def get_layout():
# df = compile_fcs()
fcs = sf.find_unique_values(fcs_df, 'runid')
fc_dropdown = dcc.Dropdown(id="flowcell-dropdown",
multi=False,
placeholder="Choose flowcell",
options=fcs)
z_sel = html.Div([
html.H5('Z Scale'),
dcc.RadioItems(id="z-scale",
options=[{
'label': ' Linear',
'value': 'linear'
}, {
'label': ' Log10',
'value': 'log'
}],
value='linear')
])
plate_slider = html.Div([
html.H5('Plate Number'),
dcc.Slider(id='plt-slider',
min=1,
max=24,
step=1,
value=1,
marks={i: str(i)
for i in range(1, 25)})
],
style={
'width': '49%',
'padding': '0px 20px 20px 20px'
})
csv_button = sf.make_row(
sf.make_col(
html.A(children=[
html.I(className="fas fa-download"),
" Download Sample Level Data"
],
id="sample-download",
download="c19_read_counts.csv",
href="",
target="_blank",
className="btn btn-default downloadButton",
role="button")))
count_hm = html.Div([dcc.Graph(id='ct-hm')], className="six columns")
pct_hm = html.Div([dcc.Graph(id='pct-hm')], className="six columns")
norm_hm = html.Div([dcc.Graph(id='plt-avg-hm')], className='six columns')
sel_row = html.Div([z_sel, plate_slider], className='row')
layout = html.Div(
[fc_dropdown, sel_row, csv_button, norm_hm, pct_hm, count_hm])
return layout
def get_layout():
site = pd.read_csv(
'/ghds/groups/labdesk/bshih/c19dash/c19_dashboard/c19_tat.csv').fillna(0)
sample_textarea = html.Div([dcc.Textarea(
id='textarea',
placeholder='Please Enter Sample ID Separated By Commas eg. HCP0327, HCP0393, HCE1369',
style={'width': '50%', 'height': 50}
)
])
date_range = html.Div([dcc.DatePickerRange(
id='date-range',
clearable=True),
html.Div(id='date-range-output')
])
site = site[site['Site Name'].notnull()]['Site Name'].unique()
site.sort()
site_dropdown = html.Div(dcc.Dropdown(
id='site-dropdown',
options=[{"label": i, "value": i} for i in site],
placeholder='Collection Site',
multi=True)
)
query_button = sf.make_row(children=[sf.make_col(html.Button('Submit', id='query-button', n_clicks=0),
col_num=1)])
textarea_button = sf.make_row(children=[sf.make_col(html.Button('Submit', id='textarea-button', n_clicks=0),
col_num=1)])
smp_id_table = sf.make_row(
html.Div(id='smp-id-table', style={'width': '100%'}))
smp_site_date_table = sf.make_row(
html.Div(id='smp-site-date-table', style={'width': '100%'}))
layout = html.Div([html.H5('Enter Sample ID'), sample_textarea, textarea_button,
html.H5('Sample Information'), smp_id_table,
html.H5('Pick Site or Date Range or Both'), date_range,
site_dropdown, query_button, smp_site_date_table
])
return layout
def get_layout():
date_range = html.Div([
dcc.DatePickerRange(id='date-picker-range'),
html.Div(id='output-container-date-picker-range')
])
fc_submit = sf.make_row(children=[
sf.make_col(html.Button(
"Submit", id="fc-button", n_clicks=0, n_clicks_timestamp=0),
col_num=1)
])
submit_res = html.Div(id='button-res-monitor')
pos_plot = sf.make_row(
dcc.Graph(id='pos-plot-monitoring',
style={
'width': '75%',
'overflowX': 'auto'
},
config={'displayModeBar': True}))
neg_plot = sf.make_row(
dcc.Graph(id='neg-plot-monitoring',
style={
'width': '75%',
'overflowX': 'auto'
},
config={'displayModeBar': True}))
pos_trip_plot = sf.make_row(
dcc.Graph(id='pos-trip-plot-monitoring',
style={
'width': '75%',
'overflowX': 'auto'
},
config={'displayModeBar': True}))
neg_trip_plot = sf.make_row(
dcc.Graph(id='neg-trip-plot-monitoring',
style={
'width': '75%',
'overflowX': 'auto'
},
config={'displayModeBar': True}))
layout = html.Div([
html.H5('Pick a date range '), date_range, fc_submit, submit_res,
html.H5('Positive Control Monitoring Triplicate'), pos_plot,
html.H5('Negative Control Monitoring Triplicate'), neg_plot,
html.H5('Positive Control Monitoring Singlicate'), pos_trip_plot,
html.H5('Negative Control Monitoring Singlicate'), neg_trip_plot
])
return layout
def get_layout():
# df = compile_fcs()
# fcs = sf.find_unique_values(fcs_df, 'runid')
fc_sel_subhead = sf.make_row(children=[
sf.make_col(html.Label("Choose Flowcell", className="mbdSelector"),
col_num=6),
sf.make_col(html.Label("Choose Experiment", className="mbdSelector"),
col_num=6)
])
fc_sel = sf.make_row(children=[
sf.make_col(dcc.Dropdown(id="flowcell-dropdown-plate",
multi=False,
placeholder="Choose flowcell"),
col_num=6),
sf.make_col(
dcc.Dropdown(
id="metric-dropdown",
multi=False,
options=[{
"label": i,
"value": i
} for i in sorted(dropdown_list)],
# placeholder = "select metric"),
value='covid_count'),
col_num=6)
])
box_header = sf.make_row(
sf.make_col(
html.Div(children="Box Plots for Each Extraction Plate",
className="mbdSubheading")))
box_plots = dcc.Loading(id="load-box-plots",
type="default",
children=[
sf.make_row(
sf.make_col(dcc.Graph(id='box-plt'),
col_num=12))
])
html.Div([dcc.Graph(id='box-plt')], className='six columns')
map_header = sf.make_row(
sf.make_col(
html.Div(children="Plate Maps for Each Extraction Plate",
className="mbdSubheading")))
norm_hm = html.Div([dcc.Graph(id='plt-all-hm')], className='six columns')
layout = html.Div(
[fc_sel_subhead, fc_sel, box_header, box_plots, map_header, norm_hm])
return layout
def get_layout():
master = sf.master_df()
positive = master[master['call'] == 'detected']
time_diff = pd.to_datetime(master['AIMS Reporting Notified Date']) \
- pd.to_datetime(master['accession_date'])
tat = (time_diff.dropna().dt.total_seconds() / 3600).mean().astype(int)
heading = sf.make_row(children=[
sf.make_col(children=[
html.H2(f"To this day, we have processed {len(master)} samples."),
html.Div(
html.H2(f"Of those samples, {len(positive)} are positive.")),
html.Div(
html.
H2(f"Average Turnaround Time: {tat} Hours from Accessioning to Reporting."
))
]),
sf.make_col(
dcc.Graph(id='location-pie',
style={'height': 500},
config={'displayModeBar': False}))
])
date_range = html.Div([
dcc.DatePickerRange(id='date-picker-range'),
html.Div(id='output-container-date-picker-range')
])
fc_submit = sf.make_row(children=[
sf.make_col(html.Button("Submit",
id="fc-button-clinical",
n_clicks=0,
n_clicks_timestamp=0),
col_num=1)
])
submit_res = html.Div(id='button-res-clinical')
site = pd.read_csv(
'/ghds/groups/labdesk/bshih/c19dash/c19_dashboard/c19_tat.csv').fillna(
0)
site = site[site['Site Name'].notnull()]['Site Name'].unique()
site.sort()
site_dropdown = html.Div(
dcc.Dropdown(id='percent-detect-site-dropdown',
options=[{
"label": i,
"value": i
} for i in site],
placeholder='Collection Site',
multi=True))
tot_smp_plot = html.Div([dav.VegaLite(id='tot-smp-plot')],
style={
'width': '100%',
'height': '400px'
})
tat_plot = html.Div([dav.VegaLite(id='tat-plot')],
style={
'width': '100%',
'height': '400px'
})
percent_detect = html.Div([dav.VegaLite(id='percent-detect-plot')],
style={
'width': '100%',
'height': '400px'
})
total_sample = html.Div([dav.VegaLite(id='total-sample-plot')],
style={
'width': '100%',
'height': '400px'
})
smp_status_plot = html.Div([dav.VegaLite(id='smp-status-plot')],
style={
'width': '100%',
'height': '400px'
})
smp_status_table = html.Div(id='smp-status-table',
style={
'width': '100%',
'overflowX': 'auto'
})
layout = html.Div([
heading,
html.H3('Pick a date range '), date_range, fc_submit, submit_res,
html.H3('Sample Statistics'), tot_smp_plot, tat_plot,
html.H3('Site Specific Metrics'), site_dropdown, percent_detect,
total_sample,
html.H3('Sample Status'), smp_status_plot, smp_status_table
],
style={'width': '100%'})
return layout
def get_layout():
date_range = html.Div([
dcc.DatePickerRange(id='date-picker-range',
end_date=dt.today(),
start_date=dt.today() - timedelta(days=30)),
html.Div(id='output-container-date-picker-range')
])
fc_submit = sf.make_row(children=[
sf.make_col(html.Button(
"Submit", id="fc-button", n_clicks=0, n_clicks_timestamp=0),
col_num=0.5),
sf.make_col(html.Button(
"Reset", id="fc-reset-button", n_clicks=0, n_clicks_timestamp=0),
col_num=0.5)
])
submit_res = html.Div(id='button-res',
children='Enter date values and press submit')
fc_metric_dropdown = html.Div(
dcc.Dropdown(id='fc-metric-dropdown',
multi=False,
value="cluster_density",
options=[{
"label": k,
"value": v
} for k, v in FC_METRICS2.items()]))
pl_metric_dropdown = html.Div(
dcc.Dropdown(id='pl-metric-dropdown',
multi=False,
value="reads_total",
options=[{
"label": k,
"value": v
} for k, v in POOL_METRICS.items()]))
smp_metric_dropdown = html.Div(
dcc.Dropdown(id='smp-metric-dropdown',
multi=False,
value="count",
options=[{
'label': x,
'value': x
} for x in ['count', 'percent']]))
control_sel = sf.make_row(children=[
sf.make_col(dcc.Dropdown(id="cont-type-dropdown",
multi=False,
value="Positive",
options=[{
'label': x,
'value': x
} for x in ['Positive', 'NTC']]),
col_num=3),
sf.make_col(dcc.Dropdown(id="cont-metric-dropdown",
multi=False,
value="count",
options=[{
'label': x,
'value': x
} for x in ['count', 'percent']]),
col_num=3),
])
discord_sel = sf.make_row(children=[
sf.make_col(dcc.Dropdown(
id="y-dropdown",
multi=False,
value='percent_detect',
options=[{
'label': x,
'value': x
} for x in [
'count_not_detect', 'count_no_call', 'count_detects',
'percent_not_detect', 'percent_detect', 'percent_no_call'
]]),
col_num=3),
sf.make_col(dcc.Dropdown(id="group-dropdown",
multi=True,
value=['0', '1', '2', '3'],
options=[{
'label': x,
'value': x
} for x in ['0', '1', '2', '3']]),
col_num=3),
])
fc_plot = sf.make_row(
dcc.Graph(id='lm-fc-plot',
style={
'width': '90%',
'overflowY': 'scroll'
}))
pl_plot = sf.make_row(
dcc.Graph(id='lm-pl-plot',
style={
'width': 1000,
'overflowY': 'scroll'
}))
smp_plot = sf.make_row(
dcc.Graph(id='smp-plot', style={
'width': 1000,
'overflowY': 'scroll'
}))
pos_plot = sf.make_row(
dcc.Graph(id='pos-plot', style={
'width': 1000,
'overflowY': 'scroll'
}))
per_plot = sf.make_row(
dcc.Graph(id='per-plot', style={
'width': 1000,
'overflowY': 'scroll'
}))
cont_plot = sf.make_row(
dcc.Graph(id='cont-plot', style={
'width': 1000,
'overflowY': 'scroll'
}))
discord_plot = sf.make_row(
dcc.Graph(id='discord-plot',
style={
'width': 1000,
'overflowY': 'scroll'
}))
layout = html.Div([
html.H5('Pick a date range '), date_range, fc_submit, submit_res,
html.H5('Flowcell Level Metrics'), fc_metric_dropdown, fc_plot,
html.H5('Pool Level Metrics'), pl_metric_dropdown, pl_plot,
html.H5('Sample Metrics'), smp_metric_dropdown, smp_plot, control_sel,
pos_plot, cont_plot, per_plot
])
return layout
def get_main_layout():
# Page header
page_header = sf.make_row(
sf.make_col(children=[
html.Nav(className="navbar navbar-light",
children=[
html.Span(children=[
html.Img(src="assets/favicon.ico",
width="41",
height="41",
className="brand-icon"),
html.Span("GUARDANT-19 Dashboard",
className="headerText")
],
className="navbar-brand brand-format"),
html.Span("v{}".format(__version__),
className="version")
])
]))
# Nav bar
nav_bar = sf.make_row(
sf.make_col(
html.Ul(
className="nav nav-tabs nav-fill",
children=[
html.Li(dcc.Link("Clinical Statistics",
href="/clinical",
id="clinical-tab",
className="nav-link fc-tab"),
className="nav-item"),
html.Li(dcc.Link("Sample Query",
href="/sample-query",
id="sample-query-tab",
className="nav-link fc-tab"),
className="nav-item"),
html.Li(dcc.Link("Monitoring",
href="/monitoring",
id="monitoring-tab",
className="nav-link fc-tab"),
className="nav-item"),
# html.Li(
# dcc.Link("% RT-PCR Fail",
# href="/rtpcr-fail",
# id="rtpcr-fail-tab",
# className="nav-link fc-tab"),
# className="nav-item"),
html.Li(dcc.Link("Flowcell Metrics",
href="/flowcell-metrics",
id="fc-metric-tab",
className="nav-link fc-tab"),
className="nav-item"),
html.Li(dcc.Link("Pool Metrics",
href="/pool-qc",
id="pool-qc-tab",
className="nav-link fc-tab"),
className="nav-item"),
html.Li(dcc.Link("All Plate Maps",
href="/plate-maps-all",
id="plate-map-all-tab",
className="nav-link fc-tab"),
className="nav-item"),
html.Li(dcc.Link("Longitudinal Monitoring",
href="/longitudinal-monitoring",
id="lm-tab",
className="nav-link fc-tab"),
className="nav-item")
])))
top_layout = html.Div(children=[
dcc.Location(id="url-start", refresh=False),
dcc.Location(id="url", refresh=False), page_header, nav_bar,
html.Div(id="interval-test", className="hidden-div"),
html.Div(id='page-content', className="container-fluid tab-container")
],
className="container-fluid page-container")
return top_layout