def show_subopts(structs, polys, energies):
srted = argsort(energies)
e = array(energies)
cols = [1.,0.,0.] * ((e - min(e)) / (max(e) - min(e)))[:,newaxis]
plf2 = myplots.fignum(7,(10,10))
rplots.grid_rnas(polys[srted],
colors =cols[srted],
size = (8,8), dims = [180,50])
def cluster_2_show(clusters, polys):
sortorder = argsort(clusters)
ct_colors = mycolors.getct(len(set(clusters)))
ct_dict = dict([(cluster, ct_colors[i]) for i, cluster in enumerate(set(clusters))])
plf2 = myplots.fignum(8,(10,10))
rplots.grid_rnas(polys[sortorder],
colors = [ct_dict[i] for i in clusters[sortorder]],
size = (5,5), dims = [180,50])
def show_conservation(fidx = 0, reset = False):
fnum = flist[fidx]
rfid = 'RF{0:05}'.format(fnum)
print rfid
if fnum ==50: ftype = 'riboswitch'
else: ftype = 'all'
out = mem.getOrSet(setFamData,
**mem.rc({}, reset =reset,
on_fail = 'compute',
hardcopy = False,
register = 'fdat'+rfid,
ftype = ftype,
rfid = rfid))
mvals, tvals, structs = mem.getOrSet(setTree,
**mem.rc({},reset = reset,
on_fail = 'compute',
hardcopy = True,
register = 'st'+rfid,
rfid = rfid,
ftype = ftype))
idxs, tidx = sutils.show_paired_v_energy(rfid,rfid,mvals,tvals,structs,ftype)
all_pairs = structs['structs']
all_energies = structs['energies']
pints,eints, mints, tints = [structs['structs'][i] for i in idxs],\
[ structs['energies'][i] for i in idxs],\
[ mvals[tidx][i] for i in idxs],\
[ tvals[tidx][i] for i in idxs]
seq = structs['seq']
if do_make_subopts:
subopts = rutils.suboptimals(seq, n = 400)
verts = rutils.struct_verts(subopts, seq, rfid)
f = myplots.fignum(4,figsize)
rplots.grid_rnas(verts, dims = [40])
f.savefig(figfile.format('{0}_grid_rnas'.\
format(rfid)))
aff = rutils.struct_affinity_matrix(all_pairs, len(seq))
pca = rutils.project_structs(all_pairs,
ptype ='pca',
affinities = aff,
n_comp = 3)
for metric in ['n_comp']:# ['frac_silent','frac_paired','n_comp']:
scolors = []
for i in range(len(tvals[tidx])):
m_silent, pidxs, frac_good = sutils.metric(
mvals[tidx][i],tvals[tidx][i],
mtype = metric)
scolors.append(mean(m_silent))
scolors = myplots.rescale(scolors, [0.,1.])[:,newaxis] * array([1.,0.,0.])
f = myplots.fignum(4,figsize)
ax = f.add_subplot(111)
xvals, yvals = pca[:,:2].T
myplots.padded_limits(ax, xvals, yvals)
ax.scatter(xvals,yvals,300,linewidth = 1,
edgecolor = 'black', color = scolors)
ax.scatter(pca[idxs,0],pca[idxs,1], 2100 ,alpha = 1,
color = 'black')
ax.scatter(pca[idxs,0],pca[idxs,1], 2000 ,alpha = 1,
color = 'white')
ax.scatter(pca[idxs,0],pca[idxs,1], 400 ,alpha = 1,
color = scolors[idxs],
)
ax.annotate('''Conservation metric: {0}
Projected onto C=2 Principal Components'''.format(metric),
[0,1],xycoords = 'axes fraction', va = 'top',
xytext = [10,-10],textcoords='offset points')
f.savefig(figfile.format('{0}_pca_{1}'.\
format(rfid, metric)))