def add_callbacks(app, trace):
add_include_transformed_callback(app, 'univariate', trace)
@app.callback(dep.Output('univariate-autocorr', 'figure'),
[dep.Input('univariate-selector', 'value')])
def update_autocorr(varname):
return autocorr_figure(trace, varname)
@app.callback(dep.Output('univariate-effective-n', 'children'),
[dep.Input('univariate-selector', 'value')])
def update_effective_n(varname):
return effective_n_p(trace, varname)
@app.callback(dep.Output('univariate-gelman-rubin', 'children'),
[dep.Input('univariate-selector', 'value')])
def update_gelman_rubin(varname):
return gelman_rubin_p(trace, varname)
@app.callback(dep.Output('univariate-hist', 'figure'),
[dep.Input('univariate-selector', 'value')])
def update_hist(varname):
return hist_figure(trace, varname)
@app.callback(dep.Output('univariate-lines', 'figure'),
[dep.Input('univariate-selector', 'value')])
def update_lines(varname):
return lines_figure(trace, varname)
def build_degroot_callbacks(app):
build_step_callback(app, id_degroot_slider_steps_value,
id_degroot_slider_steps, 'Steps')
build_init_callback(app, id_degroot_modal, id_degroot_modal_init_slider,
model_degroot['name'])
@app.callback(dp.Output('session-tracer-degroot', 'data'),
dp.Input(id_degroot_dropdown, 'value'))
def tracer_callback(value):
return [model_degroot['id'], value]
@app.callback(dp.Output('session-actions-degroot', 'data'),
dp.Input(id_degroot_button_random, 'n_clicks'),
dp.Input(id_degroot_button_stochastic, 'n_clicks'),
dp.Input(id_degroot_button_step, 'n_clicks'),
dp.Input(id_degroot_modal_generate, 'n_clicks'),
dp.State(id_degroot_modal_init_slider, 'value'),
dp.State(id_degroot_slider_steps, 'value'))
def callback(n1, n2, n3, n4, init, steps):
ctx = dash.callback_context
if not ctx.triggered: return []
source = ctx.triggered[0]['prop_id'].split('.')[0]
args = {'steps': steps, 'init': init}
ac = {
id_degroot_button_random: action_degroot_random,
id_degroot_button_stochastic: action_degroot_stochastic,
id_degroot_button_step: action_degroot_step,
id_degroot_modal_generate: action_degroot_init
}
if source in ac:
return [(model_degroot['id'], ac[source], args)]
print(
f'DeGroot callback: Could not find property with source: {source}')
raise PreventUpdate()
def tha_build_callbacks(app):
build_step_callback(app, id_tha_slider_steps_value, id_tha_slider_steps, 'Steps')
build_init_callback(app, id_tha_modal, id_tha_modal_init_slider, 'Threshold Automata')
@app.callback(
dp.Output(model_tha['session-tracer'], 'data'),
dp.Input(id_tha_dropdown, 'value'))
def tracer_callback(value):
return [model_tha['id'], value]
@app.callback(
dp.Output(model_tha['session-actions'], 'data'),
dp.Input(id_tha_button_random, 'n_clicks'),
dp.Input(id_tha_button_step, 'n_clicks'),
dp.Input(id_tha_modal_generate, 'n_clicks'),
dp.State(id_tha_modal_init_slider, 'value'),
dp.State(id_tha_slider_steps, 'value'))
def callback(n1, n2, n3, init, steps):
ctx = dash.callback_context
if not ctx.triggered: return []
source = ctx.triggered[0]['prop_id'].split('.')[0]
args = {'steps': steps, 'init': init}
ac = {
id_tha_button_random: action_tha_random,
id_tha_button_step: action_tha_step,
id_tha_modal_generate: action_tha_init,
}
if source in ac:
return [(model_tha['id'], ac[source], args)]
print(f'THA callback: Could not find property with source: {source}')
raise PreventUpdate()
def assign_callbacks(app: dash.Dash):
@app.callback(
[
dep.Output("known_index_bar", "figure"),
dep.Output("unknown_index_bar", "figure"),
dep.Output("known_unknown_pie", "figure"),
dep.Output("known_fraction", "value"),
],
[dep.Input("run_select", "value")],
)
def update_layout(run_alias):
"""
When input(run dropdown) is changed, known index bar, unknown index bar,
piechart and textarea are updated
Parameter:
run_alias: user-selected run name from dropdown
Returns:
functions update_known_index_bar, update_unknown_index_bar,
update_pie_chart's data value, and update_pie_chart's fraction value
"""
run = index[index[index_col.Run] == run_alias]
run = run[run[index_col.ReadNumber] == 1]
run = run[~run[index_col.SampleID].isna()]
run = run.drop_duplicates([index_col.SampleID, index_col.LaneNumber])
# TODO: Replace with join from Pinery (on Run, Lane, Index1, Index2)
# 10X index (SI-GA-H11) will have to be converted to nucleotide
run[COL_LIBRARY] = run[index_col.SampleID].str.extract(
r"SWID_\d+_(\w+_\d+_.*_\d+_[A-Z]{2})_"
)
run[COL_INDEX] = run[index_col.Index1].str.cat(
run[index_col.Index2].fillna(""), sep=" "
)
pruned = gsiqcetl.bcl2fastq.utility.prune_unknown_index_from_run(
run_alias, index, unknown
)
pruned[COL_INDEX] = pruned[un_col.Index1].str.cat(
pruned[un_col.Index2].fillna(""), sep=" "
)
pruned = pruned.sort_values(un_col.Count, ascending=False)
pruned = pruned.head(30)
total_clusters = gsiqcetl.bcl2fastq.utility.total_clusters_for_run(
run_alias, index
)
pie_data, textarea_fraction = create_pie_chart(
run, pruned, total_clusters
)
return (
create_known_index_bar(run),
create_unknown_index_bar(pruned),
pie_data,
textarea_fraction,
)
def register_app_callbacks(app: dash.Dash) -> None:
@app.callback(
ddp.Output("editor-euler-solution", "value"),
[ddp.Input("select-solution-number", "value")],
)
def populate_solution_code(name: str) -> str:
if not name:
return ""
module = sys.modules[__name__]
func: tp.Callable = getattr(module, name)
code: str = inspect.getsource(func)
seen: tp.List[str] = []
root: ast.Module = ast.parse(source=code)
for node in ast.walk(node=root):
if not isinstance(node, ast.Call):
continue
if not hasattr(node.func, 'value') or not hasattr(
node.func, 'attr'):
continue
if node.func.attr in seen:
continue
else:
seen.append(node.func.attr)
helper_module = getattr(module, node.func.value.id)
helper_func = getattr(helper_module, node.func.attr)
code += "\n"
code += inspect.getsource(helper_func)
return code
@app.callback(
ddp.Output("store-solution-profile", "data"),
[ddp.Input("button-solution-profile", "n_clicks")],
[ddp.State("select-solution-number", "value")],
)
def profile_solution(n_clicks: int, name: str) -> int:
if not name:
return {}
module = sys.modules[__name__]
func = getattr(module, name)
print(inspect.getsource(func))
with pi.Profiler() as profiler:
func()
profile_str = profiler.output(renderer=pi.renderers.JSONRenderer(
show_all=False))
profile_dict = json.loads(s=profile_str)
return profile_dict
@app.callback(
ddp.Output("graph-solution-profile", "figure"),
[ddp.Input("store-solution-profile", "data")],
)
def visualize_profile(data: dict) -> int:
if not data:
return {}
root_frame = data.pop("root_frame")
return {}
def build_init_callback(app, id_modal, slider_id, text):
@app.callback(dp.Output(f'{slider_id}-value', 'children'),
dp.Input(f'{slider_id}', 'value'))
def slider_update(value):
return f'{text} {value}'
@app.callback(dp.Output(f'modal-{id_modal}', 'is_open'),
dp.Input(f'modal-{id_modal}-open', 'n_clicks'),
dp.Input(f'modal-{id_modal}-close', 'n_clicks'),
dp.State(f'modal-{id_modal}', 'is_open'))
def toggle_modal_init(n1, n2, is_open):
if n1 or n2:
return not is_open
return is_open
def build_callbacks(app):
@app.callback(
[dd.Output(component_id='hyspec-fwhm_vs_Ei', component_property='figure'),
dd.Output(component_id='hyspec-flux_vs_Ei', component_property='figure'),
],
[dd.Input('hyspec_operation_mode', 'value'),
],
)
def update_figures(mode):
fwhm_data = getFWHM_vs_Ei(mode)
flux_data = getFlux_vs_Ei(mode)
return [
{
'data': fwhm_data,
'layout': dict(
title = 'Resolution vs incident energy',
showlegend=True,
xaxis=dict(
title='Ei (meV)',
type='log',
showspikes=True,
),
yaxis=dict(
title='FWHM (meV)',
type='log',
showspikes=True,
),
),
},
{
'data': flux_data,
'layout': dict(
title = 'Flux vs incident energy',
showlegend=True,
xaxis=dict(
title='Ei (meV)',
type='log',
showspikes=True,
),
yaxis=dict(
# title='Flux (counts/s/cm^2/MW)',
title='Flux (arb. unit)',
type='log',
showspikes=True,
),
),
},
]
return
def init_callbacks(app):
@app.callback(dd.Output('wordcloud', 'src'), dd.Input('wordcloud', 'id'),
dd.Input('wc_query', 'value'))
def make_image(b, query):
print(f"query : {query}")
img = BytesIO()
plot_wordcloud(data=df, query=query).save(img, format='PNG')
return 'data:image/png;base64,{}'.format(
base64.b64encode(img.getvalue()).decode())
@app.callback(dd.Output('distibution', 'figure'),
dd.Input('distribution_query', 'value'))
def distribution_selector(d_query='Pie Chart'):
print(f"d_query : {d_query}")
if (d_query == "Histogram"):
return histogram
return pie_chart
def apply(self, callbacks):
for callback in callbacks:
if len(callback[dd.Output]) == 0:
output_id = str(uuid.uuid4())
hidden_div = html.Div(id=output_id, style={"display": "none"})
callback[dd.Output] = [dd.Output(output_id, "children")]
self.hidden_divs.append(hidden_div)
return callbacks
def add_callbacks(app, trace):
add_include_transformed_callback(app, 'bivariate-x', trace)
add_include_transformed_callback(app, 'bivariate-y', trace)
@app.callback(dep.Output('bivariate-scatter', 'figure'), [
dep.Input('bivariate-x-selector', 'value'),
dep.Input('bivariate-y-selector', 'value')
])
def update_bivariate_scatter(x_varname, y_varname):
return scatter_figure(trace, x_varname, y_varname)
def sir_build_callbacks(app):
build_step_callback(app, id_sir_slider_steps_value, id_sir_slider_steps,
'Steps')
build_prob_callback(app, id_sir_slider_prob_value, id_sir_slider_prob)
build_infection_callback(app, id_sir_slider_itime_value,
id_sir_slider_itime)
build_init_callback(app, id_sir_modal, id_sir_modal_init_slider,
model_sir['name'])
@app.callback(dp.Output(model_sir['session-tracer'], 'data'),
dp.Input(id_sir_dropdown, 'value'))
def tracer_callback(value):
return [model_sir['id'], value]
@app.callback(
dp.Output(model_sir['session-actions'], 'data'),
dp.Input(id_sir_button_random, 'n_clicks'),
dp.Input(id_sir_button_step, 'n_clicks'),
dp.Input(id_sir_button_one, 'n_clicks'),
dp.Input(id_sir_modal_generate, 'n_clicks'),
dp.State(id_sir_modal_init_slider, 'value'),
dp.State(id_sir_slider_steps, 'value'),
dp.State(id_sir_slider_prob, 'value'),
dp.State(id_sir_slider_itime, 'value'),
)
def callback(n1, n2, n3, n4, init, steps, prob, itime):
ctx = dash.callback_context
if not ctx.triggered: return []
source = ctx.triggered[0]['prop_id'].split('.')[0]
args = {'steps': steps, 'prob': prob, 'itime': itime, 'init': init}
ac = {
id_sir_button_random: action_sir_random,
id_sir_button_step: action_sir_step,
id_sir_button_one: action_sir_one,
id_sir_modal_generate: action_sir_init
}
if source in ac:
return [(model_sir['id'], ac[source], args)]
print(f'SIR callback: Could not find property with source: {source}')
raise PreventUpdate()
def _assign_callbacks(self) -> None:
"""Assign callbacks to connect templated HTML with pipeline behavior"""
self.callback(ddep.Output('pipeline-cyto', 'layout'),
ddep.Input('dropdown-layout',
'value'))(callbacks.cast_layout_to_dict)
pipeline_callbacks = callbacks.PipelineStatus(
self._num_displayed_data_points, self._pipeline.connectors[0])
self.callback(ddep.Output('graph-queue-size', 'extendData'),
ddep.Input('interval', 'n_intervals'))(
pipeline_callbacks.get_queue_sizes)
system_callbacks = callbacks.SystemUsage(
self._num_displayed_data_points)
self.callback(ddep.Output('graph-cpu-usage', 'extendData'),
ddep.Input('interval', 'n_intervals'))(
system_callbacks.get_cpu_usage)
self.callback(ddep.Output('graph-mem-usage', 'extendData'),
ddep.Input('interval', 'n_intervals'))(
system_callbacks.get_memory_usage)
def add_callbacks(app, trace):
bivariate_layout = bivariate.layout(trace)
univariate_layout = univariate.layout(trace)
@app.callback(dep.Output('page-content', 'children'),
[dep.Input('url', 'pathname')])
def update_page_content(pathname):
if pathname in ['/', '/univariate']:
return univariate_layout
elif pathname == '/bivariate':
return bivariate_layout
bivariate.add_callbacks(app, trace)
univariate.add_callbacks(app, trace)
def build_callbacks(app):
@app.callback(
[
dd.Output(component_id='arcs-flux_vs_fwhm',
component_property='figure'),
],
[
dd.Input('Ei_select', 'value'),
],
)
def update_figure(Ei):
Ei = float(Ei)
data = [
getFlux_vs_FWHMdata(fc1data, Ei, 'ARCS-700-1.5'),
getFlux_vs_FWHMdata(fc2data, Ei, 'ARCS-100-1.5'),
getFlux_vs_FWHMdata(fc1_highres_data, Ei, 'ARCS-700-0.5'),
]
return {
'data':
data,
'layout':
dict(
title='Flux vs resolution',
showlegend=True,
xaxis=dict(
title='FWHM (meV)',
showspikes=True,
),
yaxis=dict(
title='Flux (counts/s/cm^2/MW)',
showspikes=True,
),
),
},
return
def build_prob_callback(app, id_value, id_slider):
@app.callback(dp.Output(id_value, 'children'),
dp.Input(id_slider, 'value'))
def slider_update(value):
return f'Probability {value}'
]),
dcc.Markdown('Apparently, you can inline a dcc.Component by listing it '
'as a child in the list of children of a html container'),
],
}
#-- 3 interaction
# subscribe to all possible triggers, even though they donot exist all
# at the same time (qresponse has either a values or a value trigger,
# but not both). This requires to disable the callback exceptions in app.config
# register answer with current question before setting new question idx
@app.callback(
dd.Output('page-content', 'children'),
[dd.Input('select-qtype', 'value')])
def setPageContent(value):
'show the new question'
# Notes:
qstn = QTYPE.get(value, value)
return qstn
@app.callback(
dd.Output('response-output', 'children'),
[dd.Input('response', 'value'),
dd.Input('response', 'values')])
def setResponseOutput(*kids):
k1 = '{}'.format(kids[0])
k2 = '{}'.format(repr(kids[1]))
return html.Div([
def add_include_transformed_callback(app, title, trace):
@app.callback(
dep.Output('{}-selector'.format(title), 'options'),
[dep.Input('{}-selector-include-transformed'.format(title), 'values')])
def update_selector_transformed(values):
return get_varname_options(trace, include_transformed=values)
},
],
values=['opt-random-q', 'opt-random-a'],
style={'display': 'block'},
labelStyle={'display': 'block'},
)
]),
]),
html.Div(className='eight columns',
id=DISPLAY,
children=['loading ...']),
])
# -- Page controls
@app.callback(dd.Output(CONTROLS, 'children'), [
dd.Input(ID('mode'), 'value'),
dd.Input(ID('max'), 'value'),
dd.Input(ID('options'), 'values'),
dd.Input(ID('limit-maxq'), 'values'),
dd.Input(ID('limit-time'), 'values'),
dd.Input(ID('max-time'), 'value'),
])
def controls(mode, maxq, options, limit_maxq, limit_time, max_time):
'store page state in cache and controls for revisits'
controls = json.dumps([
(ID('mode'), 'value', mode),
(ID('max'), 'value', maxq),
(ID('options'), 'values', options),
(ID('limit-maxq'), 'values', limit_maxq),
(ID('limit-time'), 'values', limit_time),
"x": curve[0],
"y": curve[1],
"marker_color": discrete_color_sequence[0]
}
],
layout={
"xaxis": dict(title="False Positive Rate"),
"yaxis": dict(title="True Positive Rate"),
"plot_bgcolor": bg_color,
"paper_bgcolor": bg_color,
}
)
@app.callback(
dependencies.Output("lr-feature-importance", "figure"),
[dependencies.Input("lr-importance-slider", "value")]
)
def update_lr_importance(n_features):
def get_transformer_feature_names(column_transformer):
"""Most important features from a pipeline."""
output_features = []
for name, pipe, features in column_transformer.transformers_:
if name != 'remainder':
for i in pipe:
trans_features = []
if hasattr(i, 'categories_'):
trans_features.extend(i.get_feature_names(features))
else:
trans_features = features
output_features.extend(trans_features)
def main():
usage = 'usage: %prog [options] <sad_hdf5_path>'
parser = OptionParser(usage)
parser.add_option(
'-c',
dest='chrom_hdf5',
default=False,
action='store_true',
help='HDF5 files split by chromosome [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 1:
parser.error('Must provide SAD HDF5')
else:
sad_hdf5_file = args[0]
#############################################
# precursors
print('Preparing data.', flush=True)
chr_sad_h5_open = {}
if not options.chrom_hdf5:
# open HDF5
sad_h5_open = h5py.File(sad_hdf5_file, 'r')
# with one file, hash to a fake chromosome
chr_sad_h5_open = {1: sad_h5_open}
# hash SNP ids to indexes
snps = np.array(sad_h5_open['snp'])
snp_indexes = {}
for i, snp_id in enumerate(snps):
snp_id = snp_id.decode('UTF-8')
snp_indexes[snp_id] = (1, i)
del snps
else:
snp_indexes = {}
for ci in range(1, 6):
# open HDF5
sad_h5_open = h5py.File('%s/chr%d/sad.h5' % (sad_hdf5_file, ci),
'r')
# with one file, hash to a fake chromosome
chr_sad_h5_open[ci] = sad_h5_open
# hash SNP ids to indexes
snps = np.array(sad_h5_open['snp'])
for i, snp_id in enumerate(snps):
snp_id = snp_id.decode('UTF-8')
snp_indexes[snp_id] = (ci, i)
del snps
# open chr1 HDF5 for non-chr specific data
sad_h5_open = chr_sad_h5_open[1]
# easy access to target information
target_ids = np.array(
[tl.decode('UTF-8') for tl in sad_h5_open['target_ids']])
target_labels = np.array(
[tl.decode('UTF-8') for tl in sad_h5_open['target_labels']])
# read SAD percentile indexes into memory
sad_pct = np.array(sad_h5_open['SAD_pct'])
# read percentiles
percentiles = np.around(sad_h5_open['percentiles'], 3)
percentiles = np.append(percentiles, percentiles[-1])
# initialize BigQuery client
# client = bigquery.Client('seqnn-170614')
pop_emerald = {
'EUR': '%s/popgen/1000G/phase3/eur/1000G.EUR.QC' % os.environ['HG19']
}
pop_emerald = {}
for pop in ['EUR']:
pop_vcf_stem = '%s/popgen/1000G/phase3/%s/1000G.%s.QC' % (
os.environ['HG19'], pop.lower(), pop)
pop_emerald[pop] = EmeraldVCF(pop_vcf_stem)
print('Done.', flush=True)
#############################################
# layout
app = dash.Dash()
app.css.append_css(
{"external_url": "https://codepen.io/chriddyp/pen/bWLwgP.css"})
app.layout = html.Div([
html.Div(
[
html.H1('Basenji SNP activity difference'),
dcc.Markdown('Instructions...'),
html.Div([
html.Label('Datasets'),
dcc.Dropdown(id='dataset',
options=[{
'label': 'CAGE',
'value': 'CAGE'
}, {
'label': 'DNase',
'value': 'DNASE'
}, {
'label': 'H3K4me3',
'value': 'CHIP:H3K4me3'
}, {
'label': 'All',
'value': 'All'
}],
value='CAGE')
],
style={
'width': '250',
'display': 'inline-block'
}),
html.Div([
html.Label('Population'),
dcc.Dropdown(id='population',
options=[{
'label': '-',
'value': '-'
}, {
'label': '1kG African',
'value': 'AFR'
}, {
'label': '1kG American',
'value': 'AMR'
}, {
'label': '1kG East Asian',
'value': 'EAS'
}, {
'label': '1kG European',
'value': 'EUR'
}, {
'label': '1kG South Asian',
'value': 'SAS'
}],
value='-')
],
style={
'width': '250',
'display': 'inline-block'
}),
html.Div([
html.Label('SNP ID'),
dcc.Input(id='snp_id', value='rs2157719', type='text'),
html.Button(id='snp_submit', n_clicks=0, children='Submit')
],
style={
'display': 'inline-block',
'float': 'right'
})
],
style={
'borderBottom': 'thin lightgrey solid',
'backgroundColor': 'rgb(250, 250, 250)',
'padding': '10px 5px'
}),
dcc.Graph(id='assoc_plot'),
html.Div([
dt.DataTable(id='table',
rows=[],
columns=[
'SNP', 'Association', 'Score', 'ScoreQ', 'R2',
'Experiment', 'Description'
],
column_widths=[150, 125, 125, 125, 125, 200],
editable=False,
filterable=True,
sortable=True,
resizable=True,
sortColumn='Association',
row_selectable=True,
selected_row_indices=[],
max_rows_in_viewport=20)
])
])
#############################################
# callback helpers
@memoized
def query_ld_bq(snp_id, population):
"""Query Google Genomics 1000 Genomes LD table for the given SNP."""
bq_path = 'genomics-public-data.linkage_disequilibrium_1000G_phase_3'
# construct query
query = 'SELECT tname, corr'
query += ' FROM `%s.super_pop_%s`' % (bq_path, population)
query += ' WHERE qname = "%s"' % snp_id
# run query
print('Running a BigQuery!', file=sys.stderr)
query_results = client.query(query)
return query_results
@memoized
def query_ld(population, snp_id):
if population not in pop_emerald:
print('Population unavailable.', file=sys.stderr)
return pd.DataFrame()
else:
chrm, snp_i = snp_indexes.get(snp_id, (None, None))
pos = sad_h5_open['pos'][snp_i]
if chrm is None:
return pd.DataFrame()
else:
return pop_emerald[population].query_ld(snp_id,
chrm,
pos,
ld_threshold=0.333)
@memoized
def read_pos(chrom, snp_i):
return chr_sad_h5_open[chrom]['pos'][snp_i]
@memoized
def read_sad(chrom, snp_i, verbose=True):
"""Read SAD scores from HDF5 for the given SNP index."""
if verbose:
print('Reading SAD!', file=sys.stderr)
# read SAD
snp_sad = chr_sad_h5_open[chrom]['SAD'][snp_i, :].astype('float64')
# compute percentile indexes
snp_sadq = []
for ti in range(len(snp_sad)):
snp_sadq.append(int(np.searchsorted(sad_pct[ti], snp_sad[ti])))
return snp_sad, snp_sadq
def snp_rows(snp_id, dataset, ld_r2=1., verbose=True):
"""Construct table rows for the given SNP id and its LD set
in the given dataset."""
rows = []
# search for SNP
chrom, snp_i = snp_indexes.get(snp_id, (None, None))
if chrom is not None:
# SAD
snp_sad, snp_sadq = read_sad(chrom, snp_i)
# round floats
snp_sad = np.around(snp_sad, 4)
snp_assoc = np.around(snp_sad * ld_r2, 4)
ld_r2_round = np.around(ld_r2, 4)
# extract target scores and info
for ti, tid in enumerate(target_ids):
if dataset == 'All' or target_labels[ti].startswith(dataset):
rows.append({
'SNP': snp_id,
'Association': snp_assoc[ti],
'Score': snp_sad[ti],
'ScoreQ': percentiles[snp_sadq[ti]],
'R2': ld_r2_round,
'Experiment': tid,
'Description': target_labels[ti]
})
elif verbose:
print('Cannot find %s in snp_indexes.' % snp_id)
return rows
def make_data_mask(dataset):
"""Make a mask across targets for the given dataset."""
dataset_mask = []
for ti, tid in enumerate(target_ids):
if dataset == 'All':
dataset_mask.append(True)
else:
dataset_mask.append(target_labels[ti].startswith(dataset))
return np.array(dataset_mask, dtype='bool')
def snp_scores(snp_id, dataset, ld_r2=1.):
"""Compute an array of scores for this SNP
in the specified dataset."""
dataset_mask = make_data_mask(dataset)
scores = np.zeros(dataset_mask.sum(), dtype='float64')
# search for SNP
if snp_id in snp_indexes:
chrom, snp_i = snp_indexes[snp_id]
# read SAD
snp_sad, _ = read_sad(chrom, snp_i)
# filter datasets
snp_sad = snp_sad[dataset_mask]
# add
scores += snp_sad * ld_r2
return scores
#############################################
# callbacks
@app.callback(dd.Output('table', 'rows'),
[dd.Input('snp_submit', 'n_clicks')], [
dd.State('snp_id', 'value'),
dd.State('dataset', 'value'),
dd.State('population', 'value')
])
def update_table(n_clicks, snp_id, dataset, population, verbose=True):
"""Update the table with a new parameter set."""
if verbose:
print('Tabling')
# add snp_id rows
rows = snp_rows(snp_id, dataset)
if population != '-':
# query_results = query_ld(snp_id, population)
# for ld_snp, ld_corr in query_results:
# rows += snp_rows(ld_snp, dataset, ld_corr)
df_ld = query_ld(population, snp_id)
for i, v in df_ld.iterrows():
rows += snp_rows(v.snp, dataset, v.r)
return rows
@app.callback(dd.Output('assoc_plot', 'figure'),
[dd.Input('snp_submit', 'n_clicks')], [
dd.State('snp_id', 'value'),
dd.State('dataset', 'value'),
dd.State('population', 'value')
])
def update_plot(n_clicks, snp_id, dataset, population, verbose=True):
if verbose:
print('Plotting')
target_mask = make_data_mask(dataset)
# add snp_id rows
query_scores = snp_scores(snp_id, dataset)
if population != '-':
# query_results = query_ld(snp_id, population)
# for ld_snp, ld_corr in query_results:
# query_scores += snp_scores(ld_snp, dataset, ld_corr)
df_ld = query_ld(population, snp_id)
for i, v in df_ld.iterrows():
query_scores += snp_scores(v.snp, dataset, v.r)
# sort
sorted_indexes = np.argsort(query_scores)
# range
ymax = np.abs(query_scores).max()
ymax *= 1.2
return {
'data': [
go.Scatter(x=np.arange(len(query_scores)),
y=query_scores[sorted_indexes],
text=target_ids[target_mask][sorted_indexes],
mode='markers')
],
'layout': {
'height': 400,
'margin': {
'l': 20,
'b': 30,
'r': 10,
't': 10
},
'yaxis': {
'range': [-ymax, ymax]
},
'xaxis': {
'range': [-1, 1 + len(query_scores)]
}
}
}
#############################################
# run
app.scripts.config.serve_locally = True
app.run_server(debug=False, port=8787)
# %% CALLBACKS
### These essentially control the interactions in the apps:
# Originally this was broken into lots of sub-callbacks but now we only have 2
# This probably uses marginally more processing time, but really simplifies stuff
# 1. Store selected stack as a dict() in a dcc.Store()
# 2. MEGA-CALLBACK - which does all the processing
# 3. Loci-image callback(s) UNRELATED to functioning of the game
### Setup Stack (Store & Table)
# Source df of stack from stack2df function using the name from the dropdown
# Convert to dict() twice in output; 1. for dcc.Store() and 2. for dash_table
# on dash_table need to convert with 'records' so need to do this op twice
@app.callback(
[dd.Output('stack_store', 'data'),
dd.Output('stack_table', 'data')], [dd.Input('dropdown_stack', 'value')])
def stack2store(stack):
#df = stack2df(stack=stack)
df = pd.DataFrame(stacks[stack], columns=['posn', 'card', 'loci', 'image'])
return df.to_dict(), df.to_dict('records')
### MEGA-CALLBACK OF DOOM
# An issue with Dash is a dd.Output(X) can only be triggered in 1 callback
# This is a pain for eg when we want to re-load a problem via a "reload" button
# or after the user submits their solution; we try & fix with the MEGA CALLBACK
## Helper functions
def _problem_setup(df, pType):
def main():
usage = 'usage: %prog [options] <sad_hdf5_path>'
parser = OptionParser(usage)
parser.add_option(
'-c',
dest='chrom_hdf5',
default=False,
action='store_true',
help='HDF5 files split by chromosome [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 1:
parser.error('Must provide SAD HDF5')
else:
sad_h5_path = args[0]
#############################################
# precursors
print('Preparing data...', end='', flush=True)
sad5 = ChrSAD5(sad_h5_path, index_chr=True)
print('DONE.', flush=True)
#############################################
# layout
column_widths = [('SNP', 150), ('Association', 125), ('Score', 125),
('ScoreQ', 125), ('R', 125), ('Experiment', 125),
('Description', 200)]
scc = [{
'if': {
'column_id': cw[0]
},
'width': cw[1]
} for cw in column_widths]
app = dash.Dash(__name__)
app.css.append_css(
{"external_url": "https://codepen.io/chriddyp/pen/bWLwgP.css"})
app.layout = html.Div([
html.Div(
[
html.H1('Basenji SNP activity difference'),
dcc.Markdown('Instructions...'),
html.Div([
html.Label('Datasets'),
dcc.Dropdown(id='dataset',
options=[{
'label': 'CAGE',
'value': 'CAGE'
}, {
'label': 'DNase',
'value': 'DNASE'
}, {
'label': 'H3K4me3',
'value': 'CHIP:H3K4me3'
}, {
'label': 'All',
'value': 'All'
}],
value='CAGE')
],
style={
'width': '250',
'display': 'inline-block'
}),
html.Div([
html.Label('Population'),
dcc.Dropdown(id='population',
options=[{
'label': '-',
'value': '-'
}, {
'label': '1kG African',
'value': 'AFR'
}, {
'label': '1kG American',
'value': 'AMR'
}, {
'label': '1kG East Asian',
'value': 'EAS'
}, {
'label': '1kG European',
'value': 'EUR'
}, {
'label': '1kG South Asian',
'value': 'SAS'
}],
value='-')
],
style={
'width': '250',
'display': 'inline-block'
}),
html.Div([
html.Label('SNP ID'),
dcc.Input(id='snp_id', value='rs6656401', type='text'),
html.Button(id='snp_submit', n_clicks=0, children='Submit')
],
style={
'display': 'inline-block',
'float': 'right'
})
],
style={
'borderBottom': 'thin lightgrey solid',
'backgroundColor': 'rgb(250, 250, 250)',
'padding': '10px 5px'
}),
dcc.Graph(id='assoc_plot'),
html.Div([
dt.DataTable(id='table',
data=[],
columns=[{
'id': cw[0],
'name': cw[0]
} for cw in column_widths],
style_cell_conditional=scc,
editable=False,
filtering=True,
sorting=True,
n_fixed_rows=20)
])
])
# html.Div([
# dt.DataTable(
# id='table',
# data=[],
# columns=[cw[0] for cw in column_widths],
# style_cell_conditional=scc,
# editable=False,
# filtering=True,
# sorting=True,
# n_fixed_rows=20
# )
#############################################
# callback helpers
@memoized
def query_ld(population, snp_id):
try:
sad5.set_population(population)
except ValueError:
print('Population unavailable.', file=sys.stderr)
return pd.DataFrame()
chrm, snp_i = sad5.snp_chr_index(snp_id)
pos = sad5.snp_pos(snp_i, chrm)
if chrm is None:
return pd.DataFrame()
else:
return sad5.emerald_vcf.query_ld(snp_id,
chrm,
pos,
ld_threshold=0.8)
@memoized
def read_sad(chrm, snp_i, verbose=True):
"""Read SAD scores from HDF5 for the given SNP index."""
if verbose:
print('Reading SAD!', file=sys.stderr)
# read SAD
snp_sad = sad5.chr_sad5[chrm][snp_i].astype('float64')
# read percentiles
snp_pct = sad5.chr_sad5[chrm].sad_pct(snp_sad)
return snp_sad, snp_pct
def snp_rows(snp_id, dataset, ld_r2=1., verbose=True):
"""Construct table rows for the given SNP id and its LD set
in the given dataset."""
rows = []
# search for SNP
# chrom, snp_i = snp_indexes.get(snp_id, (None,None))
chrm, snp_i = sad5.snp_chr_index(snp_id)
if chrm is not None:
# SAD
snp_sad, snp_pct = read_sad(chrm, snp_i)
# round floats
snp_sad = np.around(snp_sad, 4)
snp_assoc = np.around(snp_sad * ld_r2, 4)
ld_r2_round = np.around(ld_r2, 4)
# extract target scores and info
for ti, tid in enumerate(sad5.target_ids):
if dataset == 'All' or sad5.target_labels[ti].startswith(
dataset):
rows.append({
'SNP': snp_id,
'Association': snp_assoc[ti],
'Score': snp_sad[ti],
'ScoreQ': snp_pct[ti],
'R': ld_r2_round,
'Experiment': tid,
'Description': sad5.target_labels[ti]
})
elif verbose:
print('Cannot find %s in snp_indexes.' % snp_id)
return rows
def make_data_mask(dataset):
"""Make a mask across targets for the given dataset."""
dataset_mask = []
for ti, tid in enumerate(sad5.target_ids):
if dataset == 'All':
dataset_mask.append(True)
else:
dataset_mask.append(sad5.target_labels[ti].startswith(dataset))
return np.array(dataset_mask, dtype='bool')
def snp_scores(snp_id, dataset, ld_r2=1.):
"""Compute an array of scores for this SNP
in the specified dataset."""
dataset_mask = make_data_mask(dataset)
scores = np.zeros(dataset_mask.sum(), dtype='float64')
# search for SNP
chrm, snp_i = sad5.snp_chr_index(snp_id)
if snp_i is not None:
# read SAD
snp_sad, _ = read_sad(chrm, snp_i)
# filter datasets
snp_sad = snp_sad[dataset_mask]
# add
scores += snp_sad * ld_r2
return scores
#############################################
# callbacks
@app.callback(dd.Output('table', 'data'),
[dd.Input('snp_submit', 'n_clicks')], [
dd.State('snp_id', 'value'),
dd.State('dataset', 'value'),
dd.State('population', 'value')
])
def update_table(n_clicks, snp_id, dataset, population, verbose=True):
"""Update the table with a new parameter set."""
if verbose:
print('Tabling')
# add snp_id rows
rows = snp_rows(snp_id, dataset)
if population != '-':
df_ld = query_ld(population, snp_id)
for i, v in df_ld.iterrows():
rows += snp_rows(v.snp, dataset, v.r)
return rows
@app.callback(dd.Output('assoc_plot', 'figure'),
[dd.Input('snp_submit', 'n_clicks')], [
dd.State('snp_id', 'value'),
dd.State('dataset', 'value'),
dd.State('population', 'value')
])
def update_plot(n_clicks, snp_id, dataset, population, verbose=True):
if verbose:
print('Plotting')
target_mask = make_data_mask(dataset)
# add snp_id rows
query_scores = snp_scores(snp_id, dataset)
if population != '-':
df_ld = query_ld(population, snp_id)
for i, v in df_ld.iterrows():
query_scores += snp_scores(v.snp, dataset, v.r)
# sort
sorted_indexes = np.argsort(query_scores)
# range
ymax = np.abs(query_scores).max()
ymax *= 1.2
return {
'data': [
go.Scatter(x=np.arange(len(query_scores)),
y=query_scores[sorted_indexes],
text=sad5.target_ids[target_mask][sorted_indexes],
mode='markers')
],
'layout': {
'height': 400,
'margin': {
'l': 20,
'b': 30,
'r': 10,
't': 10
},
'yaxis': {
'range': [-ymax, ymax]
},
'xaxis': {
'range': [-1, 1 + len(query_scores)]
}
}
}
#############################################
# run
app.scripts.config.serve_locally = True
app.run_server(debug=False, port=8787)
def build_infection_callback(app, id_value, id_slider):
@app.callback(dp.Output(id_value, 'children'),
dp.Input(id_slider, 'value'))
def slider_update(value):
return f'Infection Time {value}'
def plot_wordcloud(data):
d = data
wc = WordCloud(
background_color='white',
font_path="/usr/share/fonts/truetype/msttcorefonts/times.ttf",
max_words=2000,
mask=mask,
width=1024,
height=1024,
max_font_size=90,
min_font_size=5,
mode='RGBA')
wc.fit_words(d)
wc.recolor(color_func=image_colors)
return wc.to_image()
@app.callback(dd.Output('image_wc', 'src'), [dd.Input('image_wc', 'id')])
def make_image(b):
img = BytesIO()
plot_wordcloud(data=freqs).save(img, format='PNG')
return 'data:image/png;base64,{}'.format(
base64.b64encode(img.getvalue()).decode())
if __name__ == '__main__':
app.run_server(debug=True)
from dash import dependencies as dd
from dash.exceptions import PreventUpdate
from cars.analysis import etl as etl
from .. import DashOptions, opts_from_vals
from ..layout import INPID_MAX_DIST, INPID_STATE, INPID_ZIPCODE
from . import deferred_callback
@deferred_callback(
dd.Output(INPID_STATE, "options"),
[dd.Input(INPID_ZIPCODE, "value"),
dd.Input(INPID_MAX_DIST, "value")],
)
def populate_state_options(zipcode: str, max_miles: int) -> list[DashOptions]:
"""
Generates the state refinement menu.
"""
if zipcode not in etl.LATLONG_BY_ZIP:
raise PreventUpdate
return opts_from_vals(
state.upper() for state in etl.get_states_in_range(zipcode, max_miles))
__all__ = ["populate_state_options"]
ERR_BAD_ZIP = "bad_zip"
ERR_NO_ZIP = "err_no_zip"
ERR_NO_DEALERS = "err_no_dealers"
dcc.Dropdown(id='database-name',
options=ml.dropdown_get_all_database(dbclient),
value='Database Name'),
html.Div('Table Name'),
dcc.Dropdown(id='table-name',
options=[{
'value': 'Table',
'label': 'Table'
}],
value='Table Name'),
html.Div(id='my-table')
])
@dash_app1.callback(
depend.Output(component_id='table-name', component_property='options'),
[depend.Input(component_id='database-name', component_property='value')])
def update_table_name(database):
try:
df = ml.dropdown_get_all_table(dbclient, database)
return df
except:
return html.Div('Invalid table')
@dash_app1.callback(
depend.Output(component_id='my-table', component_property='children'), [
depend.Input(component_id='database-name', component_property='value'),
depend.Input(component_id='table-name', component_property='value'),
])
def update_output_div(database, table):
def build_callbacks(app):
@app.callback(
[
dd.Output(component_id='cncs-fwhm_vs_Ei',
component_property='figure'),
dd.Output(component_id='cncs-flux_vs_Ei',
component_property='figure'),
],
[
dd.Input('cncs_chopper_mode', 'value'),
],
)
def update_figures(chopper):
if chopper == 'all':
fwhm_data = sum(
[getFWHM_vs_Ei(chopper) for chopper in chopper_modes], [])
flux_data = sum(
[getFlux_vs_Ei(chopper) for chopper in chopper_modes], [])
else:
fwhm_data = getFWHM_vs_Ei(chopper)
flux_data = getFlux_vs_Ei(chopper)
return [
{
'data':
fwhm_data,
'layout':
dict(
title='Resolution vs incident energy',
showlegend=True,
xaxis=dict(
title='Ei (meV)',
type='log',
showspikes=True,
),
yaxis=dict(
title='FWHM (meV)',
type='log',
showspikes=True,
),
),
},
{
'data':
flux_data,
'layout':
dict(
title='Flux vs incident energy',
showlegend=True,
xaxis=dict(
title='Ei (meV)',
type='log',
showspikes=True,
),
yaxis=dict(
title='Flux (counts/s/cm^2/MW)',
type='log',
showspikes=True,
),
),
},
]
return
app.css.append_css({"external_url": "/css/my.css"})
app.css.append_css(
{"external_url": "https://codepen.io/chriddyp/pen/bWLwgP.css"})
#app.css.append_css({'external_url': 'https://cdn.rawgit.com/plotly/dash-app-stylesheets/2d266c578d2a6e8850ebce48fdb52759b2aef506/stylesheet-oil-and-gas.css'}) # noqa: E501
app.layout = html.Div(children=[
html.Div([html.Button(id='button', n_clicks=0, children='STARTING...')],
style={'color': 'white'}),
html.Div([dcc.Graph(id='graph_one', figure={})],
style={'display': 'inline-block'}),
dcc.Interval(id='live-update', interval=1000),
],
style={'background-color': "#F0F0F0"})
@app.callback(dep.Output('graph_one',
'figure'), [], [dep.State('graph_one', 'figure')],
[dep.Event('live-update', 'interval')])
def do_plot(figure):
df = pd.read_csv('/tmp/mon.csv')
plt_w = uj2w(df.time, df.cpu_uj)
sys_w = uj2w(df.time, df.sys_uj) * 2
t = df.time - df.time[0]
y_data = (
df.v0 / 1e6,
df.v1 / 1e6,
df.i0 / 1e6,
df.i1 / 1e6,
df.i0 * df.v0 / 1e12,
def get_all_msg_dataframe(session_id, data):
@ cache.memoize()
def calculate_all_msg_dataframe(session_id, data):
print('starting all msg 2')
list_of_dfs = [msg_fx.get_msg_df(msg_dict) for msg_dict in data["Messages"]]
print("Working on msg df "+ str(datetime.datetime.now()))
all_msg_df = pd.concat(list_of_dfs, axis=0, sort=True)
all_msg_df['date'] = all_msg_df['sent_date'].dt.date
print('error in json')
return(all_msg_df.reset_index().to_json())
return(pd.read_json(calculate_all_msg_dataframe(session_id, data)))
@app.callback([
dd.Output('usage_hidden', 'children'),
dd.Output('all_msg_hidden', 'children')
],
[dd.Input('upload-data', 'contents', ),
dd.Input('upload-data', 'filename'),
dd.Input('session-id', 'children')])
def open_file(data, filename, session_id):
print("started open file " + str(datetime.datetime.now()))
if data is not None:
content_type, content_string = data.split(',')
if '.json' in filename:
ret_val = base64.b64decode(content_string)
data = json.load(io.BytesIO(ret_val))
else:
return(html.H1(children='File not a json'))
def register_app_callbacks(app:dash.Dash) -> None:
@app.callback(
ddp.Output("rubik-button-reset", "n_clicks"),
[ddp.Input("tabs-projects", "value")],
[ddp.State("rubik-button-reset", "n_clicks")],
)
def click_reset(tab:str, n_clicks:int) -> int:
if tab != "rubik" or n_clicks > 0:
raise dex.PreventUpdate
return n_clicks + 1
@app.callback(
[
ddp.Output("rubik-select-layer", "options"),
ddp.Output("rubik-select-layer", "value"),
ddp.Output("rubik-store-state", "data"),
ddp.Output("rubik-table-history", "data"),
],
[
ddp.Input("rubik-button-clear", "n_clicks"),
ddp.Input("rubik-button-reset", "n_clicks"),
ddp.Input("rubik-button-scramble", "n_clicks"),
ddp.Input("rubik-button-solve", "n_clicks"),
ddp.Input("rubik-graph-state", "clickData"),
ddp.Input("rubik-table-history", "rowClicked"),
ddp.Input("rubik-select-dim", "value"),
],
[
ddp.State("rubik-select-layer", "value"),
ddp.State("rubik-select-scramble", "value"),
ddp.State("rubik-store-state", "data"),
ddp.State("rubik-table-history", "data"),
],
)
def set_cube_state(*args:list) -> tp.Tuple[object, ...]:
trigger = dash.callback_context.triggered[0]
if not trigger["value"] or trigger["prop_id"].endswith("clear.n_clicks"):
# Clear cube.
return constants.EMPTY_OPTIONS, "", [], [],
# Unpack arguments and enforce data types.
*_, dim, layer, scramble, state, history = args
dim = int(dim)
layer = int(layer) if layer else 1
scramble = int(scramble)
options = [
{"label":f"Rotate {hu.ordinal(layer)} layer", "value":layer}
for layer in range(1, 1+dim)
]
layer = min(layer, dim)
if trigger["prop_id"].endswith("reset.n_clicks") or trigger["prop_id"].endswith("dim.value"):
# Load new cube.
cube = RubiksCube(dim=dim, state=None)
return options, layer, cube.get_state(), []
if trigger["prop_id"].endswith("history.rowClicked"):
# Revert cube.
i = trigger["value"]["i"]
history = [move for move in history if move["i"]<i]
cube = RubiksCube(dim=dim, state=None)
rotations = [move["move"] for move in history]
cube.rotate(rotations=rotations)
return options, layer, cube.get_state(), history
cube = RubiksCube(dim=dim, state=state)
if trigger["prop_id"].endswith("scramble.n_clicks"):
# Scramble cube.
rotations = cube.scramble(n=scramble)
if trigger["prop_id"].endswith("solve.n_clicks"):
# Solve cube.
rotations = cube.solve()
if trigger["prop_id"].endswith("state.clickData"):
# Rotate face of cube.
faces, axes = zip(*RubiksCube._face_axes.items())
point = trigger["value"]["points"][0]
coord = {axis:point[axis] for axis in ["x", "y", "z"]}
axis = max(coord.keys(), key=lambda axis:abs(coord[axis]))
axis += "+" if coord[axis]>0 else "-"
face = list(faces)[list(axes).index(axis)]
rotations = f"{layer}{face}"
rotations = cube.rotate(rotations=rotations)
n = len(history)
history.extend({"move":rotation, "i":n+i} for i, rotation in enumerate(rotations))
return options, layer, cube.get_state(), history
@app.callback(
ddp.Output("rubik-graph-state", "figure"),
[ddp.Input("rubik-store-state", "data")],
[ddp.State("rubik-select-dim", "value")],
)
def graph_cube_state(state:list, dim:str) -> dict:
if not state:
return empty_cube_figure
dim = int(dim)
cube = RubiksCube(dim=dim, state=state)
figure = cube.get_figure()
for trace in figure["data"]:
# Disable hover information.
trace.update({
"hoverinfo":"none" if trace["type"]=="mesh3d" else "skip",
"hovertemplate":"",
"name":None,
})
figure["layout"].update({
**empty_cube_figure["layout"],
# Remove center annotation.
"annotations":empty_cube_figure["layout"]["annotations"][1:],
})
return figure
@app.callback(
[
ddp.Output("rubik-button-scramble", "disabled"),
ddp.Output("rubik-button-solve", "disabled"),
],
[ddp.Input("rubik-store-state", "data")],
[ddp.State("rubik-select-dim", "value")],
)
def disable_buttons(state:tp.List[str], dim:str) -> tp.Tuple[bool, bool]:
if not state or not dim:
return True, True
if int(dim) not in RubiksCube._solvable_dims:
return False, True
return False, False