def analyze():
f = myplots.fignum(1)
gl = get_data()['gluc']
cl = get_data()['cluc']
ax = f.add_subplot(111)
ax.imshow(cl / gl, aspect='auto', interpolation='nearest')
ax.set_title('Enrichment of Cluc over control Gluc')
path = myplots.figpath('corr_matrix.pdf')
f.savefig(path)
f.clear()
ax = f.add_subplot(121)
glf = gl.flatten()[:-6]
clf = cl.flatten()[:-6]
n_mm = array([[e, e, e]
for e in [0, 2, 2, 2, 3, 3, 3, 0, 2, 2, 2, 3, 3, 3]],
float).flatten()
ax.set_title('cluc enrichment vs mm count')
ax.set_xlabel('mismatch count')
ax.set_ylabel('fold enrichment ocluc')
ax.scatter(n_mm, clf / glf)
pf1 = polyfit(n_mm, clf / glf, 1)
pf2 = polyfit(n_mm, clf / glf, 2)
ax.plot(polyval(pf1, [0, 2, 3]))
path = myplots.figpath('enrichment_vs_mm.pdf')
f.savefig(path)
ax2 = f.add_subplot(121)
def analyze():
f = myplots.fignum(1)
gl = get_data()['gluc']
cl = get_data()['cluc']
ax = f.add_subplot(111)
ax.imshow(cl / gl, aspect = 'auto', interpolation = 'nearest')
ax.set_title('Enrichment of Cluc over control Gluc')
path = myplots.figpath('corr_matrix.pdf')
f.savefig(path)
f.clear()
ax = f.add_subplot(121)
glf = gl.flatten()[:-6]
clf = cl.flatten()[:-6]
n_mm = array([ [e,e,e] for e in [0,2,2,2,3,3,3,0,2,2,2,3,3,3]], float).flatten()
ax.set_title('cluc enrichment vs mm count')
ax.set_xlabel('mismatch count')
ax.set_ylabel('fold enrichment ocluc')
ax.scatter(n_mm,clf/glf)
pf1 = polyfit(n_mm, clf/glf, 1)
pf2 = polyfit(n_mm, clf/glf, 2)
ax.plot(polyval(pf1,[0,2,3]))
path = myplots.figpath('enrichment_vs_mm.pdf')
f.savefig(path)
ax2 = f.add_subplot(121)
def peak_thr_histograms(**kwargs):
'''histograms of score and distance'''
dthr = 1500
sthr = 1e-2
dsign = -1
simple = wp.get_simple_thr(**mem.rc(kwargs,
dthr = dthr,
sthr = sthr,
dsign = dsign
)
)
min_score = -1
max_score = -1
for k,v in simple.iteritems():
smax = np.max(v['scores'])
if max_score == -1 or smax > max_score:
max_score = smax
smin = np.min(v['scores'])
if min_score == -1 or smin < min_score:
min_score = smin
lrange = [int(floor(log10(min_score))), int(ceil(log10(max_score)))]
sbin_mids = range(lrange[0],lrange[1]+1)
nsb = len(sbin_mids)
sbins = zeros((nsb))
dbin_size = 50
dbin_mids = range(-dthr, dthr, dbin_size)
ndb = len(dbin_mids)
dbins = zeros(( ndb))
for k,v in simple.iteritems():
for d in v['dists']:
dbins[int(d + dthr)/dbin_size] += 1
for s in v['scores']:
sbins[int(log10(s) - lrange[0])] += 1
f= myplots.fignum(1,(10,6))
ax = f.add_subplot(121)
ax.set_ylabel('log 10 counts')
ax.set_xlabel('distance')
ax.set_title('simplified tss distances (d<{0})'.format(dthr))
ax.plot(dbin_mids,log10(dbins), color = 'black')
f.savefig(myplots.figpath('chip_simple_distance.pdf'))
ax = f.add_subplot(122)
ax.set_title('simplified tss scores (s<{0:2.2})'.format(sthr))
ax.set_ylabel('log10 counts')
ax.set_xlabel('log10 peak score')
ax.plot(sbin_mids,log10(sbins), color = 'black')
f.savefig(myplots.figpath('chip_simple_scores.pdf'))
def snp_counts(indy_arr, indy_info):
regions = indy_regions(indy_arr, indy_info)
ct = mycolors.getct(len(regions))
skip = 1
ofs = 4
f = myplots.fignum(4, (8,8))
ax = f.add_subplot(111)
n_snps = 20
rset = set(regions)
rcounts = zeros((len(rset), n_snps))
xs = []
ys = []
cs = []
rs = []
for i, snp in enumerate(indy_arr.T[4::5][:50]):
rsub = array(regions[::100],float) / max(regions[:20])
inds = argsort(rsub)
ys.extend([i] *len(rsub))
rs.extend([10 + 30 * (1 - snp[:2:100])])
xs.extend(rsub)
print i
ax.scatter(xs,ys,rs)
f.savefig(myplots.figpath('regional_snp_counts_first.pdf'))
return
def run(meth = 'moment'):
out,srts = bs.run0(arr = arr, itr = 2, meth = meth)
f = myplots.fignum(3,(12,6))
ax = f.add_subplot(111)
csrts = [s for s in srts if len(s) == len(cols)][0]
rsrts = [s for s in srts if len(s) == len(rows)][0]
cprint = [rows[rs] for rs in rsrts]
rprint = [cols[cs] for cs in csrts]
im = ax.imshow(out,
interpolation= 'nearest',
cmap = plt.get_cmap('OrRd'),
)
#flip the rows and columns... looks better.
ax.set_xticks(arange(len(cols))+.25)
ax.set_yticks(arange(len(rows))+.25)
ax.set_yticklabels([e for e in cprint])
ax.set_xticklabels(rprint)
print 'rows: \n{0}'.format(', '.join([e.strip() for e in rprint]))
print
print 'cols: \n{0}'.format(', '.join([e.strip() for e in cprint]))
plt.colorbar(im)
f.savefig(myplots.figpath('correlation_plot_2_4_{0}.pdf')
.format(meth))
return
def make_degree_plots_0():
cxns = get_synapse_array()
rows = get_rows()
imaps = get_array_imaps()
ctypes =imaps['ctypes']
ctypes_imap = imaps['ctypes_imap']
nnames = imaps['nnames']
nnames_imap = imaps['nnames_imap']
f2 = myplots.fignum(2, (12,6))
ax1 = f2.add_subplot(121)
ax2 = f2.add_subplot(122)
var_degs = np.sum(cxns,1)
maxval = log10(np.max(var_degs) + 1)
ct = mycolors.getct(len(ctypes))
for z in range(len(ctypes)):
vals = var_degs[:,z]
vals = log10(1 + vals)
count,kde = make_kde(vals)
xax = linspace(0,maxval,10)
h = histogram(vals, xax)
ax1.hist(vals,xax,
color = ct[z],
zorder = 10,
alpha = .25)
ax1.plot(xax,kde(xax)*sum(h[0]),
label = ctypes[z],
color = ct[z],
zorder = 5)
ax1.set_xlabel('$log_10$ of edge degrees of various types')
ax1.legend()
logxy = [ log10(1 +var_degs[:,ctypes_imap['S']]),
log10(1 +var_degs[:,ctypes_imap['R']])]
max_inode =np.argmax(logxy[0] + logxy[1])
max_nodename = [k
for k,v in nnames_imap.iteritems()
if v == max_inode][0]
ax2.scatter(logxy[0]+.15*random.rand(len(nnames))
,logxy[1] + .15*random.rand(len(nnames)),
color = 'red',
alpha = .3)
ax2.set_xlabel('Sending Degree')
ax2.set_ylabel('Receiving Degree')
r2 = corrcoef(logxy[0],logxy[1])[1,0]
myplots.maketitle(ax2, ('correlation coeff: {0:2.2},\n'+\
'max {1} has {2} $e_{{out}}$, {3} $e_{{in}}$')\
.format(r2, max_nodename,
var_degs[max_inode, ctypes_imap['S']],
var_degs[max_inode, ctypes_imap['R']]))
myplots.maketitle(ax1, 'histogram and KDE of\nvarious edge degrees')
f2.savefig(myplots.figpath('degree_histograms_{0}'.format(edge_set)))
def align_len_histogram(parsed):
p0 = parsed.values()[0]
bitlens = array( [sorted([e['bits'] for e in val.values()])[:-1]
for val in p0.values()]).flatten()
bitlens = array(list(it.chain(*bitlens)))
bitlens = 2 * (bitlens - np.min(bitlens.flatten())) + 8
mind= 8 #min(deg_c.values())+.00001
maxd = max(bitlens) #max(deg_c.values())/3
bins = linspace(mind,maxd,8)
h_paths,bin_edges = histogram(bitlens,bins)
h_paths = array(h_paths,float)
h_paths/= sum(h_paths)
f = myplots.fignum(3, (8,8))
ax = f.add_subplot(111)
ax.plot(bins[:-1], h_paths, color = 'red')
ax.set_xlabel('alignment hit length')
ax.set_ylabel('frequency')
ax.set_title('best matched substring lengths')
raise Exception()
f.savefig(myplots.figpath('walk_centrality'))
paths_cat = paths.flat
n = len(paths_cat)
degs = [deg_c[p]for p in paths_cat[::10]]
mind= min(deg_c.values())+.00001
maxd = max(deg_c.values())/3
bins = linspace(mind,maxd,8)
h_paths,bin_edges = histogram(degs,bins)
h_rand,bin_edges = histogram(deg_c.values(), bins)
h_paths = array(h_paths,float)
h_rand = array(h_rand,float)
h_paths/= sum(h_paths)
h_rand/= sum(h_rand)
f = myplots.fignum(3, (8,8))
ax = f.add_subplot(111)
ax.plot(bins[:-1], h_paths, color = 'red')
ax.plot(bins[:-1], h_rand, color = 'black')
ax.set_xlabel('node centrality')
ax.set_ylabel('frequency')
ax.set_title('distribution of centrality in walks vs. random')
def align_len_histogram(parsed):
p0 = parsed.values()[0]
bitlens = array([
sorted([e['bits'] for e in val.values()])[:-1] for val in p0.values()
]).flatten()
bitlens = array(list(it.chain(*bitlens)))
bitlens = 2 * (bitlens - np.min(bitlens.flatten())) + 8
mind = 8 #min(deg_c.values())+.00001
maxd = max(bitlens) #max(deg_c.values())/3
bins = linspace(mind, maxd, 8)
h_paths, bin_edges = histogram(bitlens, bins)
h_paths = array(h_paths, float)
h_paths /= sum(h_paths)
f = myplots.fignum(3, (8, 8))
ax = f.add_subplot(111)
ax.plot(bins[:-1], h_paths, color='red')
ax.set_xlabel('alignment hit length')
ax.set_ylabel('frequency')
ax.set_title('best matched substring lengths')
raise Exception()
f.savefig(myplots.figpath('walk_centrality'))
paths_cat = paths.flat
n = len(paths_cat)
degs = [deg_c[p] for p in paths_cat[::10]]
mind = min(deg_c.values()) + .00001
maxd = max(deg_c.values()) / 3
bins = linspace(mind, maxd, 8)
h_paths, bin_edges = histogram(degs, bins)
h_rand, bin_edges = histogram(deg_c.values(), bins)
h_paths = array(h_paths, float)
h_rand = array(h_rand, float)
h_paths /= sum(h_paths)
h_rand /= sum(h_rand)
f = myplots.fignum(3, (8, 8))
ax = f.add_subplot(111)
ax.plot(bins[:-1], h_paths, color='red')
ax.plot(bins[:-1], h_rand, color='black')
ax.set_xlabel('node centrality')
ax.set_ylabel('frequency')
ax.set_title('distribution of centrality in walks vs. random')
def plot_easy_inference():
dg = io.getGraph()
pos = gd.getpos(dg)
f = myplots.fignum(4, (8,8))
ax = f.add_subplot(111)
ax.set_title('putative worm chip network')
gd.easy_draw(dg, pos)
f.savefig(myplots.figpath('worm_chip_graph.pdf'))
def plot_mers(mer_cts):
f = myplots.fignum(3, (8, 8))
ax = f.add_subplot(111)
hist, bin_edges = histogram(mer_cts.values(), 20)
ax.fill_between(bin_edges[:-1], log(hist), edgecolor='black', linewidth=5)
ax.set_xlabel('mer rediscovery rate')
ax.set_ylabel('$log(n)$')
ax.set_title('Frequencies of 5-mer reoccurence across 10,000 walks.')
f.savefig(myplots.figpath('mer_ct_hist'))
return
def peak_distance_histogram(**kwargs):
atype = kwargs.get('atype', wp. default_atype)
chips = wp.get_assay_gprops(**mem.rc(kwargs))
chiplist = chips.values()
chipkeys = chips.keys()
xs = []
ys = []
sec_spread = np.max([
np.max([
np.max(np.abs([e['dist'] for e in v2['secondaries']]))
for v2 in v.values()])
for v in chips.values()
])
hist_spread = 10000
bin_wid = 200
bin_mids = arange(-1* hist_spread, 1*hist_spread,bin_wid)
bin_starts = bin_mids - bin_wid/2
nb = len(bin_starts)
prim_hists = zeros((len(chips), len(bin_starts)))
sec_hists = zeros((len(chips), len(bin_starts)))
for i,e in enumerate(chiplist):
for k,v in e.iteritems():
pbins = array([e2['dist']/bin_wid for e2 in v['primaries']],int)
sbins = array([e2['dist']/bin_wid for e2 in v['secondaries']],int)
pbins += nb /2
sbins += nb /2
sbins[less(sbins,0)] = 0
sbins[greater(sbins,nb-1)] = nb-1
pbins[less(pbins,0)] = 0
pbins[greater(pbins,nb-1)] = nb-1
for b in pbins: prim_hists[i][b]+=1
for b in sbins: sec_hists[i][b]+=1
f= myplots.fignum(1,(8,6))
ax = f.add_subplot(111)
ax.set_title('chip peak distances to primary/sec tss for {0}'.format(atype))
for p in prim_hists:
ax.plot(bin_mids,p, color = 'green')
for s in sec_hists:
ax.plot(bin_mids,s, color = 'red')
f.savefig(myplots.figpath('chip_distance_hists_for{0}.pdf'.format(atype)))
def plot_mers(mer_cts):
f = myplots.fignum(3, (8,8))
ax = f.add_subplot(111)
hist,bin_edges = histogram(mer_cts.values(), 20)
ax.fill_between(bin_edges[:-1], log(hist),
edgecolor = 'black',
linewidth = 5)
ax.set_xlabel('mer rediscovery rate')
ax.set_ylabel('$log(n)$')
ax.set_title('Frequencies of 5-mer reoccurence across 10,000 walks.')
f.savefig(myplots.figpath('mer_ct_hist'))
return
def load(res = 25):
if res == 25: fpath = '/data/brain_atlas/AtlasAnnotation25.sva'
else: raise Exception()
print 'path: ', fpath
size = os.path.getsize(fpath)
n = 10000
skip = size / n
f = open(fpath)
f.readline()
f.readline()
coords = []
evals = []
while( len(coords) < n):
f.seek(skip, 1)
l0 = f.readline()
l = f.readline()
if( l == ''): break;
lvals =[float(v) for v in l.split(',')]
coords.append(tuple(lvals[0:3]))
evals.append(lvals[3])
print 'len: ', (len(coords))
fig = myplots.fignum(1,(8,6))
ax = fig.add_subplot(111, projection='3d')
xyvals = array([[x[0],x[1], x[2]] for x in coords])
evals = array(evals)
evals = (evals / np.max(evals) )[:,newaxis] * array([1.,0,0])
print shape(xyvals)
ax.scatter(xyvals[:,0], xyvals[:,1], xyvals[:,2],
s = 5,
edgecolor = 'none',
facecolor = evals)
#raise Exception()
path = myplots.figpath('brainmap_spatial_coords_{0}'.format(res))
fig.savefig(path)
return coords
def process_rc(cc, rows, cols, meth="binary"):
rmembers = zeros(len(rows)) + 4
cmembers = zeros(len(rows)) + 4
for i, r in enumerate(rows):
rmembers[i] = argmax(r) if np.max(r) > 0 else len(r)
for i, c in enumerate(cols):
cmembers[i] = argmax(c) if np.max(c) > 0 else len(c)
rorder = argsort(rmembers)
corder = argsort(cmembers)
f = myplots.fignum(3, (8, 8))
ax = f.add_subplot(111)
ax.imshow(cc[rorder][:, corder], aspect="auto", interpolation="nearest")
f.savefig(myplots.figpath("biclustered_expr_{0}.pdf".format(meth)))
raise Exception()
def plot_charges(coords, charges, strand_coords):
f0 = mp.fignum(1, (6,6))
ax = f0.add_subplot(111)
colors = [ 'red' if q > 0 else 'blue' for q in charges]
ax.scatter(*coords[:,:2].T, c = colors, s = 50, zorder = 5)
ax.scatter(*strand_coords[0][:,:2].T, c = 'black', alpha = 1, zorder = -1)
ax.scatter(*strand_coords[1][:,:2].T, c = 'black', alpha = 1, zorder = -1)
ax.scatter(*strand_coords[0][:,:2].T, c = 'black', alpha = .5, zorder = 6)
ax.scatter(*strand_coords[1][:,:2].T, c = 'black', alpha = .5, zorder = 6)
#ax.scatter(*txy.T, c = 'red')
fp = mp.figpath(figt.format('tal_xy_charge_scatter'))
f0.savefig(fp)
return
def plot_grids(params, name = 'tasks_followed.data'):
path =os.path.join('data',name)
fopen = open(path)
lines = [l.strip().split(' ') for l in fopen.readlines() if l.strip() != '']
f = plt.gcf()
f.clear()
ofs = 0
cols = len(lines[0])
last = None
while ofs + cols < len(lines):
sub = lines[ofs:ofs+cols]
ofs += cols * 100
if sub == last:
continue
sxs = color_grid(sub,params)
if not sxs: continue
f.savefig(myplots.figpath(name + 'iter={0}.png'.format(ofs)),format = 'png')
f.clear()
last = sub
print ofs
def check_results(locii, results, n_runs = 400):
a0 = fetch_num_ali()
names = fetch_alinames()
f = myplots.fignum(3,(8,8))
ax = f.add_subplot(211)
vec = zeros(len(a0[0]))
xys = {}
for k in results.keys():
xys[k] = array([[l,v['Mean z-score']] for v,l in zip(results[k],locii[k]) if len(v) >= 19],float).T
raise Exception()
ax2 = f.add_subplot(111)
ax2.scatter(xys[3][0],xys[3][1])
#ax2.scatter(xys[8][0],xys[8][1], color = 'red')
f.savefig(myplots.figpath('run0_zscores_{0}runs'.format(n_runs)))
def get_coexpression(gc, **kwargs):
gc = gc / sum(gc, 0)
f = myplots.fignum(3, (8, 8))
ax = f.add_subplot(111)
for c in gc[:1]:
# cplot = nonzero(greater(c,-1))[0][::10]
# xs = array([genome_coords[k[0]]
# for k in sorted(gene_srtidxs.iteritems(),
# key = lambda x: x[1])])
ys = c
# ax.scatter(*array([[gene_srtidxs[k],genome_coords[k]] for k in gene_union]).T)
# ax.plot(xs, ys + random.rand(len(ys))*.1, color = random.rand(3),
# alpha = .25)
cc = corrcoef(gc.T)
ax.imshow(cc[:1000:1, :1000:1], aspect="auto")
f.savefig(myplots.figpath("coex_counts_per_tissue.pdf"))
return cc
return genes, gene_counts, gene_info
def show_fixations(all_fixations, cmaps):
fstats = fixation_stats(all_fixations)
ranked_tasks = fstats['ranked_ages']
names = ['s_star', 'torus', 'torus_repl']
#argsort(ages, key = lambda)
mut_vals = [0.0005, 0.001, 0.002, 0.003, 0.004]
xs = []
ys = []
cs = []
name_colors = mycolors.getct(3)
task_colors = mycolors.getct(9)
all_deltas = zeros((len(mut_vals), len(all_fixations.values()[0]), 8))
all_fracs = zeros((len(mut_vals), len(all_fixations.values()[0])))
all_counts = zeros((len(mut_vals), len(all_fixations.values()[0])))
mut_spool = []
for i, m in enumerate(mut_vals):
fix_map = all_fixations[m]
for j, e in enumerate(fix_map):
name_c = name_colors[j]
task_10ptime = array([[item[1] for item in e[rt[0]]['1']]
for rt in ranked_tasks])
idxs_allowed = nonzero(greater(np.min(task_10ptime, 0), 0))[0]
frac_allowed = float(len(idxs_allowed)) / shape(task_10ptime)[1]
'''roll deltas for all sxsful completions'''
if len(idxs_allowed) != 0:
nrml = task_10ptime[:, idxs_allowed]
#nrml = 1
deltas = np.mean((roll(task_10ptime[:,idxs_allowed],-1) \
- task_10ptime[:,idxs_allowed]) / \
nrml ,1)
all_deltas[i, j, :] = deltas[:-1]
all_counts[i, j] = len(idxs_allowed)
all_fracs[i, j] = frac_allowed
mut_spool.append({'tuple': (i, j), 'mut': m, 'name': j})
for k, e2 in enumerate(e.iteritems()):
t, v = e2
task_c = task_colors[k]
p10_times = [item[1] for item in v['5'] if item[0] != -1]
n = len(p10_times)
these_x = (zeros(n) + i) + random.uniform(size=n) / 3
xs.extend(these_x)
ys.extend(p10_times)
cs.extend([task_c] * n)
f = myplots.fignum(2, (6, 6))
ax = f.add_subplot(111)
ax.set_title('fixation times for all tasks')
ax.set_xlabel('mutation rate')
ax.set_ylabel('fixation time')
#ax.scatter(xs, ys, 20, color = cs,alpha = .4)
f2 = myplots.fignum(3, (8, 8))
ax = f2.add_axes([.3, .3, .6, .6])
ax.set_title('fixation time (fold change over previous tasks)')
ax.set_xlabel('task')
ax.set_ylabel('condition')
xlabels = [(cmaps[e[0][0]], cmaps[e[1][0]])
for e in zip(ranked_tasks, roll(ranked_tasks, -1, 0))][0:-1]
ax.set_xticks(range(len(xlabels)))
ax.set_xticklabels(['{0} -> {1}'.format(*xl) for xl in xlabels],
rotation=-90,
va='top',
ha='left')
rows = []
labels = []
for ms in sorted(mut_spool, key=lambda x: x['name']):
tup = ms['tuple']
rows.append(all_deltas[tup[0], tup[1], :])
ct = all_counts[tup]
frac = all_fracs[tup]
mut = ms['mut']
labels.append('{0}: mut rate={1};n={2}'.\
format(names[ms['name']],mut,int(ct),frac)
)
im = ax.imshow(rows, interpolation='nearest')
f2.colorbar(im)
ax.set_yticks(range(len(mut_spool)))
ax.set_yticklabels(labels)
f2.savefig(myplots.figpath('graph_evolution_acceleration.pdf'))
def show_fixations(all_fixations,cmaps):
fstats = fixation_stats(all_fixations)
ranked_tasks = fstats['ranked_ages']
names = ['s_star','torus','torus_repl']
#argsort(ages, key = lambda)
mut_vals = [0.0005, 0.001, 0.002, 0.003, 0.004]
xs = []
ys = []
cs = []
name_colors = mycolors.getct(3)
task_colors = mycolors.getct(9)
all_deltas = zeros((len(mut_vals),
len(all_fixations.values()[0]),
8))
all_fracs = zeros((len(mut_vals),
len(all_fixations.values()[0])))
all_counts = zeros((len(mut_vals),
len(all_fixations.values()[0])))
mut_spool = []
for i, m in enumerate(mut_vals):
fix_map = all_fixations[m]
for j, e in enumerate(fix_map):
name_c= name_colors[j]
task_10ptime = array([ [item[1] for item in e[rt[0]]['1']]
for rt in ranked_tasks])
idxs_allowed = nonzero(greater(np.min(task_10ptime, 0),0))[0]
frac_allowed =float( len(idxs_allowed))/ shape(task_10ptime)[1]
'''roll deltas for all sxsful completions'''
if len(idxs_allowed )!= 0:
nrml = task_10ptime[:,idxs_allowed]
#nrml = 1
deltas = np.mean((roll(task_10ptime[:,idxs_allowed],-1) \
- task_10ptime[:,idxs_allowed]) / \
nrml ,1)
all_deltas[i,j,:] = deltas[:-1]
all_counts[i,j] = len(idxs_allowed)
all_fracs[i,j] = frac_allowed
mut_spool.append({'tuple':(i,j),
'mut':m,
'name': j})
for k, e2 in enumerate(e.iteritems()):
t,v = e2
task_c = task_colors[k]
p10_times = [item[1]
for item in v['5'] if item[0] != -1]
n= len(p10_times)
these_x = (zeros(n) + i ) + random.uniform(size = n)/3
xs.extend(these_x)
ys.extend(p10_times)
cs.extend([task_c] * n)
f = myplots.fignum(2,(6,6))
ax = f.add_subplot(111)
ax.set_title('fixation times for all tasks')
ax.set_xlabel('mutation rate')
ax.set_ylabel('fixation time')
#ax.scatter(xs, ys, 20, color = cs,alpha = .4)
f2 = myplots.fignum(3, (8,8))
ax = f2.add_axes([.3,.3,.6,.6])
ax.set_title('fixation time (fold change over previous tasks)')
ax.set_xlabel('task')
ax.set_ylabel('condition')
xlabels = [(cmaps[e[0][0]],cmaps[e[1][0]])
for e in zip(ranked_tasks, roll(ranked_tasks,-1,0))][0:-1]
ax.set_xticks(range(len(xlabels)))
ax.set_xticklabels(['{0} -> {1}'.format(*xl) for xl in xlabels],
rotation = -90,
va = 'top',
ha = 'left')
rows = []
labels = []
for ms in sorted(mut_spool, key = lambda x:x['name']):
tup = ms['tuple']
rows.append(all_deltas[tup[0],tup[1],:])
ct = all_counts[tup]
frac =all_fracs[tup]
mut = ms['mut']
labels.append('{0}: mut rate={1};n={2}'.\
format(names[ms['name']],mut,int(ct),frac)
)
im = ax.imshow(rows,interpolation = 'nearest')
f2.colorbar(im)
ax.set_yticks(range(len(mut_spool)))
ax.set_yticklabels(labels)
f2.savefig(myplots.figpath('graph_evolution_acceleration.pdf'))
def show_clusters(mods, genes, tfs,
switch_axes = False,
axes = 'space'):
mod_srt = sorted(mods.iteritems(), key =lambda x: len(x[1]))[::-1]
mod_ofinterest = mod_srt[0]
f = myplots.fignum(3, (14,8))
ids,tis, cs = [[] for i in range(3)]
n_tis = 60; ct = mycolors.getct(n_tis)
for i,t in enumerate(tsrt[:n_tis]):
nucs = [x[0] for x in t[1]['cts'] if x[1] == time_val][::5]
ids.extend(nucs)
tis.extend([i] * len(nucs))
cs.extend([ct[i] for j in range( len(nucs))])
#GET COORDS
coords = array(list(get_coords(axes = axes,
time_val = time_val,
spatial_idxs = spatial_idxs,
rows = rows,
ids = ids)))
print shape(coords)
print np.min(coords), np.max(coords)
#GET ELPSES
all_elps = cluster_elps(coords, tis)
module_scores = {}
mods_of_interest = mod_srt[:3]
for m in mods_of_interest:
mcounts = []
for i, e in enumerate(all_elps[0]):
t = tsrt[i]
tkey = t[0]
mcounts.append( len([e
for elt in m[1]
if elt['tissue'] == tkey]))
mvals = array(mcounts, float) / max(mcounts)
module_scores[m[0]] = mvals
#PLOT EM
all_axes = [f.add_subplot(ax_str) for ax_str in ['221', '222', '223', '224']]
ax0 = all_axes[0]
ax1 = all_axes[1]
cnv = mpl.colors.ColorConverter()
for j, ax in enumerate([ ax0, ax1]):
if switch_axes: myplots.padded_limits(ax, coords[0,:], coords[j+1,:])
else: myplots.padded_limits(ax, coords[0,:], coords[1,:])
elps = all_elps[j]
for i, e in enumerate(elps):
yellow =squeeze(\
mpl.colors.rgb_to_hsv( array(cnv.to_rgb('yellow'))[na, na, :]))
red = array([0.,1,1])
mscore = module_scores.values()[j][i]
hsv = yellow * (1 - mscore) + red * mscore
e.set_alpha(.75)
e.width = e.width/3
e.height = e.width/3
e.set_zorder(mscore)
color = squeeze([1,0,0])
alpha = mscore
e.set_facecolor(color)
e.set_alpha(alpha)
e.set_edgecolor('none')
ax.add_patch(e)
for annote_axis , plane in zip(*[[ax0, ax1],['XY','XZ']]):
annote_axis.set_title('\n'.join(tw.wrap('''PCA projection in gene space of'''+\
' blastoderm nuclei for time = {0}.'.format(time_val)+\
'Colors represent clusters used in'+\
'model building\n{1} Axes, {2} Plane'.\
format(time_val,axes, plane),50)))
annote_axis.set_xticks([])
annote_axis.set_yticks([])
f.savefig(myplots.figpath('first_filtering_time{0}_Axis={1}.pdf'.\
format(time_val,axes), delete = True))
raise Exception()
def map_pca(indy_arr, indy_info, pca = None,
metagroup = 'all',
**kwargs):
'''
output of indy_arr must be set to linear.
'''
metagroups = region_groups(indy_info)
if metagroup == 'all':
inds_allowed = arange(len(indy_arr))
else:
inds_allowed = metagroups[metagroup]['indy_idxs']
#fetch some global variables
regions = array(indy_regions(indy_arr, indy_info))
iis = [x[1] for x in sorted([(k,v) for k,v in indy_info.iteritems()],
key = lambda x:x[0])]
#and then extract the metaregion
indy_arr = indy_arr[inds_allowed]
regions = regions[inds_allowed]
iis = [iis[ia] for ia in inds_allowed]
#compute pca if none is given
if pca == None:
corr = cc(indy_arr)
indy_pcs, gene_pcs, s = cc_svd(corr, indy_arr)
pca = gene_pcs
#and from pca, coordinates
xys = dot(indy_arr, pca[:,:2]).T
#then plot
ct = array(mycolors.getct(max(regions)+1))
r_abbrevs = region_abbrevs()
f = myplots.fignum(1,(14,8))
ax = f.add_subplot(111)
ax.set_title('top two principle component projection of individual genotypes')
for k,g in it.groupby(sorted(enumerate(regions),
key = lambda x: x[1]),
key = lambda x: x[1]):
grp = list(g)
e0 = grp[0][0]
i0 = iis[e0]
ax.scatter(xys[0,[e[0] for e in grp]],
xys[1,[e[0] for e in grp]]
, color = ct[k],
label = '{0} - {1}'.format(i0['region_symb'],
i0['region_desc']))
#plot regionwide ellipses
c_imap = dict([(v,k) for k,v in enumerate(set(regions))])
c_rmap = dict([(v,k) for k,v in c_imap.iteritems()])
clusters = array([c_imap[r] for r in regions])
csort = argsort(clusters)
elps, infos = elpsfit.cluster_ellipses(xys[:,csort],clusters[csort])
for i, e in enumerate(elps):
e.set_alpha(.75)
e.set_facecolor(ct[c_rmap[i]])
e.set_edgecolor('none')
maj = e.width
minor = e.height
e.height = maj * 2
e.width = minor * 2
ax.add_patch(e)
ax.legend()
f.savefig(myplots.figpath('pca_grouping={0}.pdf'.format(metagroup)))
return
def load(plots = defplots,
reset = False):
kwargs = dict(reset = reset)
edge_set = get_edge_set()
g = get_graph(**mem.sr(kwargs))
pos = get_pos(**mem.sr(kwargs))
trips = set([])
for k1 in g:
for k2 in g[k1].keys():
for k3 in g[k1].keys():
if g[k2].has_key(k3):
trips.add((k2,k3,k1))
tripoints = dict([((e[0],e[1]),pos[e[2]]) for e in trips])
if plots.get('basic_structure', False):
f = myplots.fignum(1)
ax = f.add_subplot(111)
gd.easy_draw(g, pos)
f.savefig(myplots.figpath('basic_structure_edges={0}'.format(edge_set)))
if plots.get('feed_forward', True):
gd.overlay(g,pos,g.edges(),
tripoints = tripoints,
alphas = dict([(e,.1) for e in g.edges()]))
f.savefig(myplots.figpath('feed_forward_edges={0}'.format(edge_set)))
if plots.get('degrees' , False):
make_degree_plots_0();
maxflow = nx.algorithms.ford_fulkerson(g, 'AVAL','PVPL','weight')
imaps = get_array_imaps()
nnames = imaps['nnames']
node_stats = dict([(k,{}) for k in nnames])
for k,v in node_stats.iteritems():
v['out_degree'] = len([e for e in g.edges() if e[0] == k])
v['in_degree'] = len([e for e in g.edges() if e[1] == k])
f = myplots.fignum(3, (12,6))
outs = [v['out_degree'] for k, v in node_stats.iteritems()]
ins =[v['in_degree'] for k , v in node_stats.iteritems()]
raw_data= array([outs,ins]).T
make_data_transform(raw_data)
data = transform_data(raw_data)
kd = make_kdtree(data)
k = 5
nn = compute_nns(kd, k)
knn= nn['nn']
knn_dists = nn['dists']
dists = compute_dists(data)
mean_dists = np.mean(knn_dists[:,1:],1)
mean_colors =sqrt(mean_dists[:,newaxis] * [1/np.max(mean_dists), 0,0])
ax = f.add_subplot(121)
ax.scatter(data[:,0],data[:,1],s = 15,
facecolor = mean_colors,
edgecolor = 'none'
)
ax.set_xlabel('scaled out degree')
ax.set_ylabel('scaled in degree')
ax2 = f.add_subplot(122)
ax2.imshow(dists,
interpolation = 'nearest',
aspect = 'auto')
ax2.set_title('distance matrix for scaled degrees')
f.savefig(myplots.figpath('distances_{0}'.format(edge_set)))
return g
def run():
chains = parse_all()
c0 = chains[0]
ksrt =sorted(c0.keys())
charges = array([ sum([float(e['charge']) for e in c0[k]['pqr']]) for k in ksrt])
coords = array([ mean([e.get_coord() for e in c0[k]['pdb']], 0 ) for k in ksrt])
c1,c2 = chains[1:]
strand_charges = []
strand_coords = []
for c in [c1, c2]:
ksrt =sorted(c.keys())
strand_charges.append(array([ sum([float(e['charge']) for e in c[k]['pqr']]) for k in ksrt]))
strand_coords.append(array([ mean([e.get_coord() for e in c[k]['pdb']], 0 ) for k in ksrt]))
k1 = sorted([nt for nt in c1])
k2 = sorted([nt for nt in c2])
s1_atoms = list(it.chain(*[ [e.get_coord() for e in c1[k]['pdb'] ] for k in k1]))
s2_atoms = list(it.chain(*[ [e.get_coord() for e in c2[k]['pdb'] ] for k in k2]))
dna_atoms = []
dna_atoms.extend(s1_atoms)
dna_atoms.extend(s2_atoms)
dna_atoms = array(dna_atoms)
#nearest neighbor params:
kres =0
katoms_dna = 3
kres_atoms = 3
rvd_res = rvd_residues(c0,kres)
xs = []
ys = []
cs = []
ss = []
ecs = []
rdists = []
rvd_groups = [];
for i, rvd in enumerate(rvd_res):
for r in rvd:
atoms = array([e.get_coord()
for e in r['pdb']])
dists = sum(square(atoms),1)[:,newaxis] + \
sum(square(dna_atoms),1)[newaxis,:] - \
2 *sum(atoms[:,newaxis,:] * dna_atoms[newaxis,:,:],2)
atom_srt_dists = np.sort(dists, 1)
atom_knn_avgdist = np.mean(atom_srt_dists[:,:katoms_dna],1)
res_srt_dists = np.sort(atom_knn_avgdist)
res_k_avgdist = res_srt_dists[:kres_atoms]
xs.append(mean(atoms[:,0]))
ys.append(mean(atoms[:,1]))
#colors = array([1,0,0]) * 1/atom_knn_avgdist[:,newaxis]
cs.append(1/res_k_avgdist)
rdists.append(res_k_avgdist)
ss.append(50)
ecs.append('none')
rvd_groups.append(i)
show_helix = False
if show_helix:
cs = array(cs)
cs /= np.max(cs)
f = mp.fignum(1, (12,12))
ax = f.add_subplot(111)
ax.scatter(xs,ys,c = cs, s= ss, edgecolor = ecs)
f.savefig(mp.figpath(figt.format('tal_rvd_neighborhoods')))
rvd_dists = [(k,[e[1] for e in list(g)])
for k,g in it.groupby(zip(rvd_groups,rdists), lambda x: x[0])]
rs = rvds()
tags = [ seq()[r:r+2] for r in rs ]
nt = len(set(tags))
tag_idx_in_ct = dict([(e,i) for i,e in enumerate(set(tags))])
rvd_ct_map = dict([(i,tag_idx_in_ct[e]) for i,e in enumerate(tags)])
ct = mycolors.getct(nt)
f = mp.fignum(3, (12,12))
ax= f.add_subplot(111)
ax.set_xlabel('linear distance')
ax.set_ylabel('nearest neighbor distance to DNA')
labels_set = set([])
for k, g in rvd_dists:
if tags[k] in labels_set:
ax.plot(g, color = ct[rvd_ct_map[k]])
else:
labels_set.add(tags[k])
print 'labelling'
ax.plot(g, color = ct[rvd_ct_map[k]],label = tags[k])
ax.legend()
f.savefig(mp.figpath(figt.format('tal_rvd_distances')))
#plot_charges(coords, charges, strand_coords)
return