def srt_heatmap(net = 3,
all_module = False):
import compbio.projects.bsort.bsort as bs
arr, cols, rows = load(net = net,
max_go_modules = 15,
min_go_size = 5,
min_module_size = 10)
arr2_510, srts = bs.run0(arr = arr, itr = 2, meth = 'moment')
arr2_510 = arr2_510[:,::-1]
csrts = [s for s in srts if len(s) == len(cols)]
rsrts = [s for s in srts if len(s) == len(rows)]
c0 = array(cols)
r0 = array(rows)
for c in csrts: cols = cols[c]
for r in rsrts: rows = rows[r]
fopen =open( cfg.dataPath('daniel/heatmaps_sorted/hm_net{0}.txt'.format(net)), 'w')
fopen.write('FORMAT: L1 :GO Terms (Columns), L2: Modules (Rows), L3+ Pvals thresholded between .01, .001\n')
fopen.write('\t'.join([str(elt) for elt in cols]) + '\n')
fopen.write('\t'.join([str(squeeze(elt)) for elt in rows]) + '\n')
dmat = arr2_510
for row in dmat:
fopen.write('\t'.join(['{0}'.format(elt) for elt in row])+'\n')
fopen.close()
f = myplots.fignum(3, (8,40)) if net == 3 else myplots.fignum(3, (8,10))
ax = f.add_axes([.4,.05,.55,.9], aspect = 'auto')
goterms = [str(elt) for elt in cols]
if not all_module:
idx_omit = goterms.index('all')
arr2_510 = vstack((arr2_510[:idx_omit],arr2_510[idx_omit+1:]))
goterms = goterms[:idx_omit] + goterms[idx_omit+1:]
fopen = open(cfg.dataPath('daniel/go_accession_name_map.txt'))
gotexts = {}
for l in fopen.xreadlines():
k,v = l.split('\t')
gotexts[k] = v
row_labels = []
for g in goterms:
if g in gotexts.keys(): row_labels.append(gotexts[g].strip())
else: row_labels.append(g.strip())
ax.set_yticks(arange(len(goterms))+.25)
ax.set_yticklabels(row_labels, size = '4')
ax.set_xticks([])
ax.set_xlabel('Modules')
ax.set_xticks(arange(len(rows))+.25)
ax.set_xticklabels([str(int(r[0])) for r in rows],
rotation= 90,
size = 'small')
cm = mycolors.blackbody(flip = True)
im =ax.imshow(arr2_510[:,:] * 4 + 2,
cmap = plt.get_cmap('OrRd'),
aspect = 'auto',
interpolation = 'nearest'
)
plt.colorbar(im)
f.savefig(cfg.dataPath('daniel/heatmaps_sorted/hm_net{0}_{1}.pdf'.\
format(net, 'with_all' if all_module else 'no_all')))
def show_sims(sims):
ax = plt.gca()
ax.imshow(sims, cmap = mycolors.blackbody(),interpolation = 'nearest')
