def set_simple_description(**kwargs):
props = get_assay_gprops(**mem.sr(kwargs))
chips = get_assay_info(**mem.sr(kwargs))
simple = {}
for tf, assays in props.iteritems():
simple[tf] = {}
assay_keys = assays.keys()
idfun = lambda g: g.qualifiers['db_xref'][1][9:]
simple[tf]['gnames'] = list(it.chain(*[
[idfun(e['gene']) for e in assays[k]['primaries']]
for k in assay_keys
]))
simple[tf]['genes'] = list(it.chain(*[
[e['gene'] for e in assays[k]['primaries']]
for k in assay_keys
]))
simple[tf]['dists'] = array(list(it.chain(*[
[e['dist'] for e in assays[k]['primaries']]
for k in assay_keys
])))
simple[tf]['scores'] = array(list(it.chain(*[
[e['score'] for e in chips[tf][k]]
for k in assay_keys
])))
return simple
def set_synapse_array(**kwargs):
imaps = get_array_imaps(**mem.sr(kwargs))
ctypes =imaps['ctypes']
ctypes_imap = imaps['ctypes_imap']
nnames = imaps['nnames']
nnames_imap = imaps['nnames_imap']
all_out_cxns = get_synapse_dict(**mem.sr(kwargs))
cxns = zeros((len(nnames),len(nnames), len(ctypes)))
for k1,rows in all_out_cxns.iteritems():
for row in rows:
cxns[nnames_imap[k1],nnames_imap[row[1]],
ctypes_imap[row[2]]] +=row[3]
return cxns
def plot_city_posts(**kwargs):
cp = city_posts(**mem.sr(kwargs))
xs = cp["lons"]
ys = cp["lats"]
rs = [len(x) for x in cp["posts"]]
f = myplots.fignum(3, (4, 4))
ax = f.add_subplot(111)
ax.scatter(xs, ys, s=rs)
def set_assay_gprops(**kwargs):
chips = get_assay_info(**mem.sr(kwargs))
genes = parse_genes()
tf_stats = {}
for k, v in chips.iteritems():
tf_stats[k] = {}
for k2,v2 in v.iteritems():
print 'n_exps = {0}'.\
format(np.sum([len(v)
for v in tf_stats.values()]))
tf_stats[k][k2] = {}
cs = [e['chr'] for e in v2]
f_gups=[genes[cs[i]][e['fup_gene']] for i,e in enumerate(v2)]
f_gdowns=[genes[cs[i]][e['fdown_gene']] for i,e in enumerate(v2)]
fup_deltas = [e['mean'] - f_gups[i].location.start.position
for i,e in enumerate(v2)]
fdown_deltas=[e['mean'] - f_gdowns[i].location.start.position
for i,e in enumerate(v2)]
r_gups=[genes[cs[i]][e['rup_gene']] for i,e in enumerate(v2)]
r_gdowns=[genes[cs[i]][e['rdown_gene']] for i,e in enumerate(v2)]
rup_deltas = [e['mean'] - r_gups[i].location.end.position
for i,e in enumerate(v2)]
rdown_deltas=[e['mean'] - r_gdowns[i].location.end.position
for i,e in enumerate(v2)]
deltas = array([fdown_deltas,
fup_deltas,
rdown_deltas,
rup_deltas]).T
closest = argmin(np.abs(deltas),1)
csrt = argsort(np.abs(deltas),1)
primaries = []
secondaries = []
for i,c in enumerate(csrt):
for j,e in enumerate(c[:2]):
arr = primaries if j == 0 else secondaries
d = {}
if e == 0 : d['gene'] = f_gdowns[i]
elif e==1 : d['gene'] = f_gups[i]
elif e==2 : d['gene'] = r_gdowns[i]
elif e==3 : d['gene'] = r_gups[i]
d['dist'] = deltas[i,e] * (-1 if e < 2 else 1)
arr.append(d)
tf_stats[k][k2]['primaries'] = primaries
tf_stats[k][k2]['secondaries'] = secondaries
return tf_stats
def set_graph(**kwargs):
edge_set = get_edge_set()
rows = get_rows(**mem.sr(kwargs))
sub_cxns = dict([(k, [ e for e in list(val) if e[2] in edge_set])
for k,val in it.groupby(\
sorted(rows, key = lambda x: x[0]),
key = lambda x: x[0])])
g = nx.DiGraph();
for k, v in sub_cxns.iteritems():
g.add_weighted_edges_from([(e[0], e[1], e[3]) for e in v])
return g
def set_term_network( **kwargs):
nterms = kwargs.get('nterms')
name = kwargs.get('name')
if name == 'bdtnp': gene_list = nio.getBDTNP().keys()
elif name == 'kn': gene_list = graphs['kn'].nodes()
grps = term_groups(**mem.sr(kwargs,
name = name))
network = nx.Graph()
network.add_nodes_from(gene_list)
for g in grps:
edgelist = [[g1[0],g2[0]]
for g1 in g[1] for g2 in g[1]]
network.add_edges_from( edgelist )
return network
def set_array_imaps(**kwargs):
sdict =get_synapse_dict(**mem.sr(kwargs))
nameset = set([])
for k,v in sdict.iteritems():
nameset.add(k)
nameset.update([r[1] for r in v])
nnames = list(nameset)
ctypes = [u'Rp', u'EJ', u'Sp', u'S', u'R', u'NMJ']
ctypes_imap = dict([(k,i) for i, k in enumerate(ctypes)])
nnames_imap = dict([(k,i) for i, k in enumerate(nnames)])
return {'ctypes':ctypes,
'ctypes_imap':ctypes_imap,
'nnames':nnames,
'nnames_imap':nnames_imap}
def plot_ronn(**kwargs):
l5 = last_5(**mem.sr(kwargs))
ys = zeros((len(l5), len(l5.values()[0])))
for i, h in enumerate(l5.values()):
for j, d in enumerate(h):
if len(d) == 0:
continue
cas = [e.created_at for e in d]
secs = np.sum([(((ca.hour) * 60 + ca.minute) * 60) + ca.second for ca in cas])
ys[i, j] = secs
ys = ys[:, -20:]
ys = ys - np.min(ys, 1)[:, newaxis]
colors = mycolors.getct(len(ys))
seismic.seismic(ys, stacked=True, colors=colors)
def set_simple_thr(**kwargs):
dthr = kwargs['dthr']
dsign = kwargs['dsign']
sthr = kwargs['sthr']
simple = get_simple_description(**mem.sr(kwargs))
out = {}
for k,v in simple.iteritems():
criteria = ones(len(v['scores']))
if sthr != None:
criteria *= less(v['scores'],sthr)
if dsign != None:
criteria *= greater(v['dists']*dsign, 0)
if dthr != None:
criteria *= less(abs(v['dists']),dthr)
allowed = nonzero(criteria)[0]
out[k] = {'genes':[v['genes'][i] for i in allowed],
'gnames':[v['gnames'][i] for i in allowed],
'dists':v['dists'][allowed],
'scores':v['scores'][allowed]}
return out
def setAllGenes(**kwargs):
allPeaks = getPeaks()
all_results = {}
for num in range(1,20) + ['X']:
print 'Parsing Chromosome: chr{0}'.format(num)
genes_dict = {}
all_results['chr{0}'.format(num)] = genes_dict
chrgenes = getTrackChrGenes(**mem.sr(kwargs, num = num))
peaks = allPeaks['chr{0}'.format(num)]
for i, g in enumerate(chrgenes):
name = g['name']
startpos = g['start'] if g['strand'] == 1 else g['end']
hits = []
for p in peaks:
stranded_offset =array([ g['strand'] * (p['start'] - startpos),
g['strand'] * (p['end'] - startpos)])
if( np.min(abs(stranded_offset)) < 2000 \
or np.prod(stranded_offset) < 0):
stranded_offset.sort()
hits.append({'peak_info':p,
'peak_stranded_offset':stranded_offset})
hits = sorted(hits,key = lambda x: x['peak_stranded_offset'][0])
gene_object = {
'dnase_peaks':hits,
'name':name,
'gene_info':g,
'start':g['start'],
'end':g['end'],
'strand':g['strand']
}
genes_dict[name] = gene_object
if (mod(i,100) == 0):
print 'Gene {0}: {1}, {2} hits'.format(i, g['name'], len(hits))
return all_results;
def set_cons(**kwargs):
seqs, seqs_rndvals, keys = get_mutants(**mem.sr(kwargs))
cons = consensus_seq(seqs[::100])
return cons
def set_assay_info(**kwargs):
#peaks and keys
atype = kwargs['atype']
if atype == 'tfchip':
assay_peaks = tf_chip_peaks(**mem.sr(kwargs))
elif atype=='wormtile':
assay_peaks = tiling_peaks(**mem.sr(kwargs))
else: raise Exception()
pkeys = assay_peaks.keys()
keyvalfuns = {'tfchip':lambda x: x[:x.index(':')],
'wormtile':lambda x:re.compile('Tissue=([^\(]*)')\
.search(x).group(1)}
#index and uniquify tfs
pkeyvals = dict([(k, keyvalfuns[atype](k)) for k in pkeys])
tfnames = set(pkeyvals.values())
tfkeys= dict([(name, [k for k,v in pkeyvals.iteritems()
if v == name])
for name in tfnames])
chrmap = dict(zip(['I','II', 'III','IV', 'V', 'X'],
chromosome_names()))
all_tss = get_tss()
all_genes = parse_genes()
bind_infos = {}
#loop through tfs, assays, and finally peaks
for tfname in tfnames:
print tfname
bind_infos[tfname] = {}
for ekey in tfkeys[tfname]:
print 'n_exps = {0}'.format(np.sum([len(v)
for v in bind_infos.values()]))
exp = assay_peaks[ekey]
bind_infos[tfname][ekey] = []
for e in exp:
start = e['start']
end = e['end']
c = e['chr']
#if we have non chromosomal DNA, skip it!
if c in chrmap.keys():
crkey = chrmap[c]
else: continue
genes = all_genes[crkey]
tss = all_tss[crkey]
#grab indexes in the list of upstream and ds genes
fdownstream_idx =searchsorted(tss['fwd_tss'],(start+end) /2)
rdownstream_idx =searchsorted(tss['rev_tss'],(start+end) /2, 'right')-1
#handle the case where the factor hits past the
#last gene
fup_ofs = -1
if fdownstream_idx == len(tss['fwd_genes']):
fdownstream_idx = fdownstream_idx -1
fup_ofs = 0
rup_ofs = 1
if fdownstream_idx == len(tss['fwd_genes']):
fdownstream_idx = fdownstream_idx -1
rup_ofs = 0
#get gene indexes in the chromosomal gene dicts
#for upstream and downstream
fdown_gene = tss['fwd_genes'][fdownstream_idx]
fup_gene = tss['fwd_genes'][fdownstream_idx +fup_ofs]\
if fdownstream_idx > 0 \
else fdown_gene
rdown_gene = tss['rev_genes'][rdownstream_idx]
rup_gene = tss['rev_genes'][rdownstream_idx +rup_ofs]\
if rdownstream_idx < len(tss['rev_genes']) - 1\
else rdown_gene
bind_infos[tfname][ekey].append({
'rup_gene':rup_gene,
'rdown_gene':rdown_gene,
'fup_gene':fup_gene,
'fdown_gene':fdown_gene,
'chr':crkey,
'start':start,
'end':end,
'mean':(start+end)/2,
'score':e['score']
})
return bind_infos
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 set_pos(**kwargs):
g = get_graph(**mem.sr(kwargs))
pos = gd.getpos(g)
return pos