = $gi_LeftBorder
$gi_Top = $gi_Border
$gi_Width = $gi_ImageWidth - $gi_LeftBorder - $gi_Border
$gi_Height = $gi_ImageHeight - $gi_Border * 2 - 160.0
lk_Out.puts '<?xml version="1.0" encoding="utf-8"?>'
lk_Out.puts '<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">'
lk_Out.puts "<svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' xmlns:ev='http://www.w3.org/2001/xml-events' version='1.1' baseProfile='full' width='#{$gi_ImageWidth}px' height='#{$gi_ImageHeight}px'>"
lk_Out.puts "<rect x='0' y='0' width='#{$gi_ImageWidth}' height='#{$gi_ImageHeight}' fill='#fff' stroke='none' />"
lk_Out.puts "<rect x='#{$gi_Left}' y='#{$gi_Top}' width='#{$gi_Width}' height='#{$gi_Height}' fill='#eeeeec' stroke='#888a85' stroke-width='0.5px'/>"
y = 1
step = 0.2
while y < 4.01
sy = scaley(y)
ls_Color = '#babdb6'
ls_Color = '#888a85' if (y - y.round).abs() < 0.01
ls_Color = '#555753' if y == 1
lk_Out.puts "<line x1='#{$gi_Left}' y1='#{sy}' x2='#{$gi_Left + $gi_Width}' y2='#{sy}' stroke='#{ls_Color}' stroke-width='1px'/>"
lk_Out.puts "<text x='#{$gi_Left - 4}' y='#{sy + 4}' style='font-family: Verdana; font-size: 8pt; text-anchor: end;'>#{y}</text>"
step = 0.5 if (y >= 2.99)
y += step
end
y = 1
step = 0.2
while y < 2.01
ls_Color = '#babdb6'
ls_Color = '#888a85' if (y - y.round).abs() < 0.01
sy = scaley(1.0 / y.to_f)
if y != 1
lk_Out.puts "<line x1='#{$gi_Left}' y1='#{sy}' x2='#{$gi_Left + $gi_Width}' y2='#{sy}' stroke='#{ls_Color}' stroke-width='1px'/>"
lk_Out.puts "<text x='#{$gi_Left - 4}' y='#{sy + 4}' style='font-family: Verdana; font-size: 8pt; text-anchor: end;'>1/#{y}</text>"
end
y += step
end
=begin
(0...lk_Groups.size).each do |i|
lk_Out.puts "<rect x='#{scalex(lk_GroupStart[i].to_f - 0.5)}' y='#{$gi_Top}' width='#{scalex(lk_GroupEnd[i] + 1) - scalex(lk_GroupStart[i])}' height='#{$gi_Height}' stroke='none' fill='#{lk_GroupColorsBG[i % lk_GroupColorsBG.size]}' opacity='0.3'/>"
lk_Out.puts "<text x='#{scalex((lk_GroupStart[i].to_f + lk_GroupEnd[i].to_f) * 0.5)}' y='#{$gi_Top + $gi_Height - 6.0}' style='font-weight: bold; text-anchor: middle; font-family: Verdana; font-size: 10pt;'>#{lk_Groups[i]}</text>"
end
=end
puts lk_Items.size
(0...lk_Items.size).each do |i|
lk_Item = lk_Items[i]
#ls_Color = lk_GroupColorsFG[lk_GroupKeys[lk_Item['localization']] % lk_GroupColorsFG.size]
ls_Color = '#888a85'
# ls_Color = '#000' if lk_Item['localization'].upcase == 'CP'
# li_Count = lk_Item['count'].to_i
# if li_Count > 100
# ls_Color = '#000'
# elsif li_Count > 20
# ls_Color = '#333'
# elsif li_Count > 0
# ls_Color = '#888'
# end
ls_Color = '#000'
ls_Color = '#888a85' if lk_Item['pbcCount'].to_i == 1
ls_Style = ''
#ls_Style = 'stroke-dasharray: 2, 2;' if lk_Item['marker'].include?('unknown')
#ls_Color = '#4e9a06;' if lk_Item['localization'].upcase == 'CP-PS'
x = scalex(i)
t = Hash.new
t[0] = lk_Item['ratiomean'].to_f - lk_Item['ratiosd'].to_f
t[1] = lk_Item['ratiomean'].to_f
t[2] = lk_Item['ratiomean'].to_f + lk_Item['ratiosd'].to_f
if (t[1] > $gf_MinY)
t[0] = $gf_MinY
t[1] = $gf_MinY
t[2] = $gf_MinY
end
#puts lk_Item.to_yaml if (t[2] > 7.0)
lk_Out.puts "<line x1='#{x}' y1='#{scaley(t[0])}' x2='#{x}' y2='#{scaley(t[2])}' stroke='#{ls_Color}' stroke-width='1px' style='#{ls_Style}'/>"
#[25, 50, 75].each do |k|
[0, 1, 2].each do |k|
#y = scaley(lk_Item["p#{k}"].to_f)
y = scaley(t[k])
lk_Out.puts "<line x1='#{x - $gi_TickWidth / 2.0}' y1='#{y}' x2='#{x + $gi_TickWidth / 2.0}' y2='#{y}' stroke='#{ls_Color}' stroke-width='1px'/>"
end
[1].each do |k|
#y = scaley(lk_Item["p#{k}"].to_f)
y = scaley(t[k])
# if lk_Item['marker'].include?('unknown')
# stroke = ls_Color
# fill = '#eeeeec'
# end
stroke = 'none'
fill = ls_Color
if lk_Item['method'] == 'AMT'
fill = '#ffffff'
stroke = ls_Color
end
# r = 1.8 * Math::log(lk_Item['scancount'].to_f) / 3.0
r = Math::log(lk_Item['scancount'].to_f) * 0.7
lk_Out.puts "<circle cx='#{x}' cy='#{y}' r='#{r}' stroke='#{stroke}' fill='#{fill}'/>"
#lk_Out.puts "<circle cx='#{x}' cy='#{y}' r='2.0' stroke='none' fill='#000'/>"
end
[0].each do |k|
#y = scaley(lk_Item["p#{k}"].to_f)
y = scaley(t[k])
# if lk_Item['marker'].include?('unknown')
# stroke = ls_Color
# fill = '#eeeeec'
# end
stroke = 'none'
fill = ls_Color
if lk_Item['method'] == 'AMT'
fill = '#ffffff'
stroke = ls_Color
end
lk_Out.puts "<g transform='translate(#{x + 4.0},#{$gi_Height + 25.0}) rotate(-60)'><text x='0' y='0' style='font-family: Verdana; font-size: 8pt; text-anchor: end;'>#{lk_Item['label']}</text></g>"
# lk_Out.puts "<g transform='translate(#{x},#{y})'><text x='0' y='14' style='font-family: Verdana; font-size: 7pt; text-anchor: middle;'>#{lk_Item['scancount']}</text></g>"
end
end
lk_Out.puts "<g transform='translate(57.0, -48.0)'>"
lk_Out.puts "<rect fill='#ffffff' fill-opacity='0.8' stroke='#888a85' x='0' y='70' width='100' height='120' />"
lk_Out.puts "<text x='8.0' y='90' style='font-family: Verdana; font-size: 8pt; text-anchor: start; font-weight: bold;'>Scan counts</text>"
[5, 20, 250, 1000].each_with_index do |c, i|
r = Math::log(c.to_f) * 0.7
stroke = 'none'
fill = '#000000'
lk_Out.puts "<circle cx='#{15.0}' cy='#{107 + i * 20.0}' r='#{r}' stroke='#{stroke}' fill='#{fill}'/>"
lk_Out.puts "<text x='25.0' y='#{100 + i * 20.0 + 12.0}' style='font-family: Verdana; font-size: 8pt; text-anchor: start;'>#{c} scans</text>"
end
lk_Out.puts "</g>"
lk_Out.puts "<g transform='rotate(-90)'>"
lk_Out.puts "<text x='-13.0' y='20.0' style='font-family: Verdana; font-size: 8pt; text-anchor: end; font-weight: bold;'>Protein ratio</text>"
lk_Out.puts "</g>"
lk_Out.puts '</svg>'
end
exit
end
end
script = DrawDiagram.new