arg-dashboard 0.1.19__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- arg_dashboard/__init__.py +934 -0
- arg_dashboard/arg.py +1019 -0
- arg_dashboard/arg_layout_force.py +365 -0
- arg_dashboard/arg_layout_json.py +269 -0
- arg_dashboard/arg_layout_mindist.py +412 -0
- arg_dashboard/assets/dashboard.css +139 -0
- arg_dashboard/assets/images/arg.png +0 -0
- arg_dashboard/assets/images/placeholder286x180.png +0 -0
- arg_dashboard/assets/tabs.css +34 -0
- arg_dashboard/index.py +6 -0
- arg_dashboard-0.1.19.dist-info/METADATA +88 -0
- arg_dashboard-0.1.19.dist-info/RECORD +16 -0
- arg_dashboard-0.1.19.dist-info/WHEEL +5 -0
- arg_dashboard-0.1.19.dist-info/entry_points.txt +2 -0
- arg_dashboard-0.1.19.dist-info/licenses/LICENSE +674 -0
- arg_dashboard-0.1.19.dist-info/top_level.txt +1 -0
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import logging
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logging.basicConfig(level=logging.INFO)
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from ast import Import
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import plotly.graph_objects as go
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import json
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from textwrap import dedent as d
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import dash
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from dash import dcc
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from dash import html
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from dash.dependencies import Input, Output, State
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import dash_bootstrap_components as dbc
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import math
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import sys
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import logging
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#from app import app
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# external_stylesheets = ['https://codepen.io/chriddyp/pen/bWLwgP.css']
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# external_stylesheets = [dbc.themes.GRID]
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external_stylesheets = [dbc.themes.BOOTSTRAP]
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# app = JupyterDash(__name__, external_stylesheets=external_stylesheets)
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app = dash.Dash(__name__, external_stylesheets=external_stylesheets)
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server = app.server
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app.config.suppress_callback_exceptions = True
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import json
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###########################################e
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import pandas as pd
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import networkx as nx
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from .arg import (
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Coalescent, Recombination, Leaf,
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interval_sum, interval_diff, interval_intersect,
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get_breakpoints, get_child_lineages,
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arg2json, json2arg,
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get_arg_nodes,
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rescale_positions,
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marginal_arg, traverse_marginal, marginal_trees
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)
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# from arg import Coalescent, Recombination, Leaf, interval_sum, interval_diff, interval_intersect, get_breakpoints, get_child_lineages, rescale_positions, marginal_arg, traverse_marginal, marginal_trees
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import plotly.colors
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def get_continuous_color(colorscale, intermed):
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"""
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Plotly continuous colorscales assign colors to the range [0, 1]. This function computes the intermediate
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color for any value in that range.
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Plotly doesn't make the colorscales directly accessible in a common format.
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Some are ready to use:
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colorscale = plotly.colors.PLOTLY_SCALES["Greens"]
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Others are just swatches that need to be constructed into a colorscale:
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viridis_colors, scale = plotly.colors.convert_colors_to_same_type(plotly.colors.sequential.Viridis)
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colorscale = plotly.colors.make_colorscale(viridis_colors, scale=scale)
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:param colorscale: A plotly continuous colorscale defined with RGB string colors.
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:param intermed: value in the range [0, 1]
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:return: color in rgb string format
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:rtype: str
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"""
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if len(colorscale) < 1:
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raise ValueError("colorscale must have at least one color")
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if intermed <= 0 or len(colorscale) == 1:
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return colorscale[0][1]
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if intermed >= 1:
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return colorscale[-1][1]
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for cutoff, color in colorscale:
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if intermed > cutoff:
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low_cutoff, low_color = cutoff, color
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else:
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high_cutoff, high_color = cutoff, color
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break
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# noinspection PyUnboundLocalVariable
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return plotly.colors.find_intermediate_color(
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lowcolor=low_color, highcolor=high_color,
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intermed=((intermed - low_cutoff) / (high_cutoff - low_cutoff)),
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colortype="rgb")
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layout = html.Div(
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[
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# Hidden div inside the app that stores the intermediate value
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html.Div(id='intermediate-value', style={'display': 'none'}),
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# row for arg and marginal trees
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dbc.Row(
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[
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# column for arg
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dbc.Col(
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[
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# arg
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dbc.Container(
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[
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dbc.Container(
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[
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dbc.Row(
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[
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dbc.Col(
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[
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html.B("Simulation:"),
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# "Simulation:",
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dcc.Dropdown(
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id='sim-dropdown',
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options=[
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{'label': "ARG", 'value': 'arg'},
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# {'label': "SMC", 'value': 'smc'},
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{'label': "SMC'", 'value': 'smcprime'},
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{'label': "SMC", 'value': 'smc'}
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],
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value='arg', searchable=False, clearable=False
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),
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], width=2
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),
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dbc.Col(
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[
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html.B("Nr samples:"),
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dcc.Dropdown(
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id='samples-dropdown',
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options=[
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{'label': "3", 'value': 3},
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{'label': "4", 'value': 4},
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{'label': "5", 'value': 5}
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],
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value=5, searchable=False, clearable=False,
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style={
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# 'height': '20px',
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# 'width': '80px',
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'font-size': "0.85rem",
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# 'min-height': '1px',
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},
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),
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], width=2
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),
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dbc.Col(
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[
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html.B("Length:"),
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dcc.Dropdown(
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id='seqlen-dropdown',
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options=[
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{'label': "1kb", 'value': 1e+3},
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{'label': "2kb", 'value': 2e+3},
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{'label': "4kb", 'value': 4e+3}
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],
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value=2e+3, searchable=False, clearable=False,
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style={
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# 'height': '20px',
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# 'width': '80px',
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'font-size': "0.85rem",
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# 'min-height': '1px',
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},
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),
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], width=2
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),
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dbc.Col(
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[
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# html.Button('New simulation', id='new-arg-button')
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dbc.Button('New', id='new-arg-button',
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color="primary", #size="sm", #outline=True,
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style={'height': 35, 'font-size': "0.85rem"},
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className="mr-1"
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)
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], width=3
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),
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dbc.Col(
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[
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html.Div(id='arg-header'),
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# dcc.Markdown(d("""
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# **Ancestral recombination graph:**
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# Nodes are colored by amount of ancestral sequence.
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# """), ),
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], width=3
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),
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], justify="between", align="end", style={'padding': 3}
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),
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dcc.Graph(id='arg-figure',
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clear_on_unhover=True,
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figure={'layout': {
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# 'height': 565,
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# 'margin': {'l': 0, 'b': 0, 't': 0, 'r': 0},
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}
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}, style={'height': '85%'}
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),
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], className='pretty_container', fluid=True, style={ #'padding': 20,
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'flex-grow': 1, 'height': '100%'}
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),
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], style={#'padding-bottom': 20,
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'flex-grow': 1, 'height': '100%'}
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),
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], width=8,
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style={'display': 'flex', #'height': '650',
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'flex-direction': 'column',
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# 'background-color': 'blue',
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'overflow': 'hidden'
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}
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),
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# column for marginal trees
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dbc.Col(
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[
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dbc.Row(
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[
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dbc.Container(
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[
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dcc.Markdown(d("""
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**Marginal tree(s):** Hover over an ARG node.
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"""), ),
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dcc.Graph(id='marginal-tree',
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figure={'layout': {
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# 'autosize': True,
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# 'title': 'Marginal tree',
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# 'height': 250,
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# 'margin': {'l': 10, 'b': 0, 't': 0, 'r': 0},
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}
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}, style={'height': '85%'}
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),
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], className='pretty_container',
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),
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], style={#'padding': 10, 'padding-left': 0, 'padding-top': 0,
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'padding-bottom': 20,
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'flex-grow': 0.5, 'height': '50%'}
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),
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dbc.Row(
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[
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dbc.Container(
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[
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dcc.Markdown(d("""
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**Ancestral sequences:** Hover over an ARG node.
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"""), ),
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dcc.Graph(id='ancestral-sequence',
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figure={'layout': {
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# 'autosize': True,
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# 'height': 2, 50,
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},
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}, style={'height': '85%'}
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),
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], className='pretty_container',
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),
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], style={# 'padding': 10, 'padding-left': 0, 'padding-bottom': 0,
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'flex-grow': 0.5, 'height': '50%' #'height': 300
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# 'display': 'flex', 'flex-direction': 'column', 'justify-content': 'space-between', 'align-items': 'stretch'
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},
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),
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], width=4,
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style={'display': 'flex', 'height': '100%',
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'flex-direction': 'column',
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# 'background-color': 'red',
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'overflow': 'hidden',
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'padding-right': 25,
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'padding-left': 20}
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),
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],
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className="g-0", style={'height': 650, 'padding-bottom': 20, 'padding-top': 20}
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# style={'display': 'flex', 'height': '100%',
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# 'flex-direction': 'column',
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# # 'background-color': 'red', 'overflow': 'hidden'
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# }
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),
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dbc.Row(
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[
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dbc.Col(
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[
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dbc.Container(
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[
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dbc.Container(
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[
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dbc.Container(
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[
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dcc.Markdown(d("""
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**Coalesce and recombination events:**
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Slide to see progression of events.
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""")),
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],
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),
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dbc.Container(
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[
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dcc.Slider(
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id='event-slider',
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min=0, max=40, value=0,
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marks={str(i): str(i) for i in range(0, 40)},
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step=None,
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),
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], #style={'padding-bottom': 20}
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)
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], className='pretty_container'
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)
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], #style={'padding': 20, 'padding-top': 0},
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)
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], width=6
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),
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dbc.Col(
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dbc.Container(
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[
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dbc.Container(
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[
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dbc.Container(
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[
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dcc.Markdown(d("""
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**Recombination points:**
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Slide to see graph for only part of the sequence.
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""")),
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]
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),
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dbc.Container(
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[
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dcc.RangeSlider(
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id='seq-slider',
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min=0,
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max=1000,
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value=[0, 1000],
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# step=None,
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+
marks={0: '0', 1000: '1'},
|
|
332
|
+
pushable=30,
|
|
333
|
+
)
|
|
334
|
+
], #style={'padding-bottom': 20}
|
|
335
|
+
),
|
|
336
|
+
], className='pretty_container',
|
|
337
|
+
),
|
|
338
|
+
], #style={'padding': 20, 'padding-left': 0, 'padding-top': 0}
|
|
339
|
+
),
|
|
340
|
+
], width=6, align='start',
|
|
341
|
+
),
|
|
342
|
+
],
|
|
343
|
+
className="g-0"
|
|
344
|
+
),
|
|
345
|
+
],# style={'padding': 20}
|
|
346
|
+
)
|
|
347
|
+
|
|
348
|
+
|
|
349
|
+
def get_bezier_points(x1, y1, x2, y2, relative, absolute_limits=None):
|
|
350
|
+
mid_x = x1 + (x2 - x1) / 2
|
|
351
|
+
mid_y = y1 + (y2 - y1) / 2
|
|
352
|
+
|
|
353
|
+
dx = x2 - x1
|
|
354
|
+
dy = y2 - y1
|
|
355
|
+
length = math.sqrt(dx**2 + dy**2)
|
|
356
|
+
|
|
357
|
+
if absolute_limits is not None:
|
|
358
|
+
hyp = relative
|
|
359
|
+
else:
|
|
360
|
+
hyp = length * relative
|
|
361
|
+
|
|
362
|
+
if absolute_limits is not None:
|
|
363
|
+
hyp = min(max(hyp, absolute_limits[0]), absolute_limits[1])
|
|
364
|
+
|
|
365
|
+
if length == 0:
|
|
366
|
+
return mid_x, mid_y, mid_x, mid_y
|
|
367
|
+
|
|
368
|
+
# Perpendicular unit vector
|
|
369
|
+
perp_x = -dy / length
|
|
370
|
+
perp_y = dx / length
|
|
371
|
+
|
|
372
|
+
# Control points at distance 'hyp' perpendicular to the line
|
|
373
|
+
b11 = mid_x + perp_x * hyp
|
|
374
|
+
b12 = mid_y + perp_y * hyp
|
|
375
|
+
b21 = mid_x - perp_x * hyp
|
|
376
|
+
b22 = mid_y - perp_y * hyp
|
|
377
|
+
|
|
378
|
+
return b11, b12, b21, b22
|
|
379
|
+
|
|
380
|
+
|
|
381
|
+
def arg_figure_data(nodes):
|
|
382
|
+
|
|
383
|
+
traces = []
|
|
384
|
+
|
|
385
|
+
edge_x = []
|
|
386
|
+
edge_y = []
|
|
387
|
+
|
|
388
|
+
diamond_shapes = []
|
|
389
|
+
|
|
390
|
+
# for lineage in get_parent_lineages(nodes, root=False):
|
|
391
|
+
for lineage in get_child_lineages(nodes):
|
|
392
|
+
|
|
393
|
+
if type(lineage.down) is Recombination and \
|
|
394
|
+
type(lineage.up) is Coalescent and \
|
|
395
|
+
set(lineage.up.children) == set([lineage.down.right_parent, lineage.down.left_parent]):
|
|
396
|
+
|
|
397
|
+
# diamond recombination:
|
|
398
|
+
x1 = lineage.down.xpos
|
|
399
|
+
y1 = lineage.down.height
|
|
400
|
+
|
|
401
|
+
x2 = lineage.up.xpos
|
|
402
|
+
y2 = lineage.up.height
|
|
403
|
+
|
|
404
|
+
b11, b12, b21, b22 = get_bezier_points(x1, y1, x2, y2,
|
|
405
|
+
relative=0.2,
|
|
406
|
+
absolute_limits=(0.005, 0.05))
|
|
407
|
+
|
|
408
|
+
diamond_shapes.append(
|
|
409
|
+
dict(
|
|
410
|
+
type="path",
|
|
411
|
+
path=f"M {x1},{y1} Q {b11},{b12} {x2},{y2}",
|
|
412
|
+
# line_color="lightgray",
|
|
413
|
+
layer='below',
|
|
414
|
+
line= {'width': 2, 'color': 'gray'}
|
|
415
|
+
)
|
|
416
|
+
)
|
|
417
|
+
diamond_shapes.append(
|
|
418
|
+
dict(
|
|
419
|
+
type="path",
|
|
420
|
+
path=f"M {x1},{y1} Q {b21},{b22} {x2},{y2}",
|
|
421
|
+
# line_color="lightgray",
|
|
422
|
+
layer='below',
|
|
423
|
+
line= {'width': 2, 'color': 'gray'},
|
|
424
|
+
)
|
|
425
|
+
)
|
|
426
|
+
|
|
427
|
+
else:
|
|
428
|
+
# start
|
|
429
|
+
edge_x.append(lineage.down.xpos)
|
|
430
|
+
edge_y.append(lineage.down.height)
|
|
431
|
+
# end
|
|
432
|
+
edge_x.append(lineage.up.xpos)
|
|
433
|
+
edge_y.append(lineage.up.height)
|
|
434
|
+
# gap
|
|
435
|
+
edge_x.append(None)
|
|
436
|
+
edge_y.append(None)
|
|
437
|
+
|
|
438
|
+
traces.append(dict(
|
|
439
|
+
x=edge_x,
|
|
440
|
+
y=edge_y,
|
|
441
|
+
mode='lines',
|
|
442
|
+
opacity=1,
|
|
443
|
+
hoverinfo = 'skip',
|
|
444
|
+
line={
|
|
445
|
+
'color': 'grey',
|
|
446
|
+
},
|
|
447
|
+
name=''
|
|
448
|
+
))
|
|
449
|
+
|
|
450
|
+
node_x = []
|
|
451
|
+
node_y = []
|
|
452
|
+
node_text = []
|
|
453
|
+
node_color = []
|
|
454
|
+
for node in nodes:
|
|
455
|
+
node_x.append(node.xpos)
|
|
456
|
+
node_y.append(node.height)
|
|
457
|
+
prop_ancestral = 1
|
|
458
|
+
if type(node) is Coalescent:
|
|
459
|
+
prop_ancestral = interval_sum(node.parent.intervals)
|
|
460
|
+
elif type(node) is Recombination:
|
|
461
|
+
prop_ancestral = interval_sum(node.child.intervals)
|
|
462
|
+
node_text.append(f"Fraction ancestral: {round(prop_ancestral, 2)}<br>Event: {type(node).__name__}")
|
|
463
|
+
|
|
464
|
+
node_color.append(prop_ancestral)
|
|
465
|
+
|
|
466
|
+
traces.append(dict(
|
|
467
|
+
x=node_x,
|
|
468
|
+
y=node_y,
|
|
469
|
+
text=node_text,
|
|
470
|
+
# range_color=[0, 1],
|
|
471
|
+
# cmin=0,
|
|
472
|
+
# cmax=1,
|
|
473
|
+
mode='markers',
|
|
474
|
+
opacity=1,
|
|
475
|
+
hoverinfo ='text',
|
|
476
|
+
marker={
|
|
477
|
+
'size': 10,
|
|
478
|
+
'color': node_color,
|
|
479
|
+
'cmin': 0,
|
|
480
|
+
'cmax': 1,
|
|
481
|
+
'line': {'width': 0.7, 'color': 'white'},
|
|
482
|
+
'colorscale': 'Rainbow',
|
|
483
|
+
# 'colorscale': 'Viridis', 'reversescale': True,
|
|
484
|
+
'colorbar': {'title': 'Fraction<br>ancestral<br>sequence',
|
|
485
|
+
'titleside': 'top',
|
|
486
|
+
'thickness': 15,
|
|
487
|
+
'len': 0.5,
|
|
488
|
+
# 'tickmode': 'array',
|
|
489
|
+
'tickvals': [0, 0.5, 1],
|
|
490
|
+
# 'ticktext': ['0', '1'],
|
|
491
|
+
'ticks': 'outside',
|
|
492
|
+
},
|
|
493
|
+
},
|
|
494
|
+
name=''
|
|
495
|
+
))
|
|
496
|
+
|
|
497
|
+
return dict(data=traces,
|
|
498
|
+
layout=dict(xaxis=dict(fixedrange=True,
|
|
499
|
+
range=[-0.1, 1.1], #title='Samples',
|
|
500
|
+
showgrid=False, showline=False,
|
|
501
|
+
zeroline=False, showticklabels=False
|
|
502
|
+
),
|
|
503
|
+
yaxis=dict(fixedrange=True,
|
|
504
|
+
range=[-0.1, 1.1], #title='Time',
|
|
505
|
+
showgrid=False, showline=False,
|
|
506
|
+
zeroline=False, showticklabels=False
|
|
507
|
+
),
|
|
508
|
+
hovermode='closest',
|
|
509
|
+
range_color=[0,1],
|
|
510
|
+
margin= {'l': 50, 'b': 20, 't': 20, 'r': 20},
|
|
511
|
+
transition = {'duration': 0},
|
|
512
|
+
showlegend=False,
|
|
513
|
+
shapes=diamond_shapes,
|
|
514
|
+
)
|
|
515
|
+
)
|
|
516
|
+
|
|
517
|
+
|
|
518
|
+
def tree_figure_data(node_lists):
|
|
519
|
+
|
|
520
|
+
traces = []
|
|
521
|
+
|
|
522
|
+
edge_x = []
|
|
523
|
+
edge_y = []
|
|
524
|
+
node_x = []
|
|
525
|
+
node_y = []
|
|
526
|
+
node_color = []
|
|
527
|
+
|
|
528
|
+
max_x = -1
|
|
529
|
+
|
|
530
|
+
for i, nodes in enumerate(node_lists):
|
|
531
|
+
|
|
532
|
+
# for lineage in get_parent_lineages(nodes, root=False):
|
|
533
|
+
for lineage in get_child_lineages(nodes):
|
|
534
|
+
# start
|
|
535
|
+
edge_x.append(lineage.down.xpos)
|
|
536
|
+
edge_y.append(lineage.down.height)
|
|
537
|
+
# end
|
|
538
|
+
edge_x.append(lineage.up.xpos)
|
|
539
|
+
edge_y.append(lineage.up.height)
|
|
540
|
+
# gap
|
|
541
|
+
edge_x.append(None)
|
|
542
|
+
edge_y.append(None)
|
|
543
|
+
|
|
544
|
+
for node in nodes:
|
|
545
|
+
node_x.append(node.xpos)
|
|
546
|
+
node_y.append(node.height)
|
|
547
|
+
|
|
548
|
+
node_color.append(i/len(node_lists))
|
|
549
|
+
|
|
550
|
+
max_x = max(max_x, node.xpos)
|
|
551
|
+
|
|
552
|
+
|
|
553
|
+
|
|
554
|
+
traces.append(dict(
|
|
555
|
+
x=edge_x,
|
|
556
|
+
y=edge_y,
|
|
557
|
+
mode='lines',
|
|
558
|
+
opacity=1,
|
|
559
|
+
hoverinfo = 'skip',
|
|
560
|
+
line={
|
|
561
|
+
'color': 'grey',
|
|
562
|
+
},
|
|
563
|
+
name=''
|
|
564
|
+
))
|
|
565
|
+
|
|
566
|
+
traces.append(dict(
|
|
567
|
+
x=node_x,
|
|
568
|
+
y=node_y,
|
|
569
|
+
mode='markers',
|
|
570
|
+
opacity=1,
|
|
571
|
+
hoverinfo ='text',
|
|
572
|
+
marker={
|
|
573
|
+
'size': 7,
|
|
574
|
+
'color': node_color,
|
|
575
|
+
'cmin': 0,
|
|
576
|
+
'cmax': 1,
|
|
577
|
+
'colorscale': 'Rainbow',
|
|
578
|
+
'line': {'width': 0.3, 'color': 'white'},
|
|
579
|
+
},
|
|
580
|
+
name=''
|
|
581
|
+
))
|
|
582
|
+
|
|
583
|
+
return dict(data=traces,
|
|
584
|
+
layout=dict(xaxis=dict(fixedrange=True,
|
|
585
|
+
range=[-0.02, max_x + 0.02], #title='Samples',
|
|
586
|
+
showgrid=False, showline=False,
|
|
587
|
+
zeroline=False, showticklabels=False
|
|
588
|
+
),
|
|
589
|
+
yaxis=dict(fixedrange=True,
|
|
590
|
+
# range=[-0.1, 1.1], #title='Time',
|
|
591
|
+
range=[-0.02, 1.02], #title='Time',
|
|
592
|
+
showgrid=False, showline=False,
|
|
593
|
+
zeroline=False, showticklabels=False
|
|
594
|
+
),
|
|
595
|
+
hovermode='closest',
|
|
596
|
+
range_color=[0,1],
|
|
597
|
+
margin= {'l': 7, 'b': 10, 't': 10, 'r': 4},
|
|
598
|
+
# margin= {'l': 0, 'b': 0, 't': 0, 'r': 0},
|
|
599
|
+
transition = {'duration': 0},
|
|
600
|
+
showlegend=False,
|
|
601
|
+
)
|
|
602
|
+
)
|
|
603
|
+
|
|
604
|
+
|
|
605
|
+
@app.callback(
|
|
606
|
+
Output('arg-header', 'children'),
|
|
607
|
+
[Input('new-arg-button', 'n_clicks')])
|
|
608
|
+
def update_header(n_clicks):
|
|
609
|
+
|
|
610
|
+
if n_clicks is None:
|
|
611
|
+
n_sim = 1
|
|
612
|
+
else:
|
|
613
|
+
n_sim = n_clicks + 1
|
|
614
|
+
|
|
615
|
+
return dcc.Markdown(d("""
|
|
616
|
+
**Simulation #{}:**
|
|
617
|
+
""".format(n_sim)))
|
|
618
|
+
|
|
619
|
+
@app.callback(Output('intermediate-value', 'children'),
|
|
620
|
+
[Input('new-arg-button', 'n_clicks'),
|
|
621
|
+
Input('sim-dropdown', 'value'),
|
|
622
|
+
Input('samples-dropdown', 'value'),
|
|
623
|
+
Input('seqlen-dropdown', 'value')])
|
|
624
|
+
def new_data(n_clicks, sim, samples, length):
|
|
625
|
+
|
|
626
|
+
nodes = get_arg_nodes(L=length, n=samples, simulation=sim)
|
|
627
|
+
# rescale_positions(nodes)
|
|
628
|
+
json_str = arg2json(nodes)
|
|
629
|
+
return json_str
|
|
630
|
+
|
|
631
|
+
@app.callback(
|
|
632
|
+
[Output(component_id='event-slider', component_property='min'),
|
|
633
|
+
Output(component_id='event-slider', component_property='max'),
|
|
634
|
+
Output(component_id='event-slider', component_property='step'),
|
|
635
|
+
Output(component_id='event-slider', component_property='value')],
|
|
636
|
+
[Input('intermediate-value', 'children')])
|
|
637
|
+
def update_event_slider(jsonified_data):
|
|
638
|
+
if jsonified_data:
|
|
639
|
+
nodes = json2arg(jsonified_data)
|
|
640
|
+
else:
|
|
641
|
+
nodes = []
|
|
642
|
+
|
|
643
|
+
nr_leaves = len([n for n in nodes if type(n) is Leaf])
|
|
644
|
+
nr_events = len(nodes)-nr_leaves
|
|
645
|
+
return 0, nr_events, 1, nr_events
|
|
646
|
+
|
|
647
|
+
@app.callback(
|
|
648
|
+
[Output(component_id='seq-slider', component_property='min'),
|
|
649
|
+
Output(component_id='seq-slider', component_property='max'),
|
|
650
|
+
Output(component_id='seq-slider', component_property='value'),
|
|
651
|
+
Output(component_id='seq-slider', component_property='marks')],
|
|
652
|
+
[Input('intermediate-value', 'children')])
|
|
653
|
+
def update_seq_slider(jsonified_data):
|
|
654
|
+
if jsonified_data:
|
|
655
|
+
nodes = json2arg(jsonified_data)
|
|
656
|
+
else:
|
|
657
|
+
nodes = []
|
|
658
|
+
breakpoints = get_breakpoints(nodes)
|
|
659
|
+
marks = dict((b*1000, str(i+1)) for i, b in enumerate(breakpoints))
|
|
660
|
+
if not marks:
|
|
661
|
+
marks = None
|
|
662
|
+
return 0, 1000, [0, 1000], marks
|
|
663
|
+
|
|
664
|
+
|
|
665
|
+
@app.callback(
|
|
666
|
+
Output('arg-figure', 'figure'),
|
|
667
|
+
[Input('intermediate-value', 'children'),
|
|
668
|
+
Input('event-slider', 'value'),
|
|
669
|
+
Input('seq-slider', 'value')])
|
|
670
|
+
def update_arg_figure(jsonified_data, event, interval):
|
|
671
|
+
|
|
672
|
+
if jsonified_data:
|
|
673
|
+
nodes = json2arg(jsonified_data)
|
|
674
|
+
|
|
675
|
+
interval = [i/1000 for i in interval]
|
|
676
|
+
|
|
677
|
+
# Get marginal arg for interval
|
|
678
|
+
marg_arg_nodes = marginal_arg(nodes, interval)
|
|
679
|
+
# print(interval)
|
|
680
|
+
# get only subset of events
|
|
681
|
+
nr_leaves = len([n for n in nodes if type(n) is Leaf])
|
|
682
|
+
new_nodes = marg_arg_nodes[:nr_leaves+event]
|
|
683
|
+
else:
|
|
684
|
+
new_nodes = []
|
|
685
|
+
|
|
686
|
+
return arg_figure_data(new_nodes)
|
|
687
|
+
|
|
688
|
+
|
|
689
|
+
@app.callback(
|
|
690
|
+
Output('marginal-tree', 'figure'),
|
|
691
|
+
[Input('intermediate-value', 'children'),
|
|
692
|
+
Input('arg-figure', 'hoverData'),
|
|
693
|
+
Input('seq-slider', 'value')])
|
|
694
|
+
def update_marg_tree_figure(jsonified_data, hover, slider_interval):
|
|
695
|
+
|
|
696
|
+
marg_tree_list = []
|
|
697
|
+
if hover and jsonified_data:
|
|
698
|
+
nodes = json2arg(jsonified_data)
|
|
699
|
+
focus_node_idx = hover['points'][0]['pointIndex']
|
|
700
|
+
focus_node = nodes[focus_node_idx]
|
|
701
|
+
|
|
702
|
+
if type(focus_node) is Recombination:
|
|
703
|
+
intervals = focus_node.child.intervals
|
|
704
|
+
else:
|
|
705
|
+
intervals = focus_node.parent.intervals
|
|
706
|
+
|
|
707
|
+
# slider interval is 0-1000 not 0-1:
|
|
708
|
+
slider_interval = [x/1000 for x in slider_interval]
|
|
709
|
+
# get part of intervals that intersect slider interval:
|
|
710
|
+
intervals = interval_intersect([slider_interval], intervals)
|
|
711
|
+
|
|
712
|
+
for interval in intervals:
|
|
713
|
+
# get marginal arg under focus node
|
|
714
|
+
new_nodes = traverse_marginal(focus_node, interval)
|
|
715
|
+
new_nodes = list(new_nodes)
|
|
716
|
+
new_nodes.sort(key=lambda x: x.height)
|
|
717
|
+
|
|
718
|
+
marg_trees, _ = marginal_trees(new_nodes, interval)
|
|
719
|
+
marg_tree_list.extend(marg_trees)
|
|
720
|
+
|
|
721
|
+
nr_cols = len(marg_tree_list)
|
|
722
|
+
|
|
723
|
+
space = 0.5
|
|
724
|
+
|
|
725
|
+
for i in range(nr_cols):
|
|
726
|
+
tree = marg_tree_list[i]
|
|
727
|
+
for node in tree:
|
|
728
|
+
node.xpos = node.xpos/(nr_cols+(nr_cols-1)*space) + i/nr_cols
|
|
729
|
+
marg_tree_list[i] = tree
|
|
730
|
+
|
|
731
|
+
# TODO: Maybe keep "dangling root" branch here
|
|
732
|
+
|
|
733
|
+
if marg_tree_list:
|
|
734
|
+
return(tree_figure_data(marg_tree_list))
|
|
735
|
+
else:
|
|
736
|
+
return(tree_figure_data([]))
|
|
737
|
+
|
|
738
|
+
|
|
739
|
+
@app.callback(
|
|
740
|
+
Output('ancestral-sequence', 'figure'),
|
|
741
|
+
[Input('intermediate-value', 'children'),
|
|
742
|
+
Input('arg-figure', 'hoverData'),
|
|
743
|
+
Input('seq-slider', 'value')])
|
|
744
|
+
def update_ancestral_seq_figure(jsonified_data, hover, slider_interval):
|
|
745
|
+
|
|
746
|
+
traces = []
|
|
747
|
+
shape_list = []
|
|
748
|
+
|
|
749
|
+
if hover and jsonified_data:
|
|
750
|
+
nodes = json2arg(jsonified_data)
|
|
751
|
+
focus_node_idx = hover['points'][0]['pointIndex']
|
|
752
|
+
focus_node = nodes[focus_node_idx]
|
|
753
|
+
|
|
754
|
+
# slider interval is 0-1000 not 0-1:
|
|
755
|
+
slider_interval = [x/1000 for x in slider_interval]
|
|
756
|
+
|
|
757
|
+
gray_segments = list(map(tuple, interval_diff([[0, 1]], [slider_interval])))
|
|
758
|
+
|
|
759
|
+
def get_segments(focus_node, intervals):
|
|
760
|
+
segments = list()
|
|
761
|
+
marg_tree_list = list()
|
|
762
|
+
for interval in intervals:
|
|
763
|
+
new_nodes = traverse_marginal(focus_node, interval)
|
|
764
|
+
new_nodes = list(new_nodes)
|
|
765
|
+
new_nodes.sort(key=lambda x: x.height)
|
|
766
|
+
marg_trees, marg_segm = marginal_trees(new_nodes, interval)
|
|
767
|
+
# print(marg_trees, marg_segm)
|
|
768
|
+
marg_tree_list.extend(marg_trees)
|
|
769
|
+
segments.extend(marg_segm)
|
|
770
|
+
return segments
|
|
771
|
+
|
|
772
|
+
def get_shapes(segments, gray_segments, x, y, color_map):
|
|
773
|
+
shape_list = list()
|
|
774
|
+
shape = dict(type='rect', xref='x', yref='y', fillcolor='white', line= {'width': 1},
|
|
775
|
+
x0=x, y0=y, x1=x+2/5, y1=y+0.1)
|
|
776
|
+
shape_list.append(shape)
|
|
777
|
+
for i, segment in enumerate(segments):
|
|
778
|
+
color=color_map[segment]
|
|
779
|
+
shape = dict(type='rect', xref='x', yref='y', fillcolor=color, line= {'width': 1},
|
|
780
|
+
x0=x+segment[0]*2/5, y0=y, x1=x+segment[1]*2/5, y1=y+0.1)
|
|
781
|
+
shape_list.append(shape)
|
|
782
|
+
for i, segment in enumerate(gray_segments):
|
|
783
|
+
shape = dict(type='rect', xref='x', yref='y', fillcolor='lightgray', line= {'width': 1},
|
|
784
|
+
x0=x+segment[0]*2/5, y0=y, x1=x+segment[1]*2/5, y1=y+0.1)
|
|
785
|
+
shape_list.append(shape)
|
|
786
|
+
return shape_list
|
|
787
|
+
|
|
788
|
+
if type(focus_node) is Leaf:
|
|
789
|
+
|
|
790
|
+
colors, _ = plotly.colors.convert_colors_to_same_type(plotly.colors.sequential.Rainbow)
|
|
791
|
+
colorscale = plotly.colors.make_colorscale(colors)
|
|
792
|
+
color = get_continuous_color(colorscale, intermed=0)
|
|
793
|
+
|
|
794
|
+
shape_list = [dict(type='rect', xref='x', yref='y', fillcolor=color, line= {'width': 1},
|
|
795
|
+
x0=1.5/5, y0=0.25, x1=3.5/5, y1=0.35)]
|
|
796
|
+
for segment in gray_segments:
|
|
797
|
+
shape = dict(type='rect', xref='x', yref='y', fillcolor='lightgray', line= {'width': 1},
|
|
798
|
+
x0=1.5/5+segment[0]*2/5, y0=0.25, x1=1.5/5+segment[1]*2/5, y1=0.35)
|
|
799
|
+
shape_list.append(shape)
|
|
800
|
+
|
|
801
|
+
elif type(focus_node) is Recombination:
|
|
802
|
+
# print("###", focus_node.left_parent.intervals, focus_node.right_parent.intervals)
|
|
803
|
+
segments1 = get_segments(focus_node, focus_node.left_parent.intervals)
|
|
804
|
+
segments2 = get_segments(focus_node, focus_node.right_parent.intervals)
|
|
805
|
+
segments3 = get_segments(focus_node, focus_node.child.intervals)
|
|
806
|
+
|
|
807
|
+
# get part of intervals that intersect slider interval:
|
|
808
|
+
segments1 = list(map(tuple, interval_intersect([slider_interval], segments1)))
|
|
809
|
+
segments2 = list(map(tuple, interval_intersect([slider_interval], segments2)))
|
|
810
|
+
segments3 = list(map(tuple, interval_intersect([slider_interval], segments3)))
|
|
811
|
+
|
|
812
|
+
unique_segments = sorted(set().union(segments1, segments2, segments3))
|
|
813
|
+
color_map = dict()
|
|
814
|
+
colors, _ = plotly.colors.convert_colors_to_same_type(plotly.colors.sequential.Rainbow)
|
|
815
|
+
colorscale = plotly.colors.make_colorscale(colors)
|
|
816
|
+
for i, s in enumerate(unique_segments):
|
|
817
|
+
color_map[s] = get_continuous_color(colorscale, intermed=i/len(unique_segments))
|
|
818
|
+
|
|
819
|
+
shape_list = \
|
|
820
|
+
[dict(type='line', xref='x', yref='y', line= {'width': 2, 'color': 'gray'},
|
|
821
|
+
x0=0.5, y0=0.55, x1=0.5, y1=0.1),
|
|
822
|
+
dict(type='line', xref='x', yref='y', line= {'width': 2, 'color': 'gray'},
|
|
823
|
+
x0=0.5, y0=0.55, x1=0.05, y1=0.95),
|
|
824
|
+
# x0=0.5, y0=0.55, x1=1/5, y1=0.75),
|
|
825
|
+
dict(type='line', xref='x', yref='y', line= {'width': 2, 'color': 'gray'},
|
|
826
|
+
x0=0.5, y0=0.55, x1=0.95, y1=0.95),
|
|
827
|
+
dict(type="circle", xref="x", yref="y",
|
|
828
|
+
fillcolor="black",
|
|
829
|
+
x0=0.488, y0=0.5285, x1=0.512, y1=0.5715,
|
|
830
|
+
line_color="black")
|
|
831
|
+
] + \
|
|
832
|
+
get_shapes(segments1, gray_segments, x=0, y=0.75, color_map=color_map) + \
|
|
833
|
+
get_shapes(segments2, gray_segments, x=3/5, y=0.75, color_map=color_map) + \
|
|
834
|
+
get_shapes(segments3, gray_segments, x=1.5/5, y=0.25, color_map=color_map)
|
|
835
|
+
|
|
836
|
+
# traces.append(dict(
|
|
837
|
+
# x=[0.5, 0.5],
|
|
838
|
+
# y=[0.55, 0.55],
|
|
839
|
+
# mode='markers',
|
|
840
|
+
# # opacity=1,
|
|
841
|
+
# marker={
|
|
842
|
+
# 'size': 7,
|
|
843
|
+
# 'color': 'black',},
|
|
844
|
+
# name=''
|
|
845
|
+
# ))
|
|
846
|
+
|
|
847
|
+
|
|
848
|
+
# get_shapes(segments1, gray_segments, x=0, y=0.75, color_map=color_map) + \
|
|
849
|
+
# get_shapes(segments2, gray_segments, x=3/5, y=0.75, color_map=color_map) + \
|
|
850
|
+
# get_shapes(segments3, gray_segments, x=1.5/5, y=0.25, color_map=color_map) + \
|
|
851
|
+
# [dict(type='line', xref='x', yref='y', line= {'width': 2, 'color': 'gray'},
|
|
852
|
+
# x0=0.5, y0=0.55, x1=0.5, y1=0.35),
|
|
853
|
+
# dict(type='line', xref='x', yref='y', line= {'width': 2, 'color': 'gray'},
|
|
854
|
+
# x0=0.5, y0=0.55, x1=0, y1=1),
|
|
855
|
+
# # x0=0.5, y0=0.55, x1=1/5, y1=0.75),
|
|
856
|
+
# dict(type='line', xref='x', yref='y', line= {'width': 2, 'color': 'gray'},
|
|
857
|
+
# x0=0.5, y0=0.55, x1=4/5, y1=0.75)]
|
|
858
|
+
|
|
859
|
+
|
|
860
|
+
# print("slider", slider_interval)
|
|
861
|
+
# shape_list.append(dict(type='rect', xref='x', yref='y', fillcolor='grey', line= {'width': 1},
|
|
862
|
+
# x0=slider_interval[0], y0=0.5, x1=slider_interval[1], y1=0.5+0.1))
|
|
863
|
+
|
|
864
|
+
else:
|
|
865
|
+
segments1 = get_segments(focus_node, focus_node.children[0].intervals)
|
|
866
|
+
segments2 = get_segments(focus_node, focus_node.children[1].intervals)
|
|
867
|
+
segments3 = get_segments(focus_node, focus_node.parent.intervals)
|
|
868
|
+
|
|
869
|
+
# get part of intervals that intersect slider interval:
|
|
870
|
+
segments1 = list(map(tuple, interval_intersect([slider_interval], segments1)))
|
|
871
|
+
segments2 = list(map(tuple, interval_intersect([slider_interval], segments2)))
|
|
872
|
+
segments3 = list(map(tuple, interval_intersect([slider_interval], segments3)))
|
|
873
|
+
|
|
874
|
+
unique_segments = sorted(set().union(segments1, segments2, segments3))
|
|
875
|
+
color_map = dict()
|
|
876
|
+
colors, _ = plotly.colors.convert_colors_to_same_type(plotly.colors.sequential.Rainbow)
|
|
877
|
+
colorscale = plotly.colors.make_colorscale(colors)
|
|
878
|
+
for i, s in enumerate(unique_segments):
|
|
879
|
+
color_map[s] = get_continuous_color(colorscale, intermed=i/len(unique_segments))
|
|
880
|
+
|
|
881
|
+
shape_list = \
|
|
882
|
+
get_shapes(segments1, gray_segments, x=0, y=0.25, color_map=color_map) + \
|
|
883
|
+
get_shapes(segments2, gray_segments, x=3/5, y=0.25, color_map=color_map) + \
|
|
884
|
+
get_shapes(segments3, gray_segments, x=1.5/5, y=0.75, color_map=color_map) + \
|
|
885
|
+
[dict(type='line', xref='x', yref='y', line= {'width': 2, 'color': 'gray'},
|
|
886
|
+
x0=0.5, y0=0.55, x1=0.5, y1=0.75),
|
|
887
|
+
dict(type='line', xref='x', yref='y', line= {'width': 2, 'color': 'gray'},
|
|
888
|
+
x0=0.5, y0=0.55, x1=1/5, y1=0.35),
|
|
889
|
+
dict(type='line', xref='x', yref='y', line= {'width': 2, 'color': 'gray'},
|
|
890
|
+
x0=0.5, y0=0.55, x1=4/5, y1=0.35)]
|
|
891
|
+
|
|
892
|
+
figure_data = dict(
|
|
893
|
+
data=traces,
|
|
894
|
+
layout=dict(xaxis=dict(fixedrange=True,
|
|
895
|
+
range=[-0.01, 1.01], #title='Samples',
|
|
896
|
+
showgrid=False, showline=False,
|
|
897
|
+
zeroline=False, showticklabels=False
|
|
898
|
+
),
|
|
899
|
+
yaxis=dict(fixedrange=True,
|
|
900
|
+
range=[0, 1], #title='Time',
|
|
901
|
+
showgrid=False, showline=False,
|
|
902
|
+
zeroline=False, showticklabels=False
|
|
903
|
+
),
|
|
904
|
+
margin= {'l': 0, 'b': 0, 't': 20, 'r': 0},
|
|
905
|
+
transition = {'duration': 0},
|
|
906
|
+
showlegend=False,
|
|
907
|
+
shapes=shape_list,
|
|
908
|
+
)
|
|
909
|
+
)
|
|
910
|
+
|
|
911
|
+
# figure_data['layout']['shapes'].extend(shape_list)
|
|
912
|
+
|
|
913
|
+
return figure_data
|
|
914
|
+
|
|
915
|
+
|
|
916
|
+
|
|
917
|
+
app.layout = layout
|
|
918
|
+
|
|
919
|
+
def run():
|
|
920
|
+
|
|
921
|
+
# parse command line arguments
|
|
922
|
+
import argparse
|
|
923
|
+
parser = argparse.ArgumentParser(description='Run ARG dashboard')
|
|
924
|
+
parser.add_argument('--host', '--ip', default='127.0.0.1', help='Host address')
|
|
925
|
+
parser.add_argument('--port', type=int, default=8050, help='Port number')
|
|
926
|
+
parser.add_argument('--debug', action='store_true', help='Run in debug mode')
|
|
927
|
+
args = parser.parse_args()
|
|
928
|
+
|
|
929
|
+
import webbrowser
|
|
930
|
+
webbrowser.open(f'http://{args.host}:{args.port}/')
|
|
931
|
+
app.run(host=args.host, port=args.port, debug=args.debug)
|
|
932
|
+
|
|
933
|
+
if __name__ == '__main__':
|
|
934
|
+
app.run_server(debug=True)
|