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[simuPOP-devel] SF.net SVN: simupop:[4996] trunk
|
From: <bpe...@us...> - 2015-11-01 03:09:28
|
Revision: 4996
http://sourceforge.net/p/simupop/code/4996
Author: bpeng2000
Date: 2015-11-01 03:09:25 +0000 (Sun, 01 Nov 2015)
Log Message:
-----------
Remove rpy/rpy2 support from simuPOP
Modified Paths:
--------------
trunk/doc/refManual.lyx
trunk/doc/userGuide.py
trunk/simuOpt.py
trunk/src/plotter.py
trunk/src/sampling.py
Modified: trunk/doc/refManual.lyx
===================================================================
--- trunk/doc/refManual.lyx 2015-10-31 00:32:59 UTC (rev 4995)
+++ trunk/doc/refManual.lyx 2015-11-01 03:09:25 UTC (rev 4996)
@@ -1,5 +1,5 @@
-#LyX 2.0 created this file. For more info see http://www.lyx.org/
-\lyxformat 413
+#LyX 2.1 created this file. For more info see http://www.lyx.org/
+\lyxformat 474
\begin_document
\begin_header
\textclass manual
@@ -50,13 +50,13 @@
\font_roman default
\font_sans default
\font_typewriter beramono
+\font_math auto
\font_default_family default
\use_non_tex_fonts false
\font_sc false
\font_osf false
\font_sf_scale 100
\font_tt_scale 70
-
\graphics default
\default_output_format default
\output_sync 0
@@ -81,15 +81,24 @@
\pdf_quoted_options "linkcolor=TitleColor,urlcolor=LinkColor"
\papersize default
\use_geometry false
-\use_amsmath 1
-\use_esint 0
-\use_mhchem 1
-\use_mathdots 1
-\cite_engine natbib_authoryear
+\use_package amsmath 1
+\use_package amssymb 1
+\use_package cancel 1
+\use_package esint 0
+\use_package mathdots 1
+\use_package mathtools 1
+\use_package mhchem 1
+\use_package stackrel 1
+\use_package stmaryrd 1
+\use_package undertilde 1
+\cite_engine natbib
+\cite_engine_type authoryear
+\biblio_style plainnat
\use_bibtopic false
\use_indices false
\paperorientation portrait
\suppress_date false
+\justification true
\use_refstyle 0
\index Index
\shortcut idx
@@ -2176,20 +2185,6 @@
\backslash
-simuPOPplotternewDeviceRef
-\end_layout
-
-\begin_layout Plain Layout
-
-
-\backslash
-simuPOPplottersaveFigureRef
-\end_layout
-
-\begin_layout Plain Layout
-
-
-\backslash
simuPOPplotterVarPlotterRef
\end_layout
@@ -2200,34 +2195,6 @@
simuPOPplotterScatterPlotterRef
\end_layout
-\begin_layout Plain Layout
-
-
-\backslash
-simuPOPplotterInfoPlotterRef
-\end_layout
-
-\begin_layout Plain Layout
-
-
-\backslash
-simuPOPplotterHistPlotterRef
-\end_layout
-
-\begin_layout Plain Layout
-
-
-\backslash
-simuPOPplotterQQPlotterRef
-\end_layout
-
-\begin_layout Plain Layout
-
-
-\backslash
-simuPOPplotterBoxPlotterRef
-\end_layout
-
\end_inset
@@ -2390,13 +2357,6 @@
simuPOPsamplingdrawCombinedSamplesRef
\end_layout
-\begin_layout Plain Layout
-
-
-\backslash
-simuPOPsamplingplotPedigreeRef
-\end_layout
-
\end_inset
Modified: trunk/doc/userGuide.py
===================================================================
--- trunk/doc/userGuide.py 2015-10-31 00:32:59 UTC (rev 4995)
+++ trunk/doc/userGuide.py 2015-11-01 03:09:25 UTC (rev 4996)
@@ -4783,7 +4783,7 @@
#begin_file log/forwardTrajectory.py
import simuOpt
-simuOpt.setOptions(quiet=True, plotter='matplotlib')
+simuOpt.setOptions(quiet=True)
import simuPOP as sim
#begin_ignore
sim.setRNG(seed=12345)
@@ -4823,7 +4823,7 @@
#begin_file log/backTrajectory.py
#begin_ignore
import simuOpt
-simuOpt.setOptions(quiet=True, plotter='matplotlib')
+simuOpt.setOptions(quiet=True)
#end_ignore
import simuPOP as sim
#begin_ignore
@@ -4977,7 +4977,7 @@
#begin_file log/demoModel.py
#begin_ignore
import simuOpt
-simuOpt.setOptions(quiet=True, plotter='matplotlib')
+simuOpt.setOptions(quiet=True)
#end_ignore
import simuPOP as sim
from simuPOP.demography import *
@@ -5044,7 +5044,7 @@
#begin_file log/demoEventModel.py
#begin_ignore
import simuOpt
-simuOpt.setOptions(quiet=True, plotter='matplotlib')
+simuOpt.setOptions(quiet=True)
#end_ignore
import simuPOP as sim
from simuPOP.demography import *
@@ -5133,7 +5133,7 @@
#begin_file log/varPlotByRep.py
#begin_ignore
import simuOpt
-simuOpt.setOptions(quiet=True, plotter='matplotlib')
+simuOpt.setOptions(quiet=True)
#end_ignore
import simuPOP as sim
#begin_ignore
@@ -5149,15 +5149,6 @@
matingScheme=sim.RandomMating(),
postOps=[
sim.Stat(alleleFreq=range(4)),
- # rpy syntax
- #VarPlotter('[alleleFreq[x][0] for x in range(4)]', byRep=True,
- # update=10, saveAs='log/rpy_byRep.png',
- # legend=['Locus %d' % x for x in range(4)],
- # ylab='Allele frequency',
- # ylim=[0, 1],
- # main_rep=['Genetic drift, replicate %d' % x for x in range(3)],
- #),
- # matplotlib syntax
VarPlotter('[alleleFreq[x][0] for x in range(4)]', byRep=True,
update=10, saveAs='log/varplot_byRep.png',
figure_figsize=(10, 8),
@@ -5174,7 +5165,7 @@
#begin_file log/varPlotByDim.py
#begin_ignore
import simuOpt
-simuOpt.setOptions(quiet=True, plotter='matplotlib')
+simuOpt.setOptions(quiet=True)
#end_ignore
import simuPOP as sim
#begin_ignore
@@ -5227,7 +5218,7 @@
#begin_file log/ScatterPlotter.py
#begin_ignore
import simuOpt
-simuOpt.setOptions(quiet=True, plotter='matplotlib')
+simuOpt.setOptions(quiet=True)
#end_ignore
import simuPOP as sim
#begin_ignore
@@ -5273,62 +5264,7 @@
)
#end_file
-#begin_file log/HistPlotter.py
-#begin_ignore
-import simuOpt
-simuOpt.setOptions(quiet=True, plotter='rpy2')
-#end_ignore
-import simuPOP as sim
-#begin_ignore
-sim.setRNG(seed=12345)
-#end_ignore
-import simuPOP as sim
-from simuPOP.plotter import HistPlotter, QQPlotter, BoxPlotter
-import random
-pop = sim.Population([500], infoFields=['x', 'y', 'anc'])
-# Defines VSP 0, 1, 2, 3, 4 by anc.
-pop.setVirtualSplitter(sim.SexSplitter())
-def passInfo(x, y, anc):
- 'Parental fields will be passed as tuples'
- off_anc = (anc[0] + anc[1])/2.
- off_x = (x[0] + x[1])/2 + random.normalvariate(off_anc - 0.5, 0.1)
- off_y = (y[0] + y[1])/2 + random.normalvariate(0, 0.1)
- return off_x, off_y, off_anc
-
-pop.evolve(
- initOps=[
- sim.InitSex(),
- # random geographic location
- sim.InitInfo(random.random, infoFields=['x', 'y']),
- # anc is 0 or 1
- sim.InitInfo(lambda : random.randint(0, 1), infoFields='anc')
- ],
- matingScheme=sim.RandomMating(ops=[
- sim.MendelianGenoTransmitter(),
- sim.PyTagger(passInfo)]),
- postOps=[
- HistPlotter(infoFields='anc',
- subPops=[(0,0), (0,1)], col_sp=['blue', 'red'],
- saveAs='log/HistPlotter.png',
- main="!'Histogram of ancestry values at generation %d' % gen",
- ),
- QQPlotter(infoFields='anc',
- subPops=[(0,0), (0,1)], col_sp=['blue', 'red'],
- saveAs='log/QQPlotter.png',
- main="!'QQ plot of ancestry values at generation %d' % gen",
- ),
- BoxPlotter(infoFields='anc',
- subPops=[(0,0), (0,1)],
- saveAs='whatever',
- dev_print_file='!"log/Gen%d.png" % gen',
- main="!'Boxplots of ancestry values at generation %d' % gen",
- ),
- ],
- gen = 5,
-)
-#end_file
-
#begin_file log/getParam.py
#begin_ignore
import simuOpt
@@ -5476,16 +5412,17 @@
#end_file
-#begin_file log/plotPedigree.py
+
+#begin_file log/sampleAffectedSibpair.py
#begin_ignore
import simuOpt
simuOpt.setOptions(quiet=True)
#end_ignore
import simuPOP as sim
#begin_ignore
-sim.setRNG(seed=12311)
+sim.setRNG(seed=12347)
#end_ignore
-from simuPOP.sampling import indexToID #, plotPedigree
+from simuPOP.sampling import indexToID
pop = sim.Population(size=15, loci=5, infoFields=['father_idx', 'mother_idx'], ancGen=2)
pop.evolve(
preOps=[
@@ -5502,25 +5439,10 @@
print(pop.infoFields())
# save this population for future use
pop.save('log/pedigree.pop')
-# draw pedigree, this function is now deprecated because of the removal of
-# rpy/rpy2 support
-#plotPedigree(pop, filename='log/pedigree.png')
-#end_file
-
-#begin_file log/sampleAffectedSibpair.py
-#begin_ignore
-import simuOpt
-simuOpt.setOptions(quiet=True)
-#end_ignore
-import simuPOP as sim
-#begin_ignore
-sim.setRNG(seed=12347)
-#end_ignore
-from simuPOP.sampling import drawAffectedSibpairSample #, plotPedigree
+from simuPOP.sampling import drawAffectedSibpairSample
pop = sim.loadPopulation('log/pedigree.pop')
sample = drawAffectedSibpairSample(pop, families=2)
-#plotPedigree(sample, filename='log/affectedSibpair.png')
#end_file
@@ -5533,7 +5455,7 @@
#begin_ignore
sim.setRNG(seed=12347)
#end_ignore
-from simuPOP.sampling import drawNuclearFamilySample #, plotPedigree
+from simuPOP.sampling import drawNuclearFamilySample
pop = sim.loadPopulation('log/pedigree.pop')
sample = drawNuclearFamilySample(pop, families=2, numOffspring=(2,4),
affectedParents=(1,2), affectedOffspring=(1, 3))
@@ -5547,7 +5469,6 @@
ped1 = sample.extractIndividuals(IDs=0, idField='ped_id')
# print the ID of all individuals in the first pedigree
print([ind.ind_id for ind in ped1.allIndividuals()])
-#plotPedigree(sample, filename='log/nuclerFamily.png')
#end_file
@@ -5561,11 +5482,10 @@
#begin_ignore
sim.setRNG(seed=12347)
#end_ignore
-from simuPOP.sampling import drawThreeGenFamilySample #, plotPedigree
+from simuPOP.sampling import drawThreeGenFamilySample
pop = sim.loadPopulation('log/pedigree.pop')
sample = drawThreeGenFamilySample(pop, families=2, numOffspring=(1, 3),
pedSize=(8, 15), numOfAffected=(2, 5))
-#plotPedigree(sample, filename='log/threeGenFamily.png')
#end_file
@@ -5578,13 +5498,12 @@
#begin_ignore
sim.setRNG(seed=12347)
#end_ignore
-from simuPOP.sampling import drawCombinedSample, AffectedSibpairSampler, NuclearFamilySampler #, plotPedigree
+from simuPOP.sampling import drawCombinedSample, AffectedSibpairSampler, NuclearFamilySampler
pop = sim.loadPopulation('log/pedigree.pop')
sample = drawCombinedSample(pop, samplers = [
AffectedSibpairSampler(families=1),
NuclearFamilySampler(families=1, numOffspring=(2,4), affectedParents=(1,2), affectedOffspring=(1,3))
])
-#plotPedigree(sample, filename='log/combinedSampling.png')
#end_file
Modified: trunk/simuOpt.py
===================================================================
--- trunk/simuOpt.py 2015-10-31 00:32:59 UTC (rev 4995)
+++ trunk/simuOpt.py 2015-11-01 03:09:25 UTC (rev 4996)
@@ -195,10 +195,7 @@
commandline option ``--gui``.
plotter
- The plotting library used to draw figures. simuPOP will try to
- use ``rpy``, ``rpy2``, and ``matplotlib`` if the module is
- available. You can set this parameter to one of them to force the
- use a particular library.
+ (Deprecated)
quiet
If set to ``True``, suppress the banner message when a simuPOP module
@@ -296,10 +293,8 @@
simuOptions['NumThreads'] = numThreads
elif numThreads is not None:
raise TypeError('An integer number is expected for parameter numThreads.')
- if plotter in ['rpy', 'rpy2', 'matplotlib']:
- simuOptions['Plotter'] = plotter
- elif plotter is not None:
- raise TypeError('Only rpy and matplotlib are allowed for parameter plotter.')
+ if plotter is not None:
+ sys.stderr.write('WARNING: plotter option is deprecated because of the removal of rpy/rpy2 support\n')
#
# define some validataion functions
Modified: trunk/src/plotter.py
===================================================================
--- trunk/src/plotter.py 2015-10-31 00:32:59 UTC (rev 4995)
+++ trunk/src/plotter.py 2015-11-01 03:09:25 UTC (rev 4996)
@@ -26,38 +26,20 @@
#
'''
-This module defines several utility functions and Python operators that make
-use of the Python rpy or rpy2 module (http://rpy.sourceforge.net) to plot
-expressions and information fields of evolving populations using a popular
-statistical analysis language R (http://www.r-project.org) or matplotlib.
-You can specify the plotting library using simuOpt.setOptions(plotter='matplotlib').
+This module defines several utility functions and Python operators that plot
+expressions and information fields of evolving populations using matplotlib.
+Plotting through rpy and rpy2 was supported in version 1.1.6 and earlier but
+was removed in version 1.1.7 due to stability problems of rpy2.
-Each operator calls a sequence of R or matplotlib functions to draw and save
+Each operator calls a sequence of matplotlib functions to draw and save
figures. A special parameter passing mechanism is used so that you can specify
-arbitrary parameters to these functions. For example, you can use parameter
-``par_mfrow=[2,2]`` to pass ``mfrow=[2,2]`` to function ``par``, and use
-``lty_rep=[1,2]`` to pass ``lty=1`` and ``lty=2`` to specify different line
-types for different replicates if ``rpy`` is used. The help message of each class
-will describe which and in what sequence these R or matplotlib functions are
-called to help you figure out which parameters are allowed. The syntax
-will be different if different plotting module is used.
+arbitrary parameters to these functions.
'''
__all__ = [
- 'newDevice',
- 'saveFigure',
'DerivedArgs',
'VarPlotter',
'ScatterPlotter',
- 'InfoPlotter',
- 'HistPlotter',
- 'QQPlotter',
- 'BoxPlotter',
- # export essential piece of rpy or rpy2 so that other modules could use them
- 'r',
- # exported with rpy. Not meaningful if rpy2 is used.
- 'with_mode',
- 'NO_CONVERSION'
]
from math import ceil, sqrt
@@ -65,177 +47,14 @@
from simuOpt import simuOptions
-# used by rpy2
-def my_py2ri(o):
- '''Convert tuple to R object. This is defined because the default
- py2ri function does not support tuple type.'''
- if isinstance(o, (tuple, list)):
- if all([isinstance(x, int) for x in o]):
- res = ro.vectors.IntVector(o)
- elif all([isinstance(x, (int, float)) for x in o]):
- res = ro.vectors.FloatVector(o)
- elif all([isinstance(x, str) for x in o]):
- res = ro.vectors.StrVector(o)
- elif isinstance(o, tuple):
- raise RuntimeError('Failed to convert tuple {}'.format(o))
- else:
- # default_py2ri can handle list of
- # heterogeneous type, I guess
- res = ro.default_py2ri(o)
- else:
- res = ro.default_py2ri(o)
- return res
+import matplotlib.pylab as plt
-if simuOptions['Plotter'] is None:
- try:
- import rpy_options
- rpy_options.set_options(VERBOSE = False)
- from rpy import r, with_mode, NO_CONVERSION
- plotter = 'rpy'
- except ImportError, e:
- try:
- import rpy2.robjects as ro
- from rpy2.robjects import r, conversion
- conversion.py2ri = my_py2ri
- with_mode = None
- NO_CONVERSION = None
- plotter = 'rpy2'
- except ImportError, e:
- try:
- import matplotlib.pylab as plt
- plotter = 'matplotlib'
- except:
- print('Neither rpy nor matplotlib is available.')
- raise e
-elif simuOptions['Plotter'] == 'rpy':
- import rpy_options
- rpy_options.set_options(VERBOSE = False)
- from rpy import r, with_mode, NO_CONVERSION
- plotter = 'rpy'
-elif simuOptions['Plotter'] == 'rpy2':
- import rpy2.robjects as ro
- from rpy2.robjects import r, conversion
- conversion.py2ri = my_py2ri
- with_mode = None
- NO_CONVERSION = None
- plotter = 'rpy2'
-else:
- import matplotlib.pylab as plt
- plotter = 'matplotlib'
-
-
-# if under windows, fix a bug with rpy which uses blocking i/o so
-# R figure will not be refreshed in time. See
-# https://Stat.ethz.ch/pipermail/r-devel/2006-January/036049.html
-# for details.
-if os.name == 'nt':
- # In addition to options(windowsBuffered=False), I find that I also need to
- # call windows.options(buffered=False) to make functions such as hist work.
- #
- # This function is only available for R 2.9.0 (rev 48333)
- if plotter == 'rpy':
- r.options(windowsBuffered=False)
- if int(r.R_Version()['svn rev']) >= 48333:
- r.windows_options(buffered=False)
- elif plotter == 'rpy2':
- if int(r('R.Version()$"svn rev"')[0]) >= 48333:
- r("windows.options(buffered=False)")
-
-
from simuPOP import PyOperator, ALL_AVAIL
-def newDevice():
- '''Create a new graphics window and return its device number in R. This
- function essentially calls ``getOption('device')()`` in R.
- '''
- if plotter == 'rpy':
- # open a new window
- try:
- r('getOption("device")()')
- except Exception as e:
- raise RuntimeError("Failed to get R version to start a graphical device: {}".format(e));
- # get device number
- device = r.dev_cur()
- if device == 0:
- raise RuntimeError('Can not open new device')
- return device
- elif plotter == 'rpy2':
- # open a new window
- try:
- # 46754 is the revision number for R 2.8.0
- # For R >= 2.8.0, getOption('device') returns a function
- r('getOption("device")()')
- except Exception as e:
- raise RuntimeError("Failed to get R version to start a graphical device: {}".format(e));
- # get device number
- device = r['dev.cur']()
- if device == 0:
- raise RuntimeError('Can not open new device')
- return device
-
- else:
- return plt.figure()
-
-def saveFigure(file=None, **kwargs):
- '''
- Save current figure into ``file``. File format and graphics device are
- determined by file extension. Supported file formats include ``pdf``,
- ``png``, ``bmp``, ``jpg (jpeg)``, ``tif (tiff)``, and ``eps``, which
- correspond to R devices ``pdf``, ``png``, ``bmp``, ``jpeg``, ``tiff``
- and ``postscript``. A postscript device will be used if there is no file
- extension or the file extension is not recognizable. Additional keyword
- parameters will be passed to the underlying ``dev.print`` function.
- '''
- if file is None:
- return
- if 'rpy' in plotter:
- filename, ext = os.path.splitext(file)
- dirname = os.path.dirname(file)
- if dirname != '' and not os.path.isdir(dirname):
- # this might fail and raise an error
- os.makedirs(dirname)
- # default extension and format
- if ext == '':
- ext = '.eps'
- #
- params = {}
- # these two parameters have to be specified for raster formats
- try:
- # I need to use this more lengthy form because some
- # functions are not available in, for example, R 2.6.2
- if ext.lower() == '.pdf':
- device = r.pdf
- elif ext.lower() == '.png':
- device = r.png
- params = {'width': 800, 'height': 600}
- elif ext.lower() == '.bmp':
- device = r.bmp
- params = {'width': 800, 'height': 600}
- elif ext.lower() in ['.jpg', '.jpeg']:
- device = r.jpeg
- params = {'width': 800, 'height': 600}
- elif ext.lower() in ['.tif', '.tiff']:
- device = r.tiff
- params = {'width': 800, 'height': 600}
- elif ext.lower() == '.eps':
- device = r.postscript
- except Exception, e:
- print e
- print 'Can not determine which device to use to save file %s. A postscript driver is used.' % name
- device = r.postscript
- params.update(kwargs)
- if plotter == 'rpy':
- r.dev_print(file=file, device=device, **params)
- else:
- r['dev.print'](file=file, device=device, **params)
- else:
- plt.savefig(file)
-
-
class DerivedArgs:
'''This class implements the derived keyword argument handling mechanism that
is used by all classes defined in this module. It is provided for users who
- would like to use this mechanism for their own rpy or matplotlib-related
+ would like to use this mechanism for their own matplotlib-related
operators.
An derived keyword argument is an argument that is prefixed with a function
@@ -417,30 +236,6 @@
various formats if parameter ``saveAs`` is specified. File format is
determined by file extension. After the evolution, the graphic device could
be left open (``leaveOpen``).
-
- If the rpy module is used (default if rpy if available), arbitrary keyword
- parameters could be specified and be passed to the underlying R drawing functions
- ``plot`` and ``lines``. These parameters could be used to specify line type (``lty``),
- color (``col``), title (``main``), limit of x and y axes (``xlim`` and
- ``ylim``) and many other options (see R manual for details). As a special
- case, multiple values can be passed to each replicate and/or dimension if
- the name of a parameter ends with ``_rep``, ``_dim``, or ``_repdim``
- For example, ``lty_rep=range(1, 5)`` will pass parameters ``lty=1``, ...
- ``lty=4`` to four replicates. You can also pass parameters to specific
- R functions such as ``par``, ``plot``, ``lines``, ``legend``, ``dev_print``
- by prefixing parameter names with a function name. For example,
- ``dev_print_width=300`` will pass ``width=300`` to function ``dev.print()``
- when you save your figures using this function. In addition, if the value
- of a parameter is a string starting with ``!``, the evaluated result of
- the remaining string will be used as parameter value. Further customization
- of your figures could be achieved by writing your own hook functions that
- will be called before and after a figure is drawn, and after each ``plot``
- call.
-
- This opertor calls R functions ``par``, ``plot``, ``lines``, ``legend``,
- and ``dev.print``. Functions ``plot`` and ``lines`` are the default
- destination for keyword arguments and the ones that accept list parameters
- to customize lines by replicate and/or dimension.
'''
def __init__(self, expr, win=0, update=1, byRep=False, byDim=False,
saveAs="", leaveOpen=False, legend=[], preHook=None, postHook=None,
@@ -505,18 +300,15 @@
plotHook
A function that, if given, will be called after each ``plot``
- function. The ``r`` object from the ``rpy`` module or ``Figure``
- object from the ``matplotlib`` module , generation
- list, data being plotted, replicate number (if applicable) and
- dimension index (if applicable) will be passed as keyword arguments
- ``r``, ``gen``, ``data``, ``rep`` (optional) and ``dim``
- (optional).
+ function. The ``Figure`` object from the ``matplotlib`` module ,
+ generation list, data being plotted, replicate number (if applicable)
+ and dimension index (if applicable) will be passed as keyword arguments
+ ``gen``, ``data``, ``rep`` (optional) and ``dim`` (optional).
kwargs
Additional keyword arguments that will be interpreted and sent to
- underlying R or matplotlib functions. These arguments could have prefixes
- (destination function names) ``plot_``, ``lines_``, ``par_``,
- ``legend_`` and ``dev_print_``, and suffixes (list parameters)
+ underlying matplotlib functions. These arguments could have prefixes
+ (destination function names) and suffixes (list parameters)
``_rep``, ``_dim``, and ``_repdim`` for the ``rpy`` option. Arguments
without prefixes are sent to functions ``plot`` and ``lines``. String
values with a leading ``!`` will be replaced by its evaluated result
@@ -534,35 +326,19 @@
self.preHook = preHook
self.postHook = postHook
self.plotHook = plotHook
- if 'rpy' in plotter:
- self.args = DerivedArgs(
- defaultFuncs = ['plot', 'lines'],
- allFuncs = ['par', 'plot', 'lines', 'dev_print', 'legend'],
- suffixes = ['rep', 'dim', 'repdim'],
- defaultParams = {
- 'plot_type': 'l',
- 'plot_xlab': 'Generation',
- 'plot_ylab': '',
- 'lines_lty': 1,
- 'legend_bty': 'n',
- 'legend_x': 'topright',
- },
- **kwargs
- )
- else:
- self.args = DerivedArgs(
- defaultFuncs = ['figure', 'plot'],
- allFuncs = ['figure', 'plot', 'set_title', 'set_xlabel',
- 'set_ylabel', 'set_ylim', 'legend'],
- suffixes = ['rep', 'dim', 'repdim'],
- defaultParams = {
- 'plot_linestyle': '-',
- 'set_xlabel_xlabel': 'Generation',
- 'set_ylabel_ylabel': '',
- 'set_title_label': '',
- },
- **kwargs
- )
+ self.args = DerivedArgs(
+ defaultFuncs = ['figure', 'plot'],
+ allFuncs = ['figure', 'plot', 'set_title', 'set_xlabel',
+ 'set_ylabel', 'set_ylim', 'legend'],
+ suffixes = ['rep', 'dim', 'repdim'],
+ defaultParams = {
+ 'plot_linestyle': '-',
+ 'set_xlabel_xlabel': 'Generation',
+ 'set_ylabel_ylabel': '',
+ 'set_title_label': '',
+ },
+ **kwargs
+ )
# internal flags
self.nRep = 0
self.reps = [] # allows specification of selected replicates
@@ -574,21 +350,13 @@
self.gen = []
self.data = []
# when apply is called, self._rpy_plot is called.
- PyOperator.__init__(self, func=self._rpy_plot if 'rpy' in plotter else self._mat_plot,
+ PyOperator.__init__(self, func=self._mat_plot,
begin=begin, end=end, step=step, at=at, reps=reps,
subPops=ALL_AVAIL, infoFields=[])
def __del__(self):
- # Close the device if needed.
- if plotter == 'rpy':
- if not self.leaveOpen and hasattr(self, 'device'):
- r.dev_off(self.device)
- elif plotter == 'rpy2':
- if not self.leaveOpen and hasattr(self, 'device'):
- r['dev.off'](self.device)
- else:
- if not self.leaveOpen:
- plt.close()
+ if not self.leaveOpen:
+ plt.close()
def _pushData(self, gen, rep, data):
'''Push history data to self.data for later retrieval. Set self.min and
@@ -639,133 +407,6 @@
else:
return self.data[rep]
- def _rpy_plot(self, pop):
- "Evaluate expression in pop and save result. Plot all data if needed"
- gen = pop.dvars().gen
- rep = pop.dvars().rep
- # push data
- self._pushData(gen, rep, pop.evaluate(self.expr))
- # Draw a plot only when
- # 1. There are at least two obervations.
- # 2. rep is the last recorded replicate.
- # 3. we are self.update away from last plot.
- if len(self.gen) <= 1 or rep + 1 != len(self.data) or \
- (self.update >= 1 and gen < self.lastPlot + self.update):
- # do not plot
- return True
- else:
- self.lastPlot = gen
- # create a new graphical device if needed
- if not hasattr(self, 'device'):
- self.device = newDevice()
- else: # if there are multiple devices, set it back
- if plotter == 'rpy':
- r.dev_set(self.device)
- else:
- r['dev.set'](self.device)
- # call the preHook function if given
- if self.preHook is not None:
- self.preHook(r)
- # figure out the dimension of data
- if self.nRep == 1:
- self.byRep = False
- if self.nDim == 1:
- self.byDim = False
- # needs subplots?
- nPlots = 1
- if self.byDim:
- nPlots *= self.nDim
- if self.byRep:
- nPlots *= self.nRep
- # try to use colors
- if self.nDim > 1 and not self.byDim:
- self.args.addDefault(col_dim=r.rainbow(self.nDim))
- if self.nRep > 1 and not self.byRep:
- self.args.addDefault(col_rep=r.rainbow(self.nRep))
- # suggest how to arrange subplots
- if nPlots > 1:
- nrow = int(ceil(sqrt(nPlots)))
- ncol = int(ceil(nPlots/float(nrow)))
- if nrow > ncol:
- nrow, ncol = ncol, nrow
- self.args.addDefault(par_mfrow=[nrow, ncol])
- # users might set additional parameters and override calculated mfrow.
- r.par(**self.args.getArgs('par', pop))
- # now plot.
- if self.byRep:
- # handle each replicate separately
- for rep_idx,rep in enumerate(self.reps):
- if self.byDim:
- # separate plot for each dim
- for dim in range(self.nDim):
- data = self._getData(rep, dim)
- r.plot(self.gen, data,
- **self.args.getArgs('plot', pop, rep=rep_idx, dim=dim,
- repdim=self.nDim*rep_idx + dim, ylim=[self.min, self.max]))
- if self.plotHook is not None:
- self.plotHook(r=r, gen=self.gen, data=data, rep=rep, dim=dim)
- else:
- # all var in one subplot
- data = self._getData(rep, 0)
- r.plot(self.gen, data,
- **self.args.getArgs('plot', pop, rep=rep_idx, dim=0,
- repdim=self.nDim * rep_idx, ylim=[self.min, self.max]))
- if self.plotHook is not None:
- self.plotHook(r=r, gen=self.gen, data=data, rep=rep)
- for dim in range(1, self.nDim):
- r.lines(self.gen, self._getData(rep, dim),
- **self.args.getArgs('lines', pop, rep=rep_idx, dim=dim,
- repdim=self.nDim * rep_idx + dim))
- if len(self.legend) > 0:
- args = self.args.getLegendArgs('lines', pop, ['lty', 'col', 'lwd'],
- 'rep', range(self.nRep))
- args.update(self.args.getArgs('legend', pop))
- r.legend(legend=self.legend, **args)
- else:
- # all replicate in one figure
- if self.byDim:
- for dim in range(self.nDim):
- data = self._getData(self.reps[0], dim)
- r.plot(self.gen, data,
- **self.args.getArgs('plot', pop, rep=self.reps[0], dim=dim, repdim=dim,
- ylim=[self.min, self.max]))
- if self.plotHook is not None:
- self.plotHook(r=r, gen=self.gen, data=data, dim=dim)
- for rep_idx,rep in enumerate(self.reps[1:]):
- r.lines(self.gen, self._getData(rep, dim),
- **self.args.getArgs('lines', pop, rep=rep_idx+1, dim=dim,
- repdim=self.nDim * (rep_idx + 1) + dim))
- if len(self.legend) > 0:
- args = self.args.getLegendArgs('lines', pop, ['lty', 'col', 'lwd'],
- 'rep', range(self.nRep))
- args.update(self.args.getArgs('legend', pop))
- r.legend(legend=self.legend, **args)
- else:
- data = self._getData(0, 0)
- r.plot(self.gen, data,
- **self.args.getArgs('plot', pop, rep=0, dim=0, repdim=0,
- ylim=[self.min, self.max]))
- if self.plotHook is not None:
- self.plotHook(r=r, gen=self.gen, data=data)
- for rep_idx,rep in enumerate(self.reps):
- for dim in range(self.nDim):
- r.lines(self.gen, self._getData(rep, dim),
- **self.args.getArgs('lines', pop, rep=rep_idx, dim=dim,
- repdim=self.nDim * rep_idx + dim))
- if len(self.legend) > 0:
- args = self.args.getLegendArgs('lines', pop, ['lty', 'col', 'lwd'],
- ['rep', 'dim'], [(x,y) for x in range(self.nRep) for y in range(self.nDim)])
- args.update(self.args.getArgs('legend', pop))
- r.legend(legend=self.legend, **args)
- # call the postHook function if given
- if self.postHook is not None:
- self.postHook(r)
- if self.saveAs != '':
- file, ext = os.path.splitext(self.saveAs)
- filename = '%s_%d%s' % (file, gen, ext)
- saveFigure(**self.args.getArgs('dev_print', pop, file=filename))
- return True
-
def _mat_plot(self, pop):
"Evaluate expression in pop and save result. Plot all data if needed"
gen = pop.dvars().gen
@@ -917,18 +558,7 @@
Population, using values at two information fields as their x- and y-axis.
Arbitrary keyword parameters could be specified and be passed to the
- underlying R drawing functions ``plot`` and ``points``. These parameters
- could be used to specify point type (``pch``), color (``col``),
- title (``main``), limit of x and y axes (``xlim`` and ``ylim``) and many
- other options (see R manual for details). You can also pass parameters
- to specific R functions such as ``par``, ``plot``, ``points``, ``legend``,
- ``pdf`` by prefixing parameter names with a function name. For example,
- ``par_mar=[1]*4`` will pass ``par=[1]*4`` to function ``par()`` which is
- called before a figure is drawn. (Note that the function to save a figure
- is ``dev.print`` so parameters such as ``dev_print_width`` should be
- used.) Further customization of your figures could be achieved by writing
- your own hook functions that will be called before and after a figure is
- drawn.
+ underlying matplotlib drawing functions ``plot`` and ``scatter``.
The power of this operator lies in its ability to differentiate individuals
from different (virtual) subpopulations. If you specify IDs of (virtual)
@@ -941,11 +571,6 @@
individuals with red. In addition, if the value of a parameter is a string
starting with ``!``, the evaluated result of the remaining string will be
used as parameter value.
-
- This opertor calls R functions ``par``, ``plot``, ``points``, ``legend``,
- and ``dev.print``. Functions ``plot`` and ``points`` are the default
- destination for keyword arguments and the ones that accept list parameters
- to customize lines by (virtual) subpopulation.
'''
def __init__(self, infoFields=[], saveAs="", leaveOpen=False, legend=[],
preHook=None, postHook=None, begin=0, end=-1, step=1,
@@ -980,22 +605,18 @@
preHook
A function that, if given, will be called before the figure is
- draw. The ``r`` object from the ``plotter`` module or the ``Figure``
+ draw. The ``plotter`` module or the ``Figure``
object from matplotlib will be passed to this function.
postHook
A function that, if given, will be called after the figure is
- drawn. The ``r`` object from the ``plotter`` module or the ``Figure``
+ drawn. The ``plotter`` module or the ``Figure``
object from matplotlib will be passed to this function.
kwargs
Additional keyword arguments that will be interpreted and sent to
- underlying R functions. These arguments could have prefixes
- (destination function names) ``plot_``, ``points_``, ``par_``,
- ``legend_`` and ``dev_print_``, and suffixes (list parameters)
- ``_sp``. Arguments without prefixes are sent to functions
- ``plot`` and ``points``. String values with a leading ``!`` will be
- replaced by its evaluated result against the current population.
+ underlying matplotlib functions. String values with a leading ``!``
+ will be replaced by its evaluated result against the current population.
'''
# parameters
self.infoFields = infoFields
@@ -1007,106 +628,29 @@
self.preHook = preHook
self.postHook = postHook
self.subPops = subPops
- if 'rpy' in plotter:
- self.args = DerivedArgs(
- defaultFuncs = ['plot', 'points'],
- allFuncs = ['par', 'plot', 'points', 'dev_print', 'legend'],
- suffixes = ['sp'],
- defaultParams = {
- 'legend_bty': 'n',
- 'plot_xlab': self.infoFields[0],
- 'plot_ylab': self.infoFields[1],
- 'legend_x': 'topright',
- },
- **kwargs)
- else:
- self.args = DerivedArgs(
- defaultFuncs = ['figure', 'plot'],
- allFuncs = ['figure', 'plot', 'scatter', 'set_title', 'set_xlabel',
- 'set_ylabel', 'set_ylim', 'legend'],
- suffixes = ['sp'],
- defaultParams = {
- 'plot_linestyle': '-',
- 'set_xlabel_xlabel': self.infoFields[0],
- 'set_ylabel_ylabel': self.infoFields[1],
- 'set_title_label': '',
- },
- **kwargs
- )
+ self.args = DerivedArgs(
+ defaultFuncs = ['figure', 'plot'],
+ allFuncs = ['figure', 'plot', 'scatter', 'set_title', 'set_xlabel',
+ 'set_ylabel', 'set_ylim', 'legend'],
+ suffixes = ['sp'],
+ defaultParams = {
+ 'plot_linestyle': '-',
+ 'set_xlabel_xlabel': self.infoFields[0],
+ 'set_ylabel_ylabel': self.infoFields[1],
+ 'set_title_label': '',
+ },
+ **kwargs
+ )
if len(self.subPops) > 1:
- if 'rpy' in plotter:
- self.args.addDefault(
- pch_sp = range(1, len(self.subPops) + 1),
- col_sp = r.rainbow(len(self.subPops)))
- else:
- cm = plt.get_cmap('gist_rainbow')
- self.args.addDefault(
- scatter_c_sp=[cm(i*1.0/len(self.subPops)) for i in range(len(self.subPops))])
+ cm = plt.get_cmap('gist_rainbow')
+ self.args.addDefault(
+ scatter_c_sp=[cm(i*1.0/len(self.subPops)) for i in range(len(self.subPops))])
# when apply is called, self._rpy_plot is called.
- PyOperator.__init__(self, func=self._rpy_plot if 'rpy' in plotter else self._mat_plot,
+ PyOperator.__init__(self, func=self._mat_plot,
begin=begin, end=end, step=step, at=at, reps=reps)
- def __del__(self):
- # Close the device if needed.
- if not self.leaveOpen and hasattr(self, 'device'):
- if plotter == 'rpy':
- r.dev_off(self.device)
- elif plotter == 'rpy2':
- r['dev.off'](self.device)
-
- def _rpy_plot(self, pop):
- "Evaluate expression in pop and save result. Plot all data if needed"
- gen = pop.dvars().gen
- rep = pop.dvars().rep
- # create a new graphical device if needed
- if not hasattr(self, 'device'):
- self.device = newDevice()
- else: # if there are multiple devices, set it back
- if plotter == 'rpy':
- r.dev_set(self.device)
- else:
- r['dev.set'](self.device)
- # call the preHook function if given
- if self.preHook is not None:
- self.preHook(r)
- # call par in case some parameter is provided
- parParam = self.args.getArgs('par', pop)
- if len(parParam) > 0:
- r.par(**parParam)
- #
- x = pop.indInfo(self.infoFields[0])
- y = pop.indInfo(self.infoFields[1])
- xlim = [min(x), max(x)]
- ylim = [min(y), max(y)]
- # if there is no subpopulation, easy
- if len(self.subPops) == 0:
- r.plot(x, y,
- **self.args.getArgs('plot', pop, type='p', xlim=xlim, ylim=ylim))
- else:
- parPlot = self.args.getArgs('plot', pop, type='n', xlim=xlim, ylim=ylim)
- parPlot['type'] = 'n'
- r.plot(x[0], y[0], **parPlot)
- for idx,sp in enumerate(self.subPops):
- x = pop.indInfo(self.infoFields[0], sp)
- y = pop.indInfo(self.infoFields[1], sp)
- r.points(x, y, **self.args.getArgs('points', pop, sp=idx))
- # legend
- if len(self.legend) > 0:
- args = self.args.getLegendArgs('points', pop, ['col', 'pch', 'lwd', 'cex'],
- 'sp', range(len(self.subPops)))
- args.update(self.args.getArgs('legend', pop))
- r.legend(legend=self.legend, **args)
- # call the postHook function if given
- if self.postHook is not None:
- self.postHook(r)
- if self.saveAs != '':
- file, ext = os.path.splitext(self.saveAs)
- filename = '%s_%d_%d%s' % (file, gen, rep, ext)
- saveFigure(**self.args.getArgs('dev_print', pop, file=filename))
- return True
-
def _mat_plot(self, pop):
"Evaluate expression in pop and save result. Plot all data if needed"
gen = pop.dvars().gen
@@ -1157,464 +701,3 @@
self.device.savefig(filename)
return True
-class InfoPlotter(PyOperator):
- '''
- This operator uses a R function such as ``hist`` and ``qqplot`` to plot
- properties of one or more information fields of individuals in one or more
- (virtual) subpopulations. Separate subplots are used for different
- information fields and subpopulations.
-
- This operator essentially gets values of information fields and sends them
- to a R function such as ``hist``. The resulting figures could be customized
- by additional keyword parameters and various hook functions. For example,
- a ``qqline`` function could be called in a ``plotHook`` function to add a
- QQ line to a ``qqnorm`` plot. The ``plotHook`` can be used to draw the
- whole (sub)plot if no R function is specified for parameter ``func``.
-
- Besides regular keyword parameters, keyword parameters ending in ``_sp``,
- ``_fld`` or ``_spfld`` are expected to have multiple values which will be
- used for differnt subpopulations, information fields, and their
- combinations. You can also specify which function the keyword should be
- sent by prefixing a function name to the parameter name. For example,
- ``pch_fld=[1, 2]`` will use different symbols for different information
- fields, and ``par_mar=[1]*4`` will send parameter ``mar=[1]*4`` to function
- ``par``. In addition, if the value of a parameter is a string starting with
- ``!``, the evaluated result of the remaining string will be used as
- parameter value.
-
- This opertor calls R functions ``par``, ``dev.print``, and a user-specified
- function. Additional keyword arguments without function prefix will be sent
- to this function.
- '''
- def __init__(self, func=None, infoFields=[], saveAs="", leaveOpen=False,
- preHook=None, postHook=None, plotHook = None, begin=0,
- end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=[], **kwargs):
- '''
- func
- Name of the R or matplotlib function that will be called to draw figures
- from values of given information fields. No R function will be called
- if it is not specified. In this case, a ``plotHook`` can be used
- to plot passed values.
-
- infoFields
- Information fields whose values will be sent to the specified
- plotting function.
-
- subPops
- A list of subpopulations and virtual subpopulations. Each
- subpopulation will be plotted in a separate subplot.
-
- saveAs
- Save figures in files saveAs_gen_rep.ext (e.g. ``figure_10_0.eps``
- if ``saveAs='figure.eps'``). If ext is given, a corresponding
- device will be used. Otherwise, a default postscript driver will be
- used. Currently supported formats include ``.pdf``, ``.png``,
- ``.bmp``, ``.jpg``, and ``.tif``. The default filename could be
- overriden by derived argument ``dev_print_file``.
-
- leaveOpen
- Whether or not leave the plot open when plotting is done. Default
- to ``False`` functions. If this option is set to ``True``, you will
- have to close the graphic device explicitly using function
- ``r.dev_off()``. Note that leaving the device open allows
- further manipuation of the figures outside of this operator.
-
- preHook
- A function that, if given, will be called before the figure is
- draw. The ``r`` object for ``rpy`` will be passed to this function.
-
- postHook
- A function that, if given, will be called after the figure is
- drawn. The ``r`` object for ``rpy`` will be passed to this function.
-
- plotHook
- A function that, if given, will be called after each ``plot``
- function. The ``r`` object from the ``rpy`` module , data being
- plotted, name of the information field and index of subpopulation
- (in parameter ``subPops``, if applicable) will be passed with
- keywords ``r``, ``data``, ``field`` and ``subPop`` (optional)
- respectively.
-
- kwargs
- Additional keyword arguments that will be interpreted and sent to
- underlying R functions. These arguments could have prefixes
- (destination function names) ``par_``, ``dev_print_`` and the
- function you specify (parameter ``func``), and suffixes (list
- parameters) ``_sp``, ``_fld``, and ``_spfld``. Arguments without
- prefixes are sent to the user specified function. String values
- with a leading ``!`` will be replaced by its evaluated result
- against the current population.
- '''
- # parameters
- if type(infoFields) == type(''):
- self.infoFields = [infoFields]
- else:
- self.infoFields = infoFields
- self.func = func
- if len(self.infoFields) == 0:
- raise RuntimeError('At least one information field should be given')
- self.saveAs = saveAs
- self.leaveOpen = leaveOpen
- self.preHook = preHook
- self.postHook = postHook
- self.plotHook = plotHook
- self.subPops = subPops
- if 'rpy' in plotter:
- if self.func is not None:
- if plotter == 'rpy':
- self.rfunc = r(self.func)
- else:
- self.rfunc = r[self.func]
- self.args = DerivedArgs(
- defaultFuncs = [] if self.func is None else [self.func],
- allFuncs = ['par', 'dev_print', 'legend'] + ([] if self.func is None else [self.func]),
- suffixes = ['sp', 'fld', 'spfld'],
- defaultParams = {'legend_x': 'topright'},
- **kwargs)
- else:
- raise RuntimeError('InfoPlotter does not yet support matplotlib plotter')
- # when apply is called, self._rpy_plot is called.
- PyOperator.__init__(self, func=self._rpy_plot,
- begin=begin, end=end, step=step, at=at, reps=reps)
-
-
- def __del__(self):
- # Close the device if needed.
- if plotter == 'rpy':
- if not self.leaveOpen and hasattr(self, 'device'):
- r.dev_off(self.device)
- elif plotter == 'rpy2':
- if not self.leaveOpen and hasattr(self, 'device'):
- r['dev.off'](self.device)
- else:
- if not self.leaveOpen:
- plt.close()
-
- def _rpy_plot(self, pop):
- "Evaluate expression in pop and save result. Plot all data if needed"
- gen = pop.dvars().gen
- rep = pop.dvars().rep
- # create a new graphical device if needed
- if not hasattr(self, 'device'):
- self.device = newDevice()
- else: # if there are multiple devices, set it back
- if plotter == 'rpy':
- r.dev_set(self.device)
- else:
- r['dev.set'](self.device)
- # call the preHook function if given
- if self.preHook is not None:
- self.preHook(r)
- # subplots?
- nPlots = len(self.infoFields)
- if len(self.subPops) > 1:
- nPlots *= len(self.subPops)
- # call par in case some parameter is provided
- if nPlots > 1:
- nrow = int(ceil(sqrt(nPlots)))
- ncol = int(ceil(nPlots/float(nrow)))
- if nrow > ncol:
- nrow, ncol = ncol, nrow
- self.args.addDefault(par_mfrow=[nrow, ncol])
- #
- r.par(**self.args.getArgs('par', pop))
- #
- for fldIdx,fld in enumerate(self.infoFields):
- # if there is no subpopulation, easy
- if len(self.subPops) == 0:
- val = pop.indInfo(fld)
- if self.func is not None:
- self.rfunc(val, **self.args.getArgs(self.func, pop, fld=fldIdx, sp=0,
- spfld=fldIdx, main='%s at gen %d' % (fld, gen), xlab=fld, ylab=self.func))
- if self.plotHook is not None:
- self.plotHook(r=r, data=val, field=fld)
- else:
- for spIdx,sp in enumerate(self.subPops):
- val = pop.indInfo(fld, sp)
- if self.func is not None:
- self.rfunc(val, **self.args.getArgs(self.func, pop,
- fld=fldIdx, sp=spIdx, spfld=len(self.infoFields)*spIdx + fldIdx,
- main='%s in %s at gen %d' % (fld, pop.subPopName(sp), gen),
- xlab=fld, ylab=self.func))
- if self.plotHook is not None:
- self.plotHook(r=r, data=val, field=fld, subPop=sp)
- # call the postHook function if given
- if self.postHook is not None:
- self.postHook(r)
- if self.saveAs != '':
- file, ext = os.path.splitext(self.saveAs)
- filename = '%s_%d_%d%s' % (file, gen, rep, ext)
- saveFigure(**self.args.getArgs('dev_print', pop, file=filename))
- return True
-
-class HistPlotter(InfoPlotter):
- '''An ``InfoPlotter`` that uses function ``hist``.'''
- def __init__(self, *args, **kwargs):
- '''Returns an ``InfoPlotter`` that uses R function ``hist`` to draw
- histogram of individual information fields of specified (virtual)
- subpopulations. Please see ``InfoPlotter`` for details.
- '''
- InfoPlotter.__init__(self, 'hist', *args, **kwargs)
-
-
-class QQPlotter(InfoPlotter):
- '''An ``InfoPlotter`` that uses function ``qqnorm``.'''
- def __init__(self, *args, **kwargs):
- '''Returns an ``InfoPlotter`` that uses R function ``qqnorm`` to draw
- qq plot of individual information fields of specified (virtual)
- subpopulations. Please see ``InfoPlotter`` for details.
- '''
- InfoPlotter.__init__(self, 'qqnorm', *args, **kwargs)
-
-
-class BoxPlotter(PyOperator):
- '''
- This operator draws boxplots of one or more information fields of
- individuals in one or more (virtual) subpopulations of a population.
- Although a ``InfoPlotter`` with ``func=boxplot`` could be used to plot
- boxplots for each information field and/or subpopulation, this class allows
- multiple whiskers to share one plot. How the whiskers are oraganized is
- controlled by parameters ``byField`` and ``bySubPop``.
-
- This operator essentially gets values of information fields and sends them
- to boxplots. Individual ownerships (subpopulation or field) are also passed
- so that multiple whiskers could be drawn in the same plot. The resulting
- figures could be customized by additional keyword parameters and various
- hook functions.
-
- Besides regular keyword parameters, keyword parameters ending in ``_sp``,
- ``_fld`` or ``_spfld`` are expected to have multiple values which will be
- used for differnt subpopulations, information fields, and their
- combinations. You can also specify which function the keyword should be
- sent by prefixing a function name to the parameter name. For example,
- ``pch_fld=[1, 2]`` will use different symbols for different information
- fields, and ``par_mar=[1]*4`` will send parameter ``mar=[1]*4`` to function
- ``par``. In addition, if the value of a parameter is a string starting with
- ``!``, the evaluated result of the remaining string will be used as
- parameter value.
-
- This opertor calls R functions ``par``, ``boxplot`` and ``dev.print``.
- Keyword parameters without function prefix will be passed to ``boxplot``.
- '''
- def __init__(self, infoFields=[], byField=False, bySubPop=False, saveAs="",
- leaveOpen=False, preHook=None, postHook=None, plotHook = None,
- begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=[], **kwargs):
- '''
- infoFields
- Information fields whose values will be sent to R function
- ``boxplot``.
-
- subPops
- A list of subpopulations and virtual subpopulations. Separate
- whiskers will be drawn for individuals in these subpopulations.
-
- byField
- If multiple information fields are specified, separate the whiskers
- different subplots if this parameter is ``True``.
-
- bySubPop
- If multiple (virtual) subpopulations are specified, separate the
- whiskers to different subplots if this parameter is ``True``.
-
- saveAs
- Save figures in files saveAs_gen_rep.ext (e.g. ``figure_10_0.eps``
- if ``saveAs='figure.eps'``). If ext is given, a corresponding
- device will be used. Otherwise, a default postscript driver will be
- used. Currently supported formats include ``.pdf``, ``.png``,
- ``.bmp``, ``.jpg``, and ``.tif``. The default filename could be
- overriden by derived argument ``dev_print_file``.
-
- leaveOpen
- Whether or not leave the plot open when plotting is done. Default
- to ``False`` functions. If this option is set to ``True``, you will
- have to close the graphic device explicitly using function
- ``r.dev_off()``. Note that leaving the device open allows
- further manipuation of the figures outside of this operator.
-
- preHook
- A function that, if given, will be called before the figure is
- draw. The ``r`` object for ``rpy`` will be passed to this function.
-
- postHook
- A function that, if given, will be called after the figure is
- drawn. The ``r`` object for ``rpy`` will be passed to this function.
-
- plotHook
- A function that, if given, will be called after each ``plot``
- function. The ``r`` object from the ``rpy`` module, current field
- and subpopulation will be passed with keywords ``r``, ``field`` and
- ``subPop`` if applicable.
-
- kwargs
- Additional keyword arguments that will be interpreted and sent to
- underlying R functions. These arguments could have prefixes
- (destination function names) ``plot_``, ``boxplot_``, ``par_``,
- and ``dev_print_``, and suffixes (list parameters) ``_sp``,
- ``_fld`` and ``_spfld``. Arguments without prefixes are sent to
- function ``boxplot``. String values with a leading ``!`` will be
- replaced by its evaluated result against the current population.
- '''
- # parameters
- if type(infoFields) == type(''):
- self.infoFields = [infoFields]
- else:
- self.infoFields = infoFields
- if len(self.infoFields) == 0:
- raise RuntimeError('At least one information field should be given')
- if 'rpy' not in plotter:
- raise RuntimeError('BoxPlotter function does not support matplotlib plotter')
- self.saveAs = saveAs
- self.leaveOpen = leaveOpen
- self.preHook = preHook
- self.postHook = postHook
- self.plotHook = plotHook
- self.subPops = subPops
- self.byField = byField
- if len(self.infoFields) == 1:
- self.byField = False
- self.bySubPop = bySubPop
- if len(self.subPops) <= 1:
- self.bySubPop = False
- self.args = DerivedArgs(
- defaultFuncs = ['boxplot'],
- allFuncs = ['par', 'boxplot', 'dev_print', 'legend'],
- suffixes = ['sp', 'fld', 'spfld'],
- defaultParams = {'legend_x': 'topright'},
- **kwargs)
- # when apply is called, self.plot is called, additional keyword
- # parameters are passed by kwargs.
- PyOperator.__init__(self, func=self._rpy_plot, begin=begin, end=end,
- step=step, at=at, reps=reps)
-
- def __del__(self):
- # Close the device if needed.
- if not self.leaveOpen and hasattr(self, 'device'):
- if plotter == 'rpy':
- r.dev_off(self.device)
- elif plotter == 'rpy2':
- r['dev.off'](self.device)
-
-
- def _rpy_plot(self, pop):
- "Evaluate expression in pop and save result. Plot all data if needed"
- gen = pop.dvars().gen
- rep = pop.dvars().rep
- # create a new graphical device if needed
- if not hasattr(self, 'device'):
- self.device = newDevice()
- else: # if there are multiple devices, set it back
- if plotter == 'rpy':
- r.dev_set(self.device)
- else:
- r['dev.set'](self.device)
- # call the preHook function if given
- if self.preHook is not None:
- self.preHook(r)
- # subplots?
- nPlots = 1
- if len(self.infoFields) > 1 and self.byField:
- nPlots *= len(self.infoFields)
- if len(self.subPops) > 1 and self.bySubPop:
- nPlots *= len(self.subPops)
- # call par in case some parameter is provided
- if nPlots > 1:
- nrow = int(ceil(sqrt(nPlots)))
- ncol = int(ceil(nPlots/float(nrow)))
- if nrow > ncol:
- nrow, ncol = ncol, nrow
- self.args.addDefault(par_mfrow=[nrow, ncol])
- #
- r.par(**self.args.getArgs('par', pop))
- #
- if self.byField:
- for fldIdx,fld in enumerate(self.infoFields):
- if self.bySubPop:
- # multiple Field and subpop, each has its own subplot
- for spIdx,sp in enumerate(self.subPops):
- val = pop.indInfo(fld, sp)
- r.boxplot(val, **self.args.getArgs('boxplot', pop,
- fld=fld, sp=sp, spfld=len(self.infoFields)*spIdx + fldIdx,
- main='%s in %s at gen %d' % (fld, pop.subPopName(sp), gen)))
- if self.plotHook is not None:
- self.plotHook(r=r, field=fld, subPop=spIdx)
- else:
- # combine data
- data = []
- owner = []
- if len(self.subPops) == 0:
- data = pop.indInfo(fld)
- owner = [fld]*len(data)
- ...
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