def __call__(self, track, slice=None):
edir = EXPORTDIR
method = "utr_extension"
blocks = ResultBlocks()
filepath = "%(edir)s/%(method)s/%(track)s.readextension_%(region)s_%(direction)s.%(slice)s.png"
block = \
'''
.. figure:: %(filename)s
:height: 300
'''
# append spaces for file extension
block = "\n".join([x + " " * 200 for x in block.split("\n")])
for region, direction in itertools.product(
("downstream", "upstream"), ("sense", "antisense", "anysense")):
filename = filepath % locals()
if os.path.exists(filename):
blocks.append(
ResultBlock(text=block % locals(),
title="%(track)s %(region)s %(direction)s" %
locals()))
# else:
# blocks.append( ResultBlock( "",
# title = "%(track)s %(region)s %(direction)s" % locals() ) )
return odict(
(("rst", "\n".join(Utils.layoutBlocks(blocks,
layout="columns-3"))), ))
def __call__(self, track, slice=None):
# note there are spaces behind the %(image)s directive to accomodate
# for path substitution
block = '''
.. figure:: %(image)s
:height: 300
'''
blocks = ResultBlocks()
tracks = sorted([x.asFile() for x in TRACKS])
for track in tracks:
files = glob.glob(
os.path.join(EXPORTDIR, "fastqc", "%s*_fastqc" % track))
for x, fn in enumerate(sorted(files)):
y = x + 1
image = os.path.abspath(
os.path.join(fn, "Images", "%s.png" % slice))
if not os.path.exists(image):
continue
blocks.append(
ResultBlock(text=block % locals(),
title=os.path.basename(fn)))
return odict(
(("rst", "\n".join(Utils.layoutBlocks(blocks,
layout="columns-2"))), ))
def __call__(self, data, path):
colorbar, factors, unique, xkcd = self.getColorBar(data)
n_samples = data.shape[0]
data = data.iloc[:, :n_samples]
col_dict = dict(list(zip(unique, xkcd)))
print(data.head())
seaborn.set(font_scale=.5)
ax = seaborn.clustermap(data,
row_colors=colorbar, col_colors=colorbar)
plt.setp(ax.ax_heatmap.yaxis.set_visible(False))
for label in unique:
ax.ax_col_dendrogram.bar(
0, 0, color=seaborn.xkcd_rgb[col_dict[label]],
label=label, linewidth=0)
ax.ax_col_dendrogram.legend(loc="center", ncol=len(unique))
return ResultBlocks(ResultBlock(
'''#$mpl %i$#\n''' % ax.cax.figure.number,
title='ClusterMapPlot'))
