Python matplotlib_venn.venn3() Examples

def venn_diagram(names,labels,ax=None,**kwargs):
    """Plot venn diagrams"""

    from matplotlib_venn import venn2,venn3
    f=None
    if ax==None:
        f=plt.figure(figsize=(4,4))
        ax=f.add_subplot(111)
    if len(names)==2:
        n1,n2=names
        v = venn2([set(n1), set(n2)], set_labels=labels, **kwargs)
    elif len(names)==3:
        n1,n2,n3=names
        v = venn3([set(n1), set(n2), set(n3)], set_labels=labels, **kwargs)
    ax.axis('off')
    #f.patch.set_visible(False)
    ax.set_axis_off()
    return 

def venn(data, names=None, fill="number", show_names=True, show_plot=True, outputDir=False, **kwds):
    """
data: a list
names: names of groups in data
fill = ["number"|"logic"|"both"], fill with number, logic label, or both
show_names = [True|False]
show_plot = [True|False]
"""

    if data is None:
        raise Exception("No data!")
    if len(data) == 2:
        venn2(data, names, fill, show_names, show_plot, outputDir, **kwds)
    elif len(data) == 3:
        venn3(data, names, fill, show_names, show_plot, outputDir, **kwds)
    elif len(data) == 4:
        venn4(data, names, fill, show_names, show_plot, outputDir, **kwds)
    else:
        print len(data), 'files submitted, must be less than 4 and greater than 1...'
        #raise Exception("currently only 2-4 sets venn diagrams are supported")

#-------------------------------------------------------------------- 

def test():
    """ a test function to show basic usage of venn()"""

    # venn3()
    venn([range(10), range(5,15), range(3,8)], ["aaaa", "bbbb", "cccc"], fill="both", show_names=False)
    # venn2()
    venn([range(10), range(5,15)])
    venn([range(10), range(5,15)], ["aaaa", "bbbb"], fill="logic", show_names=False)
    # venn4()
    venn([range(10), range(5,15), range(3,8), range(4,9)], ["aaaa", "bbbb", "cccc", "dddd"], figsize=(12,12))

######### Added for AltAnalyze ######### 

def make_venn3_region_patch(region):
    '''
    Given a venn3 region (as returned from compute_venn3_regions) produces a Patch object,
    depicting the region as a curve.

    >>> centers, radii = solve_venn3_circles((1, 1, 1, 1, 1, 1, 1))
    >>> regions = compute_venn3_regions(centers, radii)
    >>> patches = [make_venn3_region_patch(r) for r in regions]
    '''
    if region is None or len(region[0]) == 0:
        return None
    if region[0] == "CIRCLE":
        return Circle(region[1][0], region[1][1])
    pts, arcs, label_pos = region
    path = [pts[0]]
    for i in range(len(pts)):
        j = (i + 1) % len(pts)
        (center, radius, direction) = arcs[i]
        fromangle = vector_angle_in_degrees(pts[i] - center)
        toangle = vector_angle_in_degrees(pts[j] - center)
        if direction:
            vertices = Path.arc(fromangle, toangle).vertices
        else:
            vertices = Path.arc(toangle, fromangle).vertices
            vertices = vertices[np.arange(len(vertices) - 1, -1, -1)]
        vertices = vertices * radius + center
        path = path + list(vertices[1:])
    codes = [1] + [4] * (len(path) - 1)
    return PathPatch(Path(path, codes)) 

def venn3_circles(subsets, normalize_to=1.0, alpha=1.0, color='black', linestyle='solid', linewidth=2.0, **kwargs):
    '''
    Plots only the three circles for the corresponding Venn diagram.
    Useful for debugging or enhancing the basic venn diagram.
    parameters sets and normalize_to are the same as in venn3()
    kwargs are passed as-is to matplotlib.patches.Circle.
    returns a list of three Circle patches.

    >>> plot = venn3_circles({'001': 10, '100': 20, '010': 21, '110': 13, '011': 14})
    '''
    complete_subets = subsets
    subsets_abrev = []
    for i in subsets:
        subsets_abrev.append(len(i))
    subsets = tuple(subsets_abrev)
    
    # Prepare parameters
    if isinstance(subsets, dict):
        subsets = [subsets.get(t, 0) for t in ['100', '010', '110', '001', '101', '011', '111']]
    areas = compute_venn3_areas(subsets, normalize_to)
    centers, radii = solve_venn3_circles(areas)
    ax = gca()
    prepare_venn3_axes(ax, centers, radii)
    result = []
    for (c, r) in zip(centers, radii):
        circle = Circle(c, r, alpha=alpha, edgecolor=color, facecolor='none', linestyle=linestyle, linewidth=linewidth, **kwargs)
        ax.add_patch(circle)
        result.append(circle)
    return result 

def check_vcf(vcf):
    """Check if vcf is suited for this script

    returns
    - appropriate venn function
    - appropriate empty list of lists for identifiers
    """
    if len(vcf.samples) == 2:
        return venn2, [[] for i in range(len(vcf.samples))]
    elif len(vcf.samples) == 3:
        return venn3, [[] for i in range(len(vcf.samples))]
    else:
        sys.exit("Fatal: Script only written for vcf files containing 2 or 3 samples") 

def SimpleMatplotVenn(names,data,outputDir=False,display=True):
    """ Uses http://pypi.python.org/pypi/matplotlib-venn (code combined into one module) to export
    simple or complex, overlapp weighted venn diagrams as an alternative to the default methods in
    this module """

    import numpy as np
    pylab.figure(figsize=(11,7),facecolor='w')
    
    vd = get_labels(data, fill="number")
    set_labels=[]
    for i in names:
        set_labels.append(string.replace(i,'.txt',''))
        
    if len(set_labels)==2:
        from matplotlib_venn import venn2, venn2_circles
        set_colors = ('r', 'g')
        subsets = (vd['10'], vd['01'], vd['11'])
        v = venn2(subsets=subsets, set_labels = set_labels, set_colors=set_colors)
        c = venn2_circles(subsets=subsets, alpha=0.5, linewidth=1.5, linestyle='dashed')
        
    if len(set_labels)==3:
        from matplotlib_venn import venn3, venn3_circles
        set_colors = ('r', 'g', 'b')
        subsets = (vd['100'], vd['010'], vd['110'], vd['001'], vd['101'], vd['011'], vd['111'])
        v = venn3(subsets=subsets, set_labels = set_labels,set_colors=set_colors)
        c = venn3_circles(subsets=subsets, alpha=0.5, linewidth=1.5, linestyle='dashed')
        
    pylab.title("Overlap Weighted Venn Diagram",fontsize=24)

    try:
        if outputDir!=False:
            filename = outputDir+'/%s.pdf' % venn_export_weighted
            pylab.savefig(filename)
            filename = outputDir+'/%s.png' % venn_export_weighted
            pylab.savefig(filename, dpi=100) #,dpi=200
    except Exception:
        print 'Image file not saved...'
        
    if display:
        pylab.show()

    try:
        import gc
        fig.clf()
        pylab.close()
        gc.collect()
    except Exception:
        pass

 ######### End Added for AltAnalyze #########