def scatter_blake(a, b, which='circles', classes=[0,1], colors=['k','r'],
maxval=None, **kwargs):
if maxval:
a,b = filter_valpairs(a,b,maxval)
defaults = {'s': 50, 'alpha':.2, 'lw':0}
kwargs = ut.dict_set_defaults(kwargs, defaults)
if type(a[0]) == list or type(a[0]) == tuple:
# second value is presumed to be class--should be 0 or 1, which will be
# mapped to the colormap cmap.
# Also need to clean a and b to just be values rather than values and
# classes.
print 'using classes'
assert ut.i1(a) == ut.i1(b), "Classes not the same between a and b"
kwargs['c'] = [colors[0] if x==classes[0] else colors[1] for x in
ut.i1(a)]
a,b = ut.i0(a), ut.i0(b)
else:
c = 'k'
if which=='pointcloud':
scatter(a, b, s=50, alpha=0.08, lw=0)
scatter(a, b, **kwargs)
elif which=='points':
scatter(a, b, **kwargs)
elif which=='fadepoints':
scatter(a, b, **kwargs)
elif which=='circles':
del kwargs['lw']
scatter(a, b, facecolors='none', edgecolors=c, **kwargs)
title('R-squared: %0.3f' % ut.r_squared(a,b))
def profiles_cxs(e, cxs, **kwargs):
# blue/yellow/red map: 'jet'
defaults = {'interpolation': 'nearest', 'cmap':'hot', 'vmin':1}
kwargs = ut.dict_set_defaults(kwargs, defaults)
arr = np.array(e.mat)
dinds = ut.list_inv_to_dict(e.prots)
useps = [p for c in cxs for p in c]
useinds = [dinds[p] for p in useps if p in dinds]
vals = np.clip(np.log2(arr[useinds,:]),0,100)
imshow(vals, **kwargs)
return vals
def cluster(tested, negmult, cltype, max_pval=0.2, **kwargs):
kwargs = ut.dict_set_defaults(kwargs, clust_defaults)
command = c1_command if cltype=='c1' else mcl_command
if 'runid' in kwargs: # keep temp files separate
runid = str(kwargs['runid'])
kwargs['fin'] = ut.pre_ext(kwargs['fin'], runid)
kwargs['fout'] = ut.pre_ext(kwargs['fout'], runid)
export_cxs(tested, kwargs['fin'],negmult)
command = command % kwargs
print command
shell_call(command)
if cltype=='c1':
cxs, pvals, cx_details = read_clust_output(kwargs['fout'], max_pval)
elif cltype=='mcl':
cxs = read_mcl_output(kwargs['fout'])
pvals,cx_details=None,None
else:
assert False, "Wrong cluster type: %s" %cltype
return Struct(cxs=cxs, pvals=pvals, cx_details=cx_details)
def hexbin_blake(a, b, maxval=None, **kwargs):
defaults = {'cmap': 'binary', 'bins':'log', 'gridsize':np.floor(sqrt(len(a))/2) }
kwargs = ut.dict_set_defaults(kwargs, defaults)
if maxval:
a,b = filter_valpairs(a,b,maxval)
hexbin(a, b, **kwargs)
