def _repr_html_(self):
"""Output for the Jupyter notebook."""
is_supergroup = self.__contains_groups()
rsl = []
rsl.append(
v.tr(v.th("Pos.", style={"text-align": "right"}),
v.th("Bezeichnung", style={"text-align": "left"}),
v.th("Betrag", style={"text-align": "right"}),
v.th("Anmerkung", style={"text-align": "left"})), )
rsl += self._vdom(is_supergroup)
if is_supergroup:
rsl.append(v.tr(v.td(), v.td(), v.td(), v.td()))
rsl.append(
v.tr(
v.td(),
v.td(v.u(v.b(f"Total {self.name}"))),
v.td(
v.u(
v.b(str(self.total())),
style={"text-align": "right"},
)),
v.td(),
), )
layout = v.table(*rsl, )
return layout.to_html()
def _vdom(self, is_supergroup: bool):
rsl = []
if not is_supergroup:
rsl.append(
v.tr(
v.td(v.b(self.code), style={"text-align": "right"}),
v.td(v.b(self.name), style={"text-align": "left"}),
v.td(),
v.td(),
), )
for item in self.items:
# Blank line before new group.
if isinstance(item, Group) and not is_supergroup:
rsl.append(v.tr(v.td(), v.td(), v.td(), v.td()))
if isinstance(item, Entry) and is_supergroup:
# Render single entry in super-group.
rsl.append(v.tr(v.td(), v.td(), v.td(), v.td()))
rsl += self._from_entry(item)._vdom(False)
else:
# Render Group or Entry.
rsl += item._vdom(False)
if not is_supergroup:
rsl.append(
v.tr(
v.td(),
v.td(v.b("Total {}".format(self.name)),
style={"text-align": "left"}),
v.td(v.b(str(self.total())), style={"text-align":
"right"}),
v.td(),
))
return rsl
def template_vdom_metacluster(name,
n_patterns,
n_seqlets,
important_for,
patterns,
is_open=False):
return details(summary(
b(name), f", # patterns: {n_patterns},"
f" # seqlets: {n_seqlets}, "
"important for: ", b(important_for)),
ul([li(pattern) for pattern in patterns], start=0),
id=name,
open=is_open)
def template_vdom_motif_pair(main_motif,
motif_pair,
lpdata,
dfab,
profile_mapping,
figures_dir,
figures_url,
cache=False,
**kwargs):
motif_figs = []
other = motif_pair[0] if motif_pair[0] != main_motif else motif_pair[1]
# HACK - pass the tasks
for task in ['Oct4', 'Sox2', 'Nanog', 'Klf4']:
figs, dist_seq = motif_pair_figs(main_motif, task, motif_pair, lpdata,
dfab, **kwargs)
motif_figs += figs
if task == profile_mapping[main_motif]:
dist_seq_fig = dist_seq
return details(
summary(b(main_motif), f" (perturb {other})"), *[
details(
summary(k), *[
cache_fig(x,
figures_dir,
figures_url,
str(i) + "-" + main_motif + "<>" + other + "-" +
k,
width=840 if k is not "Distance" else 400,
cache=cache) for i, x in enumerate(v)
]) for k, v in dist_seq_fig + motif_figs
])
def write_modisco_table(df,
output_dir,
report_url=None,
prefix='pattern_table',
exclude_when_writing=["logo pwm", "logo imp"],
doc=DOC,
write_csv=True):
"""Write the pattern table to as .html and .csv
"""
from vdom.helpers import h2, h3, p, ul, ol, li, div, b
output_dir = Path(output_dir)
df = df.copy()
if write_csv:
cols_for_csv = [c for c in df.columns if c not in exclude_when_writing]
df[cols_for_csv].to_csv(output_dir / f'{prefix}.csv', index=False)
if report_url is not None:
df.pattern = [pattern_url(p, report_url) for p in df.pattern]
df.columns = [c.replace(" ", "<br>") for c in df.columns]
# Add instructions
instructions = div(
h2("Column description"),
ul([li(b(k), ": ", v) for k, v in doc.items()]),
h2("Table interaction options"),
ul([
li(b("Re-order columns: "),
"Drag column headers using the mouse pointer"),
li(
b("Sort w.r.t single column: "),
"Click on the column header to sort the table with respect two that "
"column in an ascending order and click again to sort in a descending order."
),
li(
b("Sort w.r.t multiple columns: "),
"Hold shift and click multiple column headers to sort w.r.t. multiple columns"
),
li(b("View logo images: "),
"Right-click on the images and choose 'Open image in new tab'"),
li(b("Select muliple rows: "),
"Click on the row to select/de-select it."),
li(b("Get more information about the pattern: "),
"Follow the link in the pattern column."),
]))
write_datatable_html(df, output_dir / f"{prefix}.html",
instructions.to_html())
from IPython.display import display
from vdom.helpers import h1, p, img, div, b
display(
div(
h1('Our Incredibly Declarative Example'),
p('Can you believe we wrote this ', b('in Python'), '?'),
img(src="https://media.giphy.com/media/xUPGcguWZHRC2HyBRS/giphy.gif"),
p('What will ', b('you'), ' create next?'),
))