def get(self):
args = self.request.arguments
defaultargs = get_args(args)
form = ControlsForm()
path = defaultargs['path']
current_name = defaultargs['name']
if not os.path.exists(path):
msg = help_msg()
self.render('sequence.html', form=form, status=0, name='', msg=msg, path=path)
return
names = web.get_file_lists(path)
if current_name == '': current_name = names[0]
form.path.data = path
form.name.choices = [(i,i) for i in names]
form.name.data = current_name
form.cutoff.data = defaultargs['cutoff']
form.n.data = defaultargs['n']
form.cutoff_method.data = defaultargs['cutoff_method']
form.kind.data = defaultargs['kind']
form.view.data = defaultargs['view']
preds = web.get_predictors(path, current_name)
#alleles = web.get_alleles(preds)
data = web.get_binder_tables(preds, **defaultargs)
tables = web.dataframes_to_html(data, classes='tinytable sortable')
tables = web.tabbed_html(tables)
#info = web.dict_to_html(web.get_results_info(preds[0]))
info=''
kind = defaultargs['kind']
if kind == 'grid':
seqhtml = web.sequence_to_html_grid(preds, classes="gridtable")
div = '<div class="scrolled">%s</div>' %seqhtml
script = ''
elif kind == 'text':
seqhtml = web.create_sequence_html(preds, classes="seqtable")
div = '<div class="scrolled">%s</div>' %seqhtml
script = ''
else:
plots = web.create_figures(preds, **defaultargs)
if len(plots) > 0:
grid = gridplot(plots, ncols=1, merge_tools=True, sizing_mode='scale_width',
toolbar_options=dict(logo=None))
script, div = components(grid)
else:
script = ''; div = ''
links = []
for k in data.keys():
defaultargs['pred'] = k
links.append(self.get_url(defaultargs, link=k))
self.render('sequence.html', script=script, div=div, form=form, tables=tables,
msg='', info=info, name=current_name, status=1, links=links, path=path)
def update_header(target, event):
names = web.get_file_lists(event.new)
target.object = "_total sequences: %s_" % str(len(names))
return
def predictions_dashboard(path):
"""Dashboard for viewing results from epitopepredict runs."""
#folder_input = pn.widgets.TextInput(name='path', value='../zaire_test', width=400,width_policy='fit')
#reload_btn = pn.widgets.Button(name='reload',width=100,button_type='primary')
names = web.get_file_lists(path)
if names is None:
return
preds = web.get_predictors(path, name=names[0])
print(preds)
seqname = pnw.Select(name='name', value=names[0], options=names)
cutoff_slider = pnw.FloatSlider(name='cutoff',
value=.95,
start=.75,
end=.99,
step=0.01)
cutoff_method = pnw.Select(name='cutoff method',
value='default',
options=['default', 'rank'])
n_select = pnw.FloatSlider(name='n', value=1, start=1, end=8, step=1)
plot_select = pnw.Select(name='plot view',
value='tracks',
options=['tracks', 'sequence'])
table_select = pnw.Select(name='table view',
value='promiscuous',
options=['promiscuous', 'binders'])
colorseq_box = pnw.Checkbox(name='color sequences', value=False)
header = pn.pane.Markdown('__total sequences: %s__' % len(names),
css_classes=['main'])
tables = pn.Tabs(width=900)
plot = pn.pane.Bokeh(width=800)
debug = pn.pane.Markdown('test',
style={
'font-size': '10pt',
'background-color': 'yellow'
})
summary_plot = pn.pane.Bokeh()
summary_table_tabs = pn.Tabs()
recalc_button = pnw.Button(name='recalculate', width=200)
def update_banner():
"""Update the banner"""
fullpath = os.path.abspath(path)
banner = pn.Row(
pn.pane.Markdown(
'<h4>epitopepredict: %s</h4> [help](%s) version %s' %
(fullpath, helppage, __version__),
css_classes=['divheader'],
sizing_mode='stretch_width'))
return banner
def update_header(target, event):
names = web.get_file_lists(event.new)
target.object = "_total sequences: %s_" % str(len(names))
return
def callback_getpath(event):
path = os.path.getcwd()
folder.value = path
def update_plot(preds, name, cutoff, n, kind):
"""Plot data view"""
if kind == 'tracks':
p = plotting.bokeh_plot_tracks(preds,
name=name,
cutoff=cutoff,
n=n,
width=1000,
title=name)
plot.object = p
elif kind == 'sequence':
p = plotting.bokeh_plot_sequence(preds,
name=name,
cutoff=cutoff,
n=n,
width=1000,
title=name,
color_sequence=colorseq_box.value)
plot.object = p
return p
def update_tables(preds, name, n):
"""Tabular views of results"""
P = preds[0]
view = table_select.value
tables.clear()
for P in preds:
if view == 'promiscuous':
df = P.promiscuous_binders(n=n, name=name)
else:
df = P.get_binders(name=name)
res = df.to_html(classes="tinytable sortable")
div = '<div class="scrollingArea">%s</div>' % res
tables.append((P.name, div))
#tables.append((P.name,pn.pane.HTML('<p>hddsadsadsasda</p>',width=700)))
return
def update(event):
"""Update all elements"""
name = seqname.value
n = n_select.value
cutoff = cutoff_slider.value
kind = plot_select.value
debug.object = name
preds = web.get_predictors(path, name=name)
update_plot(preds, name=name, cutoff=cutoff, n=n, kind=kind)
update_tables(preds, name, n)
return
def update_summary(path):
"""Summary info for folder"""
data = web.get_summary_tables(path)
df = pd.concat(data, sort=True).reset_index()
#plot = plotting.bokeh_summary_plot(df)
#summary_plot.object = plot
summary_table_tabs.clear()
a = web.aggregate_summary(data)
div = web.get_scrollable_table(a)
summary_table_tabs.append(('all', div))
names = list(data.keys())
for n in names:
df = data[n]
res = df.to_html(classes="tinytable sortable")
div = '<div class="scrollingArea">%s</div>' % res
summary_table_tabs.append((n, div))
return
@pn.depends(seqname.param.value, n_select.param.value)
def download_link(name, n):
if preds is None:
return
df = preds[0].promiscuous_binders(n=n, name=name)
df.to_csv()
return pn.Pane(HTML('<a>download</a>'), width=700)
info = pn.pane.Markdown(web.get_readme())
banner = update_banner()
update_summary(path)
#reload_btn.param.watch(load_predictors, 'clicks')
#reload_btn.param.trigger()
seqname.param.watch(update, 'value')
cutoff_slider.param.watch(update, 'value')
n_select.param.watch(update, 'value')
table_select.param.watch(update, 'value')
plot_select.param.watch(update, 'value')
seqname.param.trigger('options', 'value')
top = pn.Row(header) #,download_link)
left = pn.Column(plot, tables, margin=10, sizing_mode='stretch_width')
right = pn.Column(seqname,
cutoff_slider,
cutoff_method,
n_select,
plot_select,
table_select,
colorseq_box,
css_classes=['widget-box'],
width=200)
center = pn.Row(left, right)
#bottom = pn.Row(table)
main = pn.Column(top, center)
summarypane = pn.Column(recalc_button, (pn.Row(summary_table_tabs)))
tabs = pn.Tabs(('summary', summarypane), ('sequence', main),
('about', info))
#tabs.append()
app = pn.Column(banner, tabs, sizing_mode='stretch_width')
return app