def figure_to_vdom_image(figure):
buf = io.BytesIO()
figure.savefig(buf, format='png')
buf.seek(0)
string = base64.b64encode(buf.read())
return vdomh.div(vdomh.img(src='data:image/png;base64,' +
urllib.parse.quote(string)),
style={"display": "inline-block"})
async def get_dashboard():
example = div(
span(img(src=image_url, style=dict(width='100', heigth='100')),
h1('Smart 311 Dashboard')),
p('Written in Python, 100%'),
topten(),
p('Top ten complaint types'),
).to_html()
return HTMLResponse(content=example)
def vdom_modisco(mr, figdir, total_counts, dfp=None, is_open=True, **kwargs):
return div([
vdom_metacluster(mr,
metacluster,
figdir,
total_counts,
dfp=dfp,
is_open=is_open,
**kwargs) for metacluster in mr.metaclusters()
if len(mr.patterns(metacluster)) > 0
])
def vdm_heatmaps(seqlets,
d,
included_samples,
tasks,
pattern,
top_n=None,
pssm_fig=None,
opened=False,
resize_width=200):
ex_signal, ex_contrib_profile, ex_contrib_counts, ex_seq, sort_idx = get_signal(
seqlets, d, included_samples, tasks, resize_width=resize_width)
if top_n is not None:
sort_idx = sort_idx[:top_n]
return div(
details(summary("Sequence:"),
pssm_fig,
br(),
fig2vdom(
heatmap_sequence(ex_seq,
sort_idx=sort_idx,
figsize_tmpl=(10, 15),
aspect='auto')),
open=opened),
details(
summary("ChIP-nexus counts:"),
fig2vdom(
multiple_plot_stranded_profile(
ex_signal, figsize_tmpl=(20 / len(ex_signal), 3))),
# TODO - change
fig2vdom(
multiple_heatmap_stranded_profile(ex_signal,
sort_idx=sort_idx,
figsize=(20, 20))),
open=opened),
details(summary("Contribution scores (profile)"),
fig2vdom(
multiple_heatmap_contribution_profile(ex_contrib_profile,
sort_idx=sort_idx,
figsize=(20, 20))),
open=opened),
details(summary("Contribution scores (counts)"),
fig2vdom(
multiple_heatmap_contribution_profile(ex_contrib_counts,
sort_idx=sort_idx,
figsize=(20, 20))),
open=opened))
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())
def vdom_motif_pair(motif_pair_lpdata,
dfab,
profile_mapping,
figures_dir,
figures_url,
profile_width=200,
cache=False,
**kwargs):
from basepair.exp.chipnexus.spacing import remove_edge_instances
out = []
os.makedirs(figures_dir, exist_ok=True)
for motif_pair_name, lpdata in tqdm(motif_pair_lpdata.items()):
motif_pair = list(motif_pair_name.split("<>"))
dfab_subset = remove_edge_instances(
dfab[dfab.motif_pair == motif_pair_name],
profile_width=profile_width)
out.append(
template_vdom_motif_pair(motif_pair[0],
motif_pair,
lpdata,
dfab_subset,
profile_mapping,
figures_dir=figures_dir,
figures_url=figures_url,
cache=cache,
**kwargs))
if motif_pair[0] != motif_pair[1]:
out.append(
template_vdom_motif_pair(motif_pair[1],
motif_pair,
lpdata,
dfab_subset,
profile_mapping,
figures_dir=figures_dir,
figures_url=figures_url,
cache=True,
**kwargs))
# break
return div(ul([li(elem) for elem in out], start=0))
def dashboard():
return div(
span(img(src=image_url, style=dict(width='100', heigth='100')),
h1('Smart 311 Dashboard')), img(width='400', src=barplot_url),
p('Written in Python, 100%'))
def _badHTML(data):
# TODO: use xml.dom.minidom as dangerouslySetInnerHTML should be blocklisted in frontend
return div(dangerouslySetInnerHTML={'__html': data})
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?'),
))
