python-cogent 1.9-9 / usr / lib / python2.7 / dist-packages / cogent / draw / arrow_rates.py

#!/usr/bin/env python
from matplotlib import use, rc
use('Agg')  #suppress graphical rendering
from pylab import rc, gcf, xlim, ylim, xticks, yticks, sqrt, text, clip, gca, \
    array, dot, ravel, draw, show, savefig
from fancy_arrow import arrow
"""Draws arrow plots representing rate matrices.

Note: currently requires dict of dinuc freqs, but should modify to work
with Rates objects from seqsim.

Based on graphical displays by Noboru Sueoka.
"""

__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Rob Knight"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"

rc('text', usetex=True)
rates_to_bases={'r1':'AT', 'r2':'TA', 'r3':'GA','r4':'AG','r5':'CA','r6':'AC', \
            'r7':'GT', 'r8':'TG', 'r9':'CT','r10':'TC','r11':'GC','r12':'CG'}
numbered_bases_to_rates = dict([(v,k) for k, v in rates_to_bases.items()])
lettered_bases_to_rates = dict([(v, 'r'+v) for k, v in rates_to_bases.items()])
def add_dicts(d1, d2):
    """Adds two dicts and returns the result."""
    result = d1.copy()
    result.update(d2)
    return result

def make_arrow_plot(data, size=4, display='length', shape='right', \
        max_arrow_width=0.03, arrow_sep = 0.02, alpha=0.5, \
        normalize_data=False, ec=None, labelcolor=None, \
        head_starts_at_zero=True, rate_labels=lettered_bases_to_rates,\
        graph_name=None, \
        **kwargs):
    """Makes an arrow plot.

    Parameters:
    
    data: dict with probabilities for the bases and pair transitions.
    size: size of the graph in inches.
    display: 'length', 'width', or 'alpha' for arrow property to change.
    shape: 'full', 'left', or 'right' for full or half arrows.
    max_arrow_width: maximum width of an arrow, data coordinates.
    arrow_sep: separation between arrows in a pair, data coordinates.
    alpha: maximum opacity of arrows, default 0.8.
    
    **kwargs can be anything allowed by a Arrow object, e.g. 
    linewidth and edgecolor.
    """
    
    xlim(-0.5,1.5)
    ylim(-0.5,1.5)
    gcf().set_size_inches(size,size)
    xticks([])
    yticks([])
    max_text_size = size*12
    min_text_size = size
    label_text_size = size*2.5
    text_params={'ha':'center', 'va':'center', 'family':'sans-serif',\
        'fontweight':'bold'}
    r2 = sqrt(2)

    deltas = {\
        'AT':(1,0),
        'TA':(-1,0),
        'GA':(0,1),
        'AG':(0,-1),
        'CA':(-1/r2, 1/r2),
        'AC':(1/r2, -1/r2),
        'GT':(1/r2, 1/r2),
        'TG':(-1/r2,-1/r2),
        'CT':(0,1),
        'TC':(0,-1),
        'GC':(1,0),
        'CG':(-1,0)
        }

    colors = {\
        'AT':'r',
        'TA':'k',
        'GA':'g',
        'AG':'r',
        'CA':'b',
        'AC':'r',
        'GT':'g',
        'TG':'k',
        'CT':'b',
        'TC':'k',
        'GC':'g',
        'CG':'b'
        }

    label_positions = {\
        'AT':'center',
        'TA':'center',
        'GA':'center',
        'AG':'center',
        'CA':'left',
        'AC':'left',
        'GT':'left',
        'TG':'left',
        'CT':'center',
        'TC':'center',
        'GC':'center',
        'CG':'center'
        }

    def do_fontsize(k):
        return float(clip(max_text_size*sqrt(data[k]),\
            min_text_size,max_text_size))

    A = text(0,1, '$A_3$', color='r', size=do_fontsize('A'), **text_params)
    T = text(1,1, '$T_3$', color='k', size=do_fontsize('T'), **text_params)
    G = text(0,0, '$G_3$', color='g', size=do_fontsize('G'), **text_params)
    C = text(1,0, '$C_3$', color='b', size=do_fontsize('C'), **text_params)

    arrow_h_offset = 0.25  #data coordinates, empirically determined
    max_arrow_length = 1 - 2*arrow_h_offset

    max_arrow_width = max_arrow_width
    max_head_width = 2.5*max_arrow_width
    max_head_length = 2*max_arrow_width
    arrow_params={'length_includes_head':True, 'shape':shape, \
        'head_starts_at_zero':head_starts_at_zero}
    ax = gca()
    sf = 0.6   #max arrow size represents this in data coords

    d = (r2/2 + arrow_h_offset - 0.5)/r2    #distance for diags
    r2v = arrow_sep/r2                      #offset for diags
  
    #tuple of x, y for start position
    positions = {\
        'AT': (arrow_h_offset, 1+arrow_sep),
        'TA': (1-arrow_h_offset, 1-arrow_sep),
        'GA': (-arrow_sep, arrow_h_offset),
        'AG': (arrow_sep, 1-arrow_h_offset),
        'CA': (1-d-r2v, d-r2v),
        'AC': (d+r2v, 1-d+r2v),
        'GT': (d-r2v, d+r2v),
        'TG': (1-d+r2v, 1-d-r2v),
        'CT': (1-arrow_sep, arrow_h_offset),
        'TC': (1+arrow_sep, 1-arrow_h_offset),
        'GC': (arrow_h_offset, arrow_sep),
        'CG': (1-arrow_h_offset, -arrow_sep),
        }

    if normalize_data:
        #find maximum value for rates, i.e. where keys are 2 chars long
        max_val = 0
        for k, v in data.items():
            if len(k) == 2:
                max_val = max(max_val, v)
        #divide rates by max val, multiply by arrow scale factor
        for k, v in data.items():
            data[k] = v/max_val*sf

    def draw_arrow(pair, alpha=alpha, ec=ec, labelcolor=labelcolor):
        #set the length of the arrow 
        if display == 'length':
            length = max_head_length+(max_arrow_length-max_head_length)*\
                data[pair]/sf
        else:
            length = max_arrow_length
        #set the transparency of the arrow
        if display == 'alph':
            alpha = min(data[pair]/sf, alpha)
        else:
            alpha=alpha
        #set the width of the arrow
        if display == 'width':
            scale = data[pair]/sf
            width = max_arrow_width*scale
            head_width = max_head_width*scale
            head_length = max_head_length*scale
        else:
            width = max_arrow_width
            head_width = max_head_width
            head_length = max_head_length

        fc = colors[pair]
        ec = ec or fc

        x_scale, y_scale = deltas[pair]
        x_pos, y_pos = positions[pair]
        arrow(ax, x_pos, y_pos, x_scale*length, y_scale*length, \
            fc=fc, ec=ec, alpha=alpha, width=width, head_width=head_width, \
            head_length=head_length, **arrow_params)

        #figure out coordinates for text
        #if drawing relative to base: x and y are same as for arrow
        #dx and dy are one arrow width left and up
        #need to rotate based on direction of arrow, use x_scale and y_scale
        #as sin x and cos x?
        sx, cx = y_scale, x_scale

        alo = arrow_label_offset = 3.5*max_arrow_width

        where = label_positions[pair]
        if where == 'left':
            orig_position = array([[alo, alo]])
        elif where == 'absolute':
            orig_position = array([[max_arrow_length/2.0, alo]])
        elif where == 'right':
            orig_position = array([[length-alo, alo]])
        elif where == 'center':
            orig_position = array([[length/2.0, alo]])
        else:
            raise ValueError, "Got unknown position parameter %s" % where
            

        
        M = array([[cx, sx],[-sx,cx]])
        coords = dot(orig_position, M) + [[x_pos, y_pos]]
        x, y = ravel(coords)
        orig_label = rate_labels[pair]
        label = '$%s_{_{\mathrm{%s}}}$' % (orig_label[0], orig_label[1:])
   
        text(x, y, label, size=label_text_size, ha='center', va='center', \
            color=labelcolor or fc)

    for p in positions.keys():
        draw_arrow(p)
    
    if graph_name is not None:
        savefig(graph_name)

            
    #test data
all_on_max = dict([(i, 1) for i in 'TCAG'] + \
        [(i+j, 0.6) for i in 'TCAG' for j in 'TCAG'])

realistic_data = {
        'A':0.4,
        'T':0.3,
        'G':0.5,
        'C':0.2,
        'AT':0.4,
        'AC':0.3,
        'AG':0.2,
        'TA':0.2,
        'TC':0.3,
        'TG':0.4,
        'CT':0.2,
        'CG':0.3,
        'CA':0.2,
        'GA':0.1,
        'GT':0.4,
        'GC':0.1,
    }

extreme_data = {
        'A':0.75,
        'T':0.10,
        'G':0.10,
        'C':0.05,
        'AT':0.6,
        'AC':0.3,
        'AG':0.1,
        'TA':0.02,
        'TC':0.3,
        'TG':0.01,
        'CT':0.2,
        'CG':0.5,
        'CA':0.2,
        'GA':0.1,
        'GT':0.4,
        'GC':0.2,
    }

sample_data = {
        'A':0.2137,
        'T':0.3541,
        'G':0.1946,
        'C':0.2376,
        'AT':0.0228,
        'AC':0.0684,
        'AG':0.2056,
        'TA':0.0315,
        'TC':0.0629,
        'TG':0.0315,
        'CT':0.1355,
        'CG':0.0401,
        'CA':0.0703,
        'GA':0.1824,
        'GT':0.0387,
        'GC':0.1106,
    }


if __name__ == '__main__':
    from sys import argv
    if len(argv) > 1:
        if argv[1] == 'full':
            d = all_on_max
            scaled = False
        elif argv[1] == 'extreme':
            d = extreme_data
            scaled = False
        elif argv[1] == 'realistic':
            d = realistic_data
            scaled = False
        elif argv[1] == 'sample':
            d = sample_data
            scaled = True
    else:
        d = all_on_max
        scaled=False
    if len(argv) > 2:
        display = argv[2]
    else:
        display = 'length'

    size = 4
    gcf().set_size_inches(size,size)
    
    make_arrow_plot(d, display=display, linewidth=0.001, edgecolor=None,
        normalize_data=scaled, head_starts_at_zero=True, size=size,
        graph_name='arrows.png')