def label_ys(labels):
import plotting as pl
ax = pl.gca()
bottoms = [YSCALE*i for i in range(len(labels))]
for b in bottoms: pl.axhline(y=b, linewidth=.5, color='gray')
ax.axes.set_yticks([b+YSCALE/2 for b in bottoms])
ax.axes.set_yticklabels(labels)
ax.axes.yaxis.set_ticks_position('none')
def label_xs(lefts, labels):
import plotting as pl
# Draw bars separating fractionations. Were in the wrong place before
# moving to the left by one.
for left in lefts[1:]:
pl.axvline(x=left-1, linewidth=.5, color='gray')
ax = pl.gca()
# Center x-axis labels
ax.axes.set_xticks([int((lefts[i]+lefts[i+1])/2) for i in
range(len(lefts)-1)])
ax.axes.xaxis.set_ticks_position('none')
ax.axes.set_xticklabels(labels, fontsize=10)
labels = ax.get_xticklabels()
for label in labels:
label.set_rotation(35)
[i.set_linewidth(0.5) for i in ax.spines.itervalues()]
def cluster_ids(gids, unnorm_eluts, sp, gt=None, dist='cosine', do_plot=True,
norm_rows=True, bigarr=None, **kwargs):
import plotting as pl
import hcluster
arr = (bigarr if bigarr is not None else single_array(gids, unnorm_eluts,
sp, norm_rows=norm_rows))
ymat = hcluster.pdist(arr, metric=dist)
zmat = hcluster.linkage(ymat)
zmat = np.clip(zmat, 0, 10**8)
if do_plot: pl.figure()
order = hcluster.dendrogram(zmat, no_plot=bool(1-do_plot),
**kwargs)['leaves']
if do_plot:
ax = pl.gca()
ax.axes.set_xticklabels([gt.id2name[gids[ind]] for ind in order])
pl.figure()
pl.imshow(arr[order,:])
return list(np.array(list(gids))[order])
