/usr/lib/python2.7/dist-packages/pymzml/plot.py is in python-mzml 0.7.4-dfsg-3.
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# -*- coding: utf-8 -*-
# encoding: utf-8
"""
Plotting functions for pymzML
"""
# pymzml
#
# Copyright (C) 2010-2011 T. Bald, J. Barth, A. Niehues, C. Fufezan
#
# This program 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.
#
# This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
from __future__ import print_function
import math
import sys
import collections
class Factory(object):
"""
Class to plot pymzml.spec.Spectrum as svg/xhtml.
:param filename: Name for the output file. Default = "spectra.xhtml"
:type filename: string
Example:
>>> import pymzml, get_example_file
>>> mzMLFile = 'profile-mass-spectrum.mzml'
>>> example_file = get_example_file.open_example(mzMLFile)
>>> run = pymzml.run.Run("../mzML_example_files/"+mzMLFile, precisionMSn = 250e-6)
>>> p = pymzml.plot.Factory()
>>> for spec in run:
>>> p.newPlot()
>>> p.add(spec.peaks, color=(200,00,00), style='circles')
>>> p.add(spec.centroidedPeaks, color=(00,00,00), style='sticks')
>>> p.add(spec.reprofiledPeaks, color=(00,255,00), style='circles')
>>> p.save( filename="output/plotAspect.xhtml" , mzRange = [745.2,745.6] )
"""
def __init__(self,filename = None):
self.filename = filename if filename != None else "spectra.xhtml"
self.plots = [ ] # list of plots, where each plot hold a list of mz-i lists that should be plotted in the same plot
self.styles = [ ]
self.colors = [ ]
self.header = [ ]
self.labelPos = [ ]
self.mzRanges = [ ]
self.normalizations = []
pass
def newPlot(self, header = None , mzRange = [None,None] , normalize = False):
"""
Add new plot to the plotFactory.
:param header: an optional title that will be printed above the plot
:type header: string
:param mzRange: Boundaries of the new plot
:type mzRange: tuple of minMZ,maxMZ
:param normalize: whether or not the individal data sets are normalized in the plot
:type boolean:
"""
self.plots.append( [] )
self.styles.append( [] )
self.colors.append( [] )
self.labelPos.append( set() )
self.mzRanges.append( mzRange )
self.normalizations.append( normalize )
if header == None:
self.header.append( '' )
else:
self.header.append( header )
return
def add(self,data, color=(00,00,00) , style = 'sticks', mzRange = [None,None] ):
"""
Add data to the graph.
:param data: The data added to the graph
:type data: list of tuples (mz,i)
:param color: color encoded in RGB. Default = (0,0,0)
:type color: tuple (R,G,B)
:param style: plotting style. Default = "circles".
:type style: string
:param mzRange: Boundaries that should be added to the current plot
:type mzRange: tuple of minMZ,maxMZ
Currently supported styles are:
* 'emptycircles'
* 'circles'
* 'sticks'
* 'squares'
* 'area'
* 'triangle'
* 'label'
NOTE: The data format for label style is [( mz1, 'label1' ), ( mz2, 'label2' ), ( mz3, 'label3' ) ].
"""
if len(self.plots) == 0:
self.newPlot()
self.styles[-1].append(style)
self.colors[-1].append(color)
selective = True
if mzRange == [None,None]:
if self.mzRanges[-1] == [None,None]:
selective = False
self.plots[-1].append(data)
else:
mzRange = self.mzRanges[-1]
else:
self.mzRanges[-1] = mzRange
# NOTE this allows us to define the mzRange in the call of the add function, otherwise it has to be in the call of the new function
# NOTE Problem can be: mzRanges[-1] can be overwritten ... don't know what is best here
if selective:
self.plots[-1].append([(mz,i) for mz,i in data if mzRange[0] <= mz <=mzRange[1]])
#print("Added {0} data points".format(len(self.plots[-1][-1])))
return
def info(self):
"""
Returns summary about the plotting factory, i.e.how many plots and how many datasets per plot.
"""
print("""
Factory holds {0} unique plots""".format(len(self.plots)))
for i,plot in enumerate(self.plots):
print(" Plot {0} holds {1} unique datasets".format(i,len(plot)))
for j,dataset in enumerate(plot):
print(" Dataset {0} holds {1} datapoints".format(j,len(dataset)))
print()
return
def save(self, filename = None, mzRange = [None,None]):
"""
Saves all plots and their data points that have been added to the plotFactory.
:param filename: Name for the output file. Default = "spectra.xhtml"
:type filename: string
:param mzRange: m/z range which should be considered [start, end]. Default = [ ``None`` , ``None`` ]
:type mzRange: list
"""
if filename == None:
filename = self.filename
io = open("{0}".format(filename), 'w' )
# NOTE: we need to check if file exists and/or if file can be written ...
print("""<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>pymzml spectrum visualisation</title>
<style>
</style>
</head>
<body style="position:relative; z-index:0; width:100%; height:100%;">
""", file = io)
for plotNumber,plot in enumerate(self.plots):
w = 1000
h = 700
heada = self.header[plotNumber]
resolved_mzRange = [ None, None ]
if mzRange != [ None, None ]:
resolved_mzRange = mzRange
else:
if self.mzRanges[plotNumber] == [None,None]:
# we have to determine ranges ...
for dataset in plot:
print("Determing mzRanges ...")
if len(dataset) == 0:
continue
if resolved_mzRange[0] == None:
resolved_mzRange[0] = min(dataset)[0]
else:
if resolved_mzRange[0] > min(dataset)[0]:
resolved_mzRange[0] = min(dataset)[0]
if resolved_mzRange[1] == None:
resolved_mzRange[1] = max(dataset)[0]
else:
if resolved_mzRange[1] < max(dataset)[0]:
resolved_mzRange[1] = max(dataset)[0]
else:
# Ranges have been defined by newPlot()
# i.e we want to plot no matter what ...
resolved_mzRange = self.mzRanges[plotNumber]
if resolved_mzRange == [None,None]:
print("Skipping empty plot, plotNumber {0} , header :{1} ...".format(plotNumber,heada))
continue
i_max = 0
i_min = 0
for dataset in plot:
for mz,i in dataset:
if resolved_mzRange[0] <= mz <= resolved_mzRange[1]:
try:
i = float(i)
except:
continue
if i >= i_max:
i_max = i
if i_max == 0:
i_max = 0.1
if self.normalizations[plotNumber] == True:
resolved_i_max = 1.05
else:
resolved_i_max = i_max * 1.05
print("""
<svg xmlns="http://www.w3.org/2000/svg" version="1.1"
width="{w}" height="{h}"
style="position:relative; top:0; left:0; z-index:-1;">
""".format(w = w, h = h), file = io)
PADDING = (300,50,100,50) # css style convention
baseline = h-PADDING[2]
# Drawing Frame ...
for x1,y1,x2,y2 in [ (PADDING[3],PADDING[0],w-PADDING[1],PADDING[0]),
(w-PADDING[1],PADDING[0],w-PADDING[1],h-PADDING[2]),
(PADDING[3],h-PADDING[2],w-PADDING[1],h-PADDING[2]),
(PADDING[3],PADDING[0],PADDING[3],h-PADDING[2]),
]:
print("""<line x1="{0}" y1="{1}" x2="{2}" y2="{3}"
style="stroke:rgb(00,00,00);stroke-width:1"/>""".format(x1,y1,x2,y2),file=io)
if heada != '':
heada_y = 30
for subheada in heada.split("\n"):
print("""<text x="{x}" y="{y}" font-family="Courier" text-anchor="start" font-size="{fontsize}" fill="black" >{0}</text>
""".format(subheada, x = 0, y = heada_y, fontsize = 24), file = io)
heada_y += 30
pixelpermz = float( w - PADDING[1] - PADDING[3] ) / float(resolved_mzRange[1]-resolved_mzRange[0]) # NOTE this returns ZeroDivisionError if the range to plot contains only one peak
pixelper_i = float( h - PADDING[0] - PADDING[2] ) / float(resolved_i_max-i_min)
delta = resolved_mzRange[1]-resolved_mzRange[0]
sep = round(math.log(delta,10))
factor = 10**(-1*(sep-1))
# grid
# Drawing ticks and x labels
for _ in range(int(round(resolved_mzRange[0]*factor)),int(round(resolved_mzRange[1]*factor))+1 ):
x = int(round(PADDING[3] + (float(_)/float(factor) - resolved_mzRange[0] ) * pixelpermz ))
y = baseline
color = 77 #if _ % 10 == 0 else 125
# Dashed lines
# print("""<line x1="{0}" y1="{1}" x2="{0}" y2="{2}"
# style="stroke-dasharray: 9, 5;stroke:rgb({3},{3},{3});stroke-width:0.5"/>""".format(x,PADDING[0],baseline,color),file=io)
print("""<line x1="{0}" y1="{1}" x2="{0}" y2="{2}"
style="stroke:rgb(00,00,00);stroke-width:0.5;"/>""".format(x,baseline,baseline+10),file=io)
print("""<text x="{x}" y="{y}" transform="rotate(90 {x},{y})" font-family="Courier" text-anchor="start" font-size="{fontsize}" fill="black" >{0:7.3f}</text>
""".format(float(_)/float(factor), x = x, y = y + 30, fontsize = 12), file = io)
# Drawing data points .. labels first
for datasetnumber,dataset in enumerate(plot):
r,g,b = self.colors[plotNumber][datasetnumber]
style = self.styles[plotNumber][datasetnumber]
if style[:5] == 'label':
for pos,(mz,i) in enumerate(dataset):
if resolved_mzRange[0] <= mz <= resolved_mzRange[1]:
x = int(round(PADDING[3] + (mz - resolved_mzRange[0] ) * pixelpermz ))
y = baseline
y2 = baseline - (resolved_i_max * pixelper_i)
x3 = round(x,-1)
if style.upper().endswith('X1'):
y3 = round(y+10)
sign = 1
stroke_width = 0.50
else:
y3 = round(y2)
sign = -1
stroke_width = 0.40
layers = 15
while (x3,y3) in self.labelPos[plotNumber]:
y3 = y3 + sign * 15
layers -= 1
if layers <= 0:
break
print("""<line x1="{0}" y1="{1}" x2="{0}" y2="{2}"
style="stroke-opacity: 0.6;stroke:rgb({r},{g},{b});stroke-width:{o};" />""".format(x, y, y2, o=stroke_width, r=r,g=g,b=b),file=io)
self.labelPos[plotNumber].add((x3,y3))
self.labelPos[plotNumber].add((x3+10,y3 + sign * 15))
print("""<text x="{x}" y="{y}" transform="rotate({angle} {x},{y})" font-family="Courier" text-anchor="start" font-size="{fontsize}" style="fill:rgb({r},{g},{b});" >{0}</text>
""".format(i, x = x, y = y3, fontsize = 10, angle = sign * 45 , r = r, g = g, b = b), file = io)
elif style[:5] == 'area':
if self.normalizations[plotNumber] == True:
maxI = max([ i for mz,i in dataset ])
else:
maxI = None
first = True
for pos,(mz,i) in enumerate(sorted(dataset)):
if resolved_mzRange[0] <= mz <= resolved_mzRange[1]:
x = int(round(PADDING[3] + (mz - resolved_mzRange[0] ) * pixelpermz ))
if self.normalizations[plotNumber] == True:
y = baseline - ((float(i)/float(maxI)) * pixelper_i)
else:
y = baseline - (i * pixelper_i)
if first:
print('<path d="M{0} {2} L{0} {1}'.format(x,y,baseline), end=" ", file = io)
first = False
else:
print('L{0} {1}'.format(x,y ), end=" ", file = io)
if first == False:
# aka we have seen some points ;)
print(' L{0} {1} Z" style="fill:rgb({r},{g},{b}); fill-opacity:0.2; stroke:rgb({r},{g},{b}); stroke-width:1" />'.format(x,baseline,r=r,g=g,b=b), file = io)
elif style[:8] == 'triangle':
if self.normalizations[plotNumber] == True:
maxI = max([ i for mz,i in dataset ])
else:
maxI = None
#first = True
for pos,(mz,i) in enumerate(sorted(dataset)):
if resolved_mzRange[0] <= mz <= resolved_mzRange[1]:
x = int(round(PADDING[3] + (mz - resolved_mzRange[0] ) * pixelpermz ))
xl = int(round(PADDING[3] + (mz-0.075 - resolved_mzRange[0] ) * pixelpermz ))
xr = int(round(PADDING[3] + (mz+0.075 - resolved_mzRange[0] ) * pixelpermz ))
if self.normalizations[plotNumber] == True:
y = baseline - ((float(i)/float(maxI)) * pixelper_i)
else:
y = baseline - (i * pixelper_i)
print('<path d="M{0} {4} L{2} {3} L{1} {4} Z" style="fill:rgb({r},{g},{b}); fill-opacity:0.4"/>'.format(xl,xr,x,y,baseline,r=r,g=g,b=b), file = io)
#print('<line x1="{0}" y1="{1}" x2="{0}" y2="{2}" style="stroke:rgb({r},{g},{b});stroke-width:1"/>'.format(x,y,baseline,r=r,g=g,b=b), file = io)
# Drawing data ...
for datasetnumber,dataset in enumerate(plot):
r,g,b = self.colors[plotNumber][datasetnumber]
style = self.styles[plotNumber][datasetnumber]
if style[:5] not in ['label', 'area', 'trian']:
if len(dataset) == 0:
continue
if self.normalizations[plotNumber] == True:
maxI = max([ i for mz,i in dataset ])
else:
maxI = None
for pos,(mz,i) in enumerate(dataset):
if resolved_mzRange[0] <= mz <= resolved_mzRange[1]:
x = int(round(PADDING[3] + (mz - resolved_mzRange[0] ) * pixelpermz ))
if self.normalizations[plotNumber] == True:
y = baseline - ((float(i)/float(maxI)) * pixelper_i)
else:
y = baseline - (i * pixelper_i)
if style == 'circles':
print("""<circle cx="{x}" cy="{y}" r="2" style="fill:rgb({r},{g},{b});" />""".format( x = x, y = y , r = r, g = g, b = b),file=io)
elif style == 'emptycircles':
print("""<circle cx="{x}" cy="{y}" r="4" style="stroke:rgb({r},{g},{b}); stroke-width:2; fill:none" />""".format( x = x, y = y , r = r, g = g, b = b),file=io)
elif style == 'sticks':
print("""<line x1="{0}" y1="{1}" x2="{0}" y2="{2}"
style="stroke:rgb({r},{g},{b});stroke-width:0.5"/>""".format(x,y,baseline,r=r,g=g,b=b),file=io)
elif style == 'squares':
# this is experimental, the squares are not centred
print("""<rect x="{0}" y="{1}" width="4" height="4" style="fill:rgb({r},{g},{b});
fill-opacity:0.8;" />
""".format(x-2,y-2,r=r,g=g,b=b),file=io)
else:
print("Style {0} not support yet ...".format(style),file=sys.stderr)
exit(1)
print("</svg>", file = io)
print("""
</body>
</html>
""", file = io)
return
if __name__ == '__main__':
print(__doc__)
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