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Commitde93f2b

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added rob knights fancy arrow
svn path=/trunk/matplotlib/; revision=2188
1 parentdd525e4 commitde93f2b

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6 files changed

+440
-31
lines changed

6 files changed

+440
-31
lines changed

‎CHANGELOG

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2006-03-21 Added Rob Knight's arrow code; see examples/arrow_demo.py - JDH
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2006-03-20 Added support for masking values with nan's, using ADS's
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isnan module and the new API. Works for *Agg backends and
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the postscript backend- DSD

‎boilerplate.py

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@@ -47,6 +47,7 @@ def %(func)s(*args, **kwargs):
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# these methods are all simple wrappers of Axes methods by the same
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# name.
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_plotcommands= (
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'arrow',
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'axhline',
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'axhspan',
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'axvline',

‎examples/arrow_demo.py

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#!/usr/bin/env python
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"""Arrow drawing example for the new fancy_arrow facilities.
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Code contributed by: Rob Knight <rob@spot.colorado.edu>
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usage:
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python arrow_demo.py realistic|full|sample|extreme
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"""
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frompylabimport*
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rc('text',usetex=True)
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rates_to_bases={'r1':'AT','r2':'TA','r3':'GA','r4':'AG','r5':'CA','r6':'AC', \
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'r7':'GT','r8':'TG','r9':'CT','r10':'TC','r11':'GC','r12':'CG'}
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numbered_bases_to_rates=dict([(v,k)fork,vinrates_to_bases.items()])
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lettered_bases_to_rates=dict([(v,'r'+v)fork,vinrates_to_bases.items()])
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defadd_dicts(d1,d2):
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"""Adds two dicts and returns the result."""
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result=d1.copy()
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result.update(d2)
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returnresult
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defmake_arrow_plot(data,size=4,display='length',shape='right', \
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max_arrow_width=0.03,arrow_sep=0.02,alpha=0.5, \
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normalize_data=False,ec=None,labelcolor=None, \
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head_starts_at_zero=True,rate_labels=lettered_bases_to_rates,\
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**kwargs):
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"""Makes an arrow plot.
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Parameters:
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data: dict with probabilities for the bases and pair transitions.
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size: size of the graph in inches.
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display: 'length', 'width', or 'alpha' for arrow property to change.
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shape: 'full', 'left', or 'right' for full or half arrows.
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max_arrow_width: maximum width of an arrow, data coordinates.
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arrow_sep: separation between arrows in a pair, data coordinates.
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alpha: maximum opacity of arrows, default 0.8.
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**kwargs can be anything allowed by a Arrow object, e.g.
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linewidth and edgecolor.
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"""
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xlim(-0.5,1.5)
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ylim(-0.5,1.5)
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gcf().set_figsize_inches(size,size)
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xticks([])
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yticks([])
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max_text_size=size*12
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min_text_size=size
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label_text_size=size*2.5
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text_params={'ha':'center','va':'center','family':'sans-serif',\
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'fontweight':'bold'}
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r2=sqrt(2)
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deltas= {\
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'AT':(1,0),
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'TA':(-1,0),
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'GA':(0,1),
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'AG':(0,-1),
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'CA':(-1/r2,1/r2),
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'AC':(1/r2,-1/r2),
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'GT':(1/r2,1/r2),
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'TG':(-1/r2,-1/r2),
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'CT':(0,1),
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'TC':(0,-1),
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'GC':(1,0),
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'CG':(-1,0)
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}
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colors= {\
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'AT':'r',
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'TA':'k',
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'GA':'g',
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'AG':'r',
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'CA':'b',
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'AC':'r',
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'GT':'g',
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'TG':'k',
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'CT':'b',
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'TC':'k',
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'GC':'g',
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'CG':'b'
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}
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label_positions= {\
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'AT':'center',
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'TA':'center',
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'GA':'center',
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'AG':'center',
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'CA':'left',
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'AC':'left',
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'GT':'left',
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'TG':'left',
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'CT':'center',
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'TC':'center',
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'GC':'center',
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'CG':'center'
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}
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defdo_fontsize(k):
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returnfloat(clip(max_text_size*sqrt(data[k]),\
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min_text_size,max_text_size))
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A=text(0,1,'$A_3$',color='r',size=do_fontsize('A'),**text_params)
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T=text(1,1,'$T_3$',color='k',size=do_fontsize('T'),**text_params)
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G=text(0,0,'$G_3$',color='g',size=do_fontsize('G'),**text_params)
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C=text(1,0,'$C_3$',color='b',size=do_fontsize('C'),**text_params)
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arrow_h_offset=0.25#data coordinates, empirically determined
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max_arrow_length=1-2*arrow_h_offset
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max_arrow_width=max_arrow_width
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max_head_width=2.5*max_arrow_width
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max_head_length=2*max_arrow_width
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arrow_params={'length_includes_head':True,'shape':shape, \
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'head_starts_at_zero':head_starts_at_zero}
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ax=gca()
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sf=0.6#max arrow size represents this in data coords
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d= (r2/2+arrow_h_offset-0.5)/r2#distance for diags
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r2v=arrow_sep/r2#offset for diags
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#tuple of x, y for start position
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positions= {\
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'AT': (arrow_h_offset,1+arrow_sep),
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'TA': (1-arrow_h_offset,1-arrow_sep),
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'GA': (-arrow_sep,arrow_h_offset),
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'AG': (arrow_sep,1-arrow_h_offset),
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'CA': (1-d-r2v,d-r2v),
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'AC': (d+r2v,1-d+r2v),
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'GT': (d-r2v,d+r2v),
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'TG': (1-d+r2v,1-d-r2v),
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'CT': (1-arrow_sep,arrow_h_offset),
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'TC': (1+arrow_sep,1-arrow_h_offset),
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'GC': (arrow_h_offset,arrow_sep),
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'CG': (1-arrow_h_offset,-arrow_sep),
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}
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ifnormalize_data:
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#find maximum value for rates, i.e. where keys are 2 chars long
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max_val=0
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fork,vindata.items():
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iflen(k)==2:
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max_val=max(max_val,v)
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#divide rates by max val, multiply by arrow scale factor
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fork,vindata.items():
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data[k]=v/max_val*sf
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defdraw_arrow(pair,alpha=alpha,ec=ec,labelcolor=labelcolor):
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#set the length of the arrow
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ifdisplay=='length':
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length=max_head_length+(max_arrow_length-max_head_length)*\
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data[pair]/sf
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else:
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length=max_arrow_length
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#set the transparency of the arrow
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ifdisplay=='alph':
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alpha=min(data[pair]/sf,alpha)
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else:
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alpha=alpha
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#set the width of the arrow
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ifdisplay=='width':
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scale=data[pair]/sf
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width=max_arrow_width*scale
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head_width=max_head_width*scale
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head_length=max_head_length*scale
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else:
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width=max_arrow_width
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head_width=max_head_width
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head_length=max_head_length
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fc=colors[pair]
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ec=ecorfc
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x_scale,y_scale=deltas[pair]
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x_pos,y_pos=positions[pair]
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arrow(x_pos,y_pos,x_scale*length,y_scale*length, \
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fc=fc,ec=ec,alpha=alpha,width=width,head_width=head_width, \
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head_length=head_length,**arrow_params)
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#figure out coordinates for text
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#if drawing relative to base: x and y are same as for arrow
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#dx and dy are one arrow width left and up
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#need to rotate based on direction of arrow, use x_scale and y_scale
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#as sin x and cos x?
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sx,cx=y_scale,x_scale
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where=label_positions[pair]
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ifwhere=='left':
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orig_position=3*array([[max_arrow_width,max_arrow_width]])
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elifwhere=='absolute':
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orig_position=array([[max_arrow_length/2.0,3*max_arrow_width]])
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elifwhere=='right':
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orig_position=array([[length-3*max_arrow_width,\
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3*max_arrow_width]])
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elifwhere=='center':
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orig_position=array([[length/2.0,3*max_arrow_width]])
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else:
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raiseValueError,"Got unknown position parameter %s"%where
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M=array([[cx,sx],[-sx,cx]])
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coords=matrixmultiply(orig_position,M)+ [[x_pos,y_pos]]
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x,y=ravel(coords)
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orig_label=rate_labels[pair]
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label='$%s_{_{\mathrm{%s}}}$'% (orig_label[0],orig_label[1:])
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text(x,y,label,size=label_text_size,ha='center',va='center', \
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color=labelcolororfc)
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forpinpositions.keys():
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draw_arrow(p)
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#test data
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all_on_max=dict([(i,1)foriin'TCAG']+ \
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[(i+j,0.6)foriin'TCAG'forjin'TCAG'])
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realistic_data= {
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'A':0.4,
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'T':0.3,
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'G':0.5,
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'C':0.2,
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'AT':0.4,
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'AC':0.3,
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'AG':0.2,
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'TA':0.2,
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'TC':0.3,
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'TG':0.4,
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'CT':0.2,
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'CG':0.3,
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'CA':0.2,
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'GA':0.1,
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'GT':0.4,
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'GC':0.1,
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}
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extreme_data= {
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'A':0.75,
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'T':0.10,
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'G':0.10,
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'C':0.05,
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'AT':0.6,
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'AC':0.3,
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'AG':0.1,
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'TA':0.02,
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'TC':0.3,
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'TG':0.01,
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'CT':0.2,
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'CG':0.5,
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'CA':0.2,
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'GA':0.1,
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'GT':0.4,
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'GC':0.2,
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}
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sample_data= {
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'A':0.2137,
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'T':0.3541,
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'G':0.1946,
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'C':0.2376,
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'AT':0.0228,
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'AC':0.0684,
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'AG':0.2056,
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'TA':0.0315,
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'TC':0.0629,
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'TG':0.0315,
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'CT':0.1355,
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'CG':0.0401,
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'CA':0.0703,
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'GA':0.1824,
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'GT':0.0387,
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'GC':0.1106,
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}
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if__name__=='__main__':
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fromsysimportargv
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iflen(argv)>1:
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ifargv[1]=='full':
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d=all_on_max
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scaled=False
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elifargv[1]=='extreme':
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d=extreme_data
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scaled=False
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elifargv[1]=='realistic':
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d=realistic_data
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scaled=False
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elifargv[1]=='sample':
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d=sample_data
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scaled=True
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else:
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d=all_on_max
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scaled=False
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iflen(argv)>2:
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display=argv[2]
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else:
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display='length'
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size=4
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figure(figsize=(size,size))
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make_arrow_plot(d,display=display,linewidth=0.001,edgecolor=None,
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normalize_data=scaled,head_starts_at_zero=True,size=size)
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draw()
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savefig('arrows.png')
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print'Example saved to file "arrows.png"'
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show()

‎lib/matplotlib/axes.py

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@@ -33,7 +33,7 @@
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frommatplotlib.numerix.mlabimportflipud,amin,amax
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frommatplotlibimportrcParams
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frompatchesimportPatch,Rectangle,Circle,Polygon,Arrow,Wedge,Shadow,bbox_artist
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frompatchesimportPatch,Rectangle,Circle,Polygon,Arrow,Wedge,Shadow,FancyArrow,bbox_artist
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fromtableimportTable
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fromtextimportText,TextWithDash,_process_text_args
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fromtransformsimportBbox,Point,Value,Affine,NonseparableTransformation
@@ -463,6 +463,12 @@ def _set_lim_and_transforms(self):
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ifself._sharey:
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self.transData.set_funcy(self._sharey.transData.get_funcy())
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defarrow(self,x,y,dx,dy,**kwargs):
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"""Draws arrow on specified axis from (x,y) to (x+dx,y+dy)."""
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a=FancyArrow(x,y,dx,dy,**kwargs)
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self.add_artist(a)
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returna
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defaxhline(self,y=0,xmin=0,xmax=1,**kwargs):
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"""
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AXHLINE(y=0, xmin=0, xmax=1, **kwargs)

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