pico-ml 2.0.0__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.
- pico/__init__.py +3 -0
- pico/__main__.py +3 -0
- pico/cli/__init__.py +2 -0
- pico/cli/main.py +117 -0
- pico/conf/SupportedCV.py +17 -0
- pico/conf/SupportedModels.py +73 -0
- pico/conf/algo_sklearn.json +51 -0
- pico/conf/parameters.py +14 -0
- pico/domain/ClassificationDesign.py +107 -0
- pico/domain/Controller.py +397 -0
- pico/domain/DataMatrix.py +147 -0
- pico/domain/ExperimentDTO.py +17 -0
- pico/domain/MetaData.py +229 -0
- pico/domain/MetaboExperiment.py +696 -0
- pico/domain/MetaboModel.py +53 -0
- pico/domain/ModelFactory.py +45 -0
- pico/domain/Results.py +602 -0
- pico/domain/SplitGroup.py +202 -0
- pico/domain/__init__.py +9 -0
- pico/domain/dumps/metadata/.gitkeep +0 -0
- pico/domain/dumps/splits/.gitkeep +0 -0
- pico/service/DataFormat.py +180 -0
- pico/service/ExperimentDesign.py +30 -0
- pico/service/LoggerConfig.py +150 -0
- pico/service/Plots.py +472 -0
- pico/service/RunMLalgo.py +93 -0
- pico/service/SamplesPairing.py +390 -0
- pico/service/Utils.py +497 -0
- pico/service/__init__.py +7 -0
- pico/ui/__init__.py +1 -0
- pico/ui/app.py +145 -0
- pico/ui/assets/000_Stylesheet.css +464 -0
- pico/ui/assets/DecisionTree.png +0 -0
- pico/ui/assets/Figure_home_wider.png +0 -0
- pico/ui/assets/favicon.ico +0 -0
- pico/ui/assets/help_icon.png +0 -0
- pico/ui/assets/help_icon.svg +15 -0
- pico/ui/assets/update_figure_steps_MeDIC_4.svg +1 -0
- pico/ui/tabs/AggregatedResultsTab.py +394 -0
- pico/ui/tabs/InfoTab.py +440 -0
- pico/ui/tabs/InterpretTab.py +21 -0
- pico/ui/tabs/MLTab.py +487 -0
- pico/ui/tabs/MetaTab.py +23 -0
- pico/ui/tabs/ResultsTab.py +1062 -0
- pico/ui/tabs/SplitsTab.py +1227 -0
- pico/ui/tabs/__init__.py +6 -0
- pico/ui/tabs/utils.py +101 -0
- pico_ml-2.0.0.dist-info/METADATA +86 -0
- pico_ml-2.0.0.dist-info/RECORD +52 -0
- pico_ml-2.0.0.dist-info/WHEEL +4 -0
- pico_ml-2.0.0.dist-info/entry_points.txt +2 -0
- pico_ml-2.0.0.dist-info/licenses/LICENSE +437 -0
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import os
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import time
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import dash_bootstrap_components as dbc
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import dash_interactive_graphviz as dg
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import pandas as pd
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from dash import html, dcc, Output, Input, State, dash, Dash
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import dash_cytoscape as cyto
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from matplotlib import pyplot as plt
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from sklearn import tree
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from ...conf import parameters as cfg
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from . import utils
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from .MetaTab import MetaTab
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from ...domain import Controller
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from ...service import Plots, Utils, init_logger, log_exceptions
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PATH_TO_BIGRESULTS = os.path.abspath(
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os.path.join(os.path.dirname(__file__), "..", "..", "..", "big_results.p")
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)
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CONFIG = {
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"toImageButtonOptions": {
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"format": "svg", # one of png, svg, jpeg, webp
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"height": None,
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"width": None,
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"scale": 1, # Multiply title/legend/axis/canvas sizes by this factor
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}
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}
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class ResultsTab(MetaTab):
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def __init__(self, app: Dash, metabo_controller: Controller):
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super().__init__(app, metabo_controller)
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self._logger = init_logger()
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# self.r = pkl.load(open(PATH_TO_BIGRESULTS, "rb"))
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self.r = self.metabo_controller.get_all_results()
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self._plots = Plots("blues")
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def getLayout(self) -> dbc.Tab:
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__resultsMenuDropdowns = dbc.Card(
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className="results_menu_dropdowns",
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children=[
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dbc.CardBody(
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[
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html.Div(
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className="dropdowns",
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children=[
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html.H6("Classification Design : "),
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dbc.Select(
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id="design_dropdown",
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className="form_select",
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options=[{"label": "None", "value": "None"}],
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value="None",
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),
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],
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),
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html.Div(
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className="dropdowns",
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children=[
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html.H6("ML Algorithm : "),
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dbc.Select(
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id="ml_dropdown",
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className="form_select",
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options=[{"label": "None", "value": "None"}],
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value="None",
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),
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],
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),
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dbc.Button(
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"Load",
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color="primary",
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id="load_ML_results_button",
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className="custom_buttons",
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n_clicks=0,
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),
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html.Div(id="output_button_load_ML_results"),
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],
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id="menu_results",
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)
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],
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)
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__currentExperimentInfo = dbc.Card(
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children=[
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dbc.CardBody(
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children=[
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html.H6(
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"Current experiment info"
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), # , style={"marginTop": 25},
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# html.Div(id="view_info", children=[
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dcc.Loading(
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id="loading_expe_table",
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children=html.Div(id="expe_table", children=""),
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type="circle",
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),
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# dcc.Loading(id="loading-1", children=[html.Div(id="loading-output-1")],
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# type="dot", color="#13BD00")
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]
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)
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],
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className="w-25",
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)
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_resultsInfo = html.Div(
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className="Results_info",
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children=[
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__resultsMenuDropdowns,
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__currentExperimentInfo,
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],
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)
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___pcaPlot = html.Div(
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className="pca_plot_and_title",
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children=[
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html.Div(
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className="title_and_help",
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children=[
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html.H6("PCA", id="PCA_title"),
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dcc.RadioItems(
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id='pca_dimensions',
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options=[
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{'label': ' 2D', 'value': '2d'},
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{'label': ' 3D', 'value': '3d'},
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],
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value='2d',
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labelStyle={'margin': 'auto', 'padding': '5px'},
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inline=True
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),
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],
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style={"display": "flex", "justify-content": "space-between"},
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),
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# Should we put the title on the plot?
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dcc.Loading(
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dcc.Graph(id="PCA", config=CONFIG), type="dot", color="#13BD00"
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),
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dcc.Slider(
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step=None,
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value=1,
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marks={**cfg.default_marks, **cfg.all_mark},
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id="pca_slider",
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),
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],
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)
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___umap = html.Div(
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className="umap_plot_and_title",
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children=[
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html.Div(
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className="title_and_help",
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children=[
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html.H6("Umap"),
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dcc.RadioItems(
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id='umap_dimensions',
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options=[
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{'label': ' 2D', 'value': '2d'},
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{'label': ' 3D', 'value': '3d'},
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],
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value='2d',
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# add space between radio and label
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labelStyle={'margin': 'auto', 'padding': '5px'},
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inline=True
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),
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],
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style={"display": "flex", "justify-content": "space-between"},
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),
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dcc.Loading(
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dcc.Graph(id="umap_overview", config=CONFIG),
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type="dot",
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color="#13BD00",
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),
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dcc.Slider(
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step=None,
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value=1,
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marks={**cfg.default_marks, **cfg.all_mark},
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id="umap_slider",
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)
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],
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)
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___2dPlot = html.Div(
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className="umap_plot_and_title",
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children=[
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html.Div(
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className="title_and_help",
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children=[
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html.H6("2D"),
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dbc.Button(
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"[?]",
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className="text-muted btn-secondary popover_btn",
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id="help_2dPlot",
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),
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dbc.Popover(
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children=[dbc.PopoverBody("Blablabla wout wout")],
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id="pop_help_2dPlot",
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is_open=False,
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target="help_2dPlot",
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),
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],
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),
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dcc.Loading(
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dcc.Graph(id="2d_overview", config=CONFIG),
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type="dot",
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color="#13BD00",
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),
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],
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___3dPlot = html.Div(
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className="umap_plot_and_title",
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children=[
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html.Div(
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className="title_and_help",
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children=[
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html.H6("3D"),
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dbc.Button(
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"[?]",
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className="text-muted btn-secondary popover_btn",
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id="help_3dPlot",
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),
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dbc.Popover(
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children=[dbc.PopoverBody("Blablabla wout wout")],
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id="pop_help_3dPlot",
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is_open=False,
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target="help_3dPlot",
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),
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],
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),
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dcc.Loading(
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dcc.Graph(id="3d_overview", config=CONFIG),
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type="dot",
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color="#13BD00",
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),
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],
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)
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__dataResultTab = dbc.Tab(
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className="sub_tab",
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label="Data",
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children=[
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html.Div(className="fig_group", children=[___pcaPlot, ___umap]),
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html.Div(className="fig_group", children=[___2dPlot, ___3dPlot]),
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],
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)
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___accuracyPlot = html.Div(
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className="acc_plot_and_title",
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children=[
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html.Div(
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className="title_and_help",
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children=[
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html.H6("Balanced accuracy plot"),
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dbc.Button(
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"[?]",
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className="text-muted btn-secondary popover_btn",
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id="help_accPlot",
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),
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dbc.Popover(
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children=[
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dbc.PopoverBody(
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"Accuracies for each split on train and test set. Here you would want to check"
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"the difference between each set, because a really good train performance and a mediocre"
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"or bad test performance is a sign of over-fitting."
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)
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],
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id="pop_help_accPlot",
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is_open=False,
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target="help_accPlot",
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),
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],
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),
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dcc.Loading(
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dcc.Graph(id="accuracy_overview", config=CONFIG),
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type="dot",
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color="#13BD00",
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),
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],
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)
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___globalMetric = html.Div(
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className="w-25",
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children=[
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html.H6("Global confusion matrix"),
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dcc.Loading(
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dcc.Graph(id="conf_matrix", config=CONFIG),
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type="dot",
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color="#13BD00",
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),
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],
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)
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___specificFilters = html.Div(
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className="fig_group_col",
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children=[
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html.Div(
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className="",
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children=[
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html.H6("Splits number"),
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dbc.Select(
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id="splits_dropdown",
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className="form_select_large",
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options=[{"label": "None", "value": "None"}],
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value="None",
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),
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dbc.Button(
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"Update",
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color="primary",
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id="update_specific_results_button",
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className="custom_buttons",
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n_clicks=0,
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),
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html.Div(id="output_button_update_specific_results"),
|
|
313
|
+
],
|
|
314
|
+
),
|
|
315
|
+
html.Div(
|
|
316
|
+
className="",
|
|
317
|
+
style={"display": "flex", "width": "100%"},
|
|
318
|
+
children=[
|
|
319
|
+
html.Div(
|
|
320
|
+
children=[
|
|
321
|
+
html.H6("Confusion matrix"),
|
|
322
|
+
dcc.Loading(
|
|
323
|
+
dcc.Graph(id="split_conf_matrix", config=CONFIG),
|
|
324
|
+
type="dot",
|
|
325
|
+
color="#13BD00",
|
|
326
|
+
),
|
|
327
|
+
],
|
|
328
|
+
),
|
|
329
|
+
html.Div(
|
|
330
|
+
children=[
|
|
331
|
+
html.H6("Table of used hyperparameter"),
|
|
332
|
+
dcc.Loading(
|
|
333
|
+
html.Div(id="hyperparam_table", children="", style={"margin-top": "2em"}),
|
|
334
|
+
),
|
|
335
|
+
],
|
|
336
|
+
)
|
|
337
|
+
],
|
|
338
|
+
),
|
|
339
|
+
],
|
|
340
|
+
)
|
|
341
|
+
___metricsTable = html.Div(
|
|
342
|
+
className="table_features",
|
|
343
|
+
children=[
|
|
344
|
+
html.H6("Metrics table : mean(std)"),
|
|
345
|
+
dcc.Loading(
|
|
346
|
+
id="loading_metrics_table",
|
|
347
|
+
children=html.Div(id="metrics_score_table", children=""),
|
|
348
|
+
type="circle",
|
|
349
|
+
),
|
|
350
|
+
],
|
|
351
|
+
)
|
|
352
|
+
|
|
353
|
+
__algoResultsTab = dbc.Tab(
|
|
354
|
+
className="sub_tab",
|
|
355
|
+
label="Algorithm",
|
|
356
|
+
children=[
|
|
357
|
+
html.Div(
|
|
358
|
+
className="fig_group",
|
|
359
|
+
children=[
|
|
360
|
+
___accuracyPlot,
|
|
361
|
+
# ___globalMetric,
|
|
362
|
+
___metricsTable,
|
|
363
|
+
],
|
|
364
|
+
),
|
|
365
|
+
html.Div(className="fig_group", children=[___specificFilters]),
|
|
366
|
+
],
|
|
367
|
+
)
|
|
368
|
+
|
|
369
|
+
__DTTreeTab = dbc.Tab(
|
|
370
|
+
id="DTTT", className="sub_tab", label="DT Tree", disabled=True,
|
|
371
|
+
children=[
|
|
372
|
+
html.Div(dg.DashInteractiveGraphviz(
|
|
373
|
+
id="DTTT_graph"
|
|
374
|
+
),
|
|
375
|
+
style={"letter-spacing": "0"}),
|
|
376
|
+
]
|
|
377
|
+
)
|
|
378
|
+
|
|
379
|
+
___featuresTable = html.Div(
|
|
380
|
+
className="table_features",
|
|
381
|
+
children=[
|
|
382
|
+
html.H6("Top 10 features sorted by importance"),
|
|
383
|
+
dbc.Button(
|
|
384
|
+
"Export",
|
|
385
|
+
color="primary",
|
|
386
|
+
id="export_features",
|
|
387
|
+
className="custom_buttons",
|
|
388
|
+
n_clicks=0,
|
|
389
|
+
),
|
|
390
|
+
dcc.Download(id="download_dataframe_csv"),
|
|
391
|
+
dcc.Loading(
|
|
392
|
+
id="loading_features_table",
|
|
393
|
+
children=html.Div(id="features_table", children=""),
|
|
394
|
+
type="circle",
|
|
395
|
+
),
|
|
396
|
+
],
|
|
397
|
+
)
|
|
398
|
+
___stripChart = html.Div(
|
|
399
|
+
className="umap_plot_and_title",
|
|
400
|
+
children=[
|
|
401
|
+
html.Div(
|
|
402
|
+
className="title_and_help",
|
|
403
|
+
children=[
|
|
404
|
+
html.H6("StripChart of features"),
|
|
405
|
+
dbc.Button(
|
|
406
|
+
"[?]",
|
|
407
|
+
className="text-muted btn-secondary popover_btn",
|
|
408
|
+
id="help_stripChart",
|
|
409
|
+
),
|
|
410
|
+
dbc.Popover(
|
|
411
|
+
children=[dbc.PopoverBody("Blablabla wout wout")],
|
|
412
|
+
id="pop_help_stripChart",
|
|
413
|
+
is_open=False,
|
|
414
|
+
target="help_stripChart",
|
|
415
|
+
),
|
|
416
|
+
],
|
|
417
|
+
),
|
|
418
|
+
# dbc.Select(
|
|
419
|
+
# id="features_dropdown",
|
|
420
|
+
# className="form_select",
|
|
421
|
+
# options=[{"label": "None", "value": "None"}],
|
|
422
|
+
# value="None",
|
|
423
|
+
# style={"width": "35%"},
|
|
424
|
+
# ),
|
|
425
|
+
dcc.Loading(
|
|
426
|
+
dcc.Graph(id="features_stripChart", config=CONFIG),
|
|
427
|
+
type="dot",
|
|
428
|
+
color="#13BD00",
|
|
429
|
+
),
|
|
430
|
+
dcc.Slider(
|
|
431
|
+
step=None,
|
|
432
|
+
value=1,
|
|
433
|
+
marks=cfg.default_marks,
|
|
434
|
+
id="strip_chart_slider",
|
|
435
|
+
)
|
|
436
|
+
],
|
|
437
|
+
)
|
|
438
|
+
|
|
439
|
+
___coocMatrix = html.Div(
|
|
440
|
+
id="cooc_matrix",
|
|
441
|
+
style={"width": "50%", "height": "5em"},
|
|
442
|
+
children=[
|
|
443
|
+
html.H6("Co-occurence graph of features"),
|
|
444
|
+
dcc.Loading(
|
|
445
|
+
children=[
|
|
446
|
+
cyto.Cytoscape(
|
|
447
|
+
id="cooc_matrix_graph",
|
|
448
|
+
layout={"name": "cose"},
|
|
449
|
+
style={"width": "100%", "height": "100%", "border": "1px solid black"},
|
|
450
|
+
stylesheet=self._plots.get_default_stylesheet_for_cooc_graph(),
|
|
451
|
+
elements=[],
|
|
452
|
+
|
|
453
|
+
),
|
|
454
|
+
html.Div(
|
|
455
|
+
id="cooc_matrix_graph_error",
|
|
456
|
+
children="",
|
|
457
|
+
style={"color": "red", "height": "100%", "background-color": "lightgrey",
|
|
458
|
+
"text-align": "center", "vertical-align": "middle"},
|
|
459
|
+
),
|
|
460
|
+
],
|
|
461
|
+
type="dot",
|
|
462
|
+
color="#13BD00",
|
|
463
|
+
),
|
|
464
|
+
],
|
|
465
|
+
)
|
|
466
|
+
|
|
467
|
+
__featuresResultsTab = dbc.Tab(
|
|
468
|
+
className="sub_tab",
|
|
469
|
+
label="Features",
|
|
470
|
+
children=[
|
|
471
|
+
html.Div(
|
|
472
|
+
className="fig_group", children=[___featuresTable,
|
|
473
|
+
___stripChart
|
|
474
|
+
]
|
|
475
|
+
),
|
|
476
|
+
___coocMatrix
|
|
477
|
+
],
|
|
478
|
+
)
|
|
479
|
+
|
|
480
|
+
_mainPlotContent = html.Div(
|
|
481
|
+
id="main_plots-content",
|
|
482
|
+
children=[ # className="six columns",
|
|
483
|
+
dbc.Tabs(
|
|
484
|
+
className="custom_sub_tabs",
|
|
485
|
+
id="sub_tabs",
|
|
486
|
+
children=[
|
|
487
|
+
__dataResultTab,
|
|
488
|
+
__algoResultsTab,
|
|
489
|
+
__featuresResultsTab,
|
|
490
|
+
__DTTreeTab,
|
|
491
|
+
],
|
|
492
|
+
)
|
|
493
|
+
],
|
|
494
|
+
)
|
|
495
|
+
|
|
496
|
+
return dbc.Tab(
|
|
497
|
+
className="global_tab",
|
|
498
|
+
id="results_tab",
|
|
499
|
+
label="Results",
|
|
500
|
+
children=[
|
|
501
|
+
dcc.Store(id='design_dropdown_store', storage_type='session'),
|
|
502
|
+
dcc.Store(id='ml_dropdown_store', storage_type='session'),
|
|
503
|
+
dcc.Store(id='splits_dropdown_store', storage_type='session'),
|
|
504
|
+
_resultsInfo,
|
|
505
|
+
_mainPlotContent
|
|
506
|
+
],
|
|
507
|
+
)
|
|
508
|
+
|
|
509
|
+
def _registerCallbacks(self) -> None:
|
|
510
|
+
@self.app.callback(
|
|
511
|
+
Output("pop_help_accPlot", "is_open"),
|
|
512
|
+
[Input("help_accPlot", "n_clicks")],
|
|
513
|
+
[State("pop_help_accPlot", "is_open")],
|
|
514
|
+
)
|
|
515
|
+
def toggle_popover(n, is_open):
|
|
516
|
+
if n:
|
|
517
|
+
return not is_open
|
|
518
|
+
return is_open
|
|
519
|
+
|
|
520
|
+
@self.app.callback(
|
|
521
|
+
[Output("design_dropdown", "options"), Output("design_dropdown", "value")],
|
|
522
|
+
[Input("custom_big_tabs", "active_tab")],
|
|
523
|
+
State('design_dropdown_store', 'data'),
|
|
524
|
+
)
|
|
525
|
+
@log_exceptions(self._logger)
|
|
526
|
+
def update_results_dropdown_design(active, stored_value):
|
|
527
|
+
if active == "tab-3":
|
|
528
|
+
self.r = self.metabo_controller.get_all_results()
|
|
529
|
+
experiment_designs = list(self.r.keys())
|
|
530
|
+
if len(experiment_designs) == 0:
|
|
531
|
+
return dash.no_update, dash.no_update
|
|
532
|
+
if stored_value is not None and stored_value in experiment_designs:
|
|
533
|
+
return Utils.format_list_for_checklist(experiment_designs), stored_value
|
|
534
|
+
return (
|
|
535
|
+
Utils.format_list_for_checklist(experiment_designs),
|
|
536
|
+
experiment_designs[0],
|
|
537
|
+
)
|
|
538
|
+
else:
|
|
539
|
+
return dash.no_update, dash.no_update
|
|
540
|
+
|
|
541
|
+
@self.app.callback(
|
|
542
|
+
[Output("ml_dropdown", "options"), Output("ml_dropdown", "value")],
|
|
543
|
+
[Input("design_dropdown", "value")],
|
|
544
|
+
[State("custom_big_tabs", "active_tab"), State('ml_dropdown_store', 'data')],
|
|
545
|
+
)
|
|
546
|
+
@log_exceptions(self._logger)
|
|
547
|
+
def update_results_dropdown_algo(design, active, stored_value):
|
|
548
|
+
if active == "tab-3":
|
|
549
|
+
a = list(self.r[design].keys())
|
|
550
|
+
if stored_value is not None and stored_value in a:
|
|
551
|
+
return [{"label": i, "value": i} for i in a], stored_value
|
|
552
|
+
else:
|
|
553
|
+
return [{"label": i, "value": i} for i in a], a[0]
|
|
554
|
+
else:
|
|
555
|
+
return dash.no_update
|
|
556
|
+
|
|
557
|
+
@self.app.callback(
|
|
558
|
+
[Output("splits_dropdown", "options"), Output("splits_dropdown", "value")],
|
|
559
|
+
[Input("sub_tabs", "active_tab")],
|
|
560
|
+
[State("ml_dropdown", "value"), State("design_dropdown", "value"), State('splits_dropdown_store', 'data')],
|
|
561
|
+
)
|
|
562
|
+
@log_exceptions(self._logger)
|
|
563
|
+
def update_nbr_splits_dropdown(active, algo, design, stored_value):
|
|
564
|
+
if active == "tab-1":
|
|
565
|
+
a = list(self.r[design][algo].splits_number)
|
|
566
|
+
if stored_value is not None and stored_value in a:
|
|
567
|
+
return [{"label": i, "value": i} for i in a], stored_value
|
|
568
|
+
else:
|
|
569
|
+
return [{"label": i, "value": i} for i in a], a[0]
|
|
570
|
+
else:
|
|
571
|
+
return dash.no_update
|
|
572
|
+
|
|
573
|
+
@self.app.callback(
|
|
574
|
+
[Output("loading-output-1", "children")],
|
|
575
|
+
[Input("custom_big_tabs", "active_tab")],
|
|
576
|
+
)
|
|
577
|
+
def input_triggers_spinner(value):
|
|
578
|
+
time.sleep(1)
|
|
579
|
+
return
|
|
580
|
+
|
|
581
|
+
# --- Callbacks to Save Values (persist dropdown selection) ---
|
|
582
|
+
@self.app.callback(
|
|
583
|
+
Output('design_dropdown_store', 'data'),
|
|
584
|
+
Input('load_ML_results_button', 'n_clicks'),
|
|
585
|
+
State('design_dropdown', 'value'),
|
|
586
|
+
)
|
|
587
|
+
def save_design_dropdown_value(_, value):
|
|
588
|
+
return value
|
|
589
|
+
|
|
590
|
+
@self.app.callback(
|
|
591
|
+
Output('ml_dropdown_store', 'data'),
|
|
592
|
+
Input('load_ML_results_button', 'n_clicks'),
|
|
593
|
+
State('ml_dropdown', 'value'),
|
|
594
|
+
)
|
|
595
|
+
def save_ml_dropdown_value(_, value):
|
|
596
|
+
return value
|
|
597
|
+
|
|
598
|
+
@self.app.callback(
|
|
599
|
+
Output('splits_dropdown_store', 'data'),
|
|
600
|
+
Input('update_specific_results_button', 'n_clicks'),
|
|
601
|
+
State('splits_dropdown', 'value'),
|
|
602
|
+
)
|
|
603
|
+
def save_splits_dropdown_value(_, value):
|
|
604
|
+
return value
|
|
605
|
+
|
|
606
|
+
# @self.app.callback(
|
|
607
|
+
# Output("2features", "figure"),
|
|
608
|
+
# [Input("load_ML_results_button", "n_clicks"), Input("pca_slider", "value")],
|
|
609
|
+
# [State("ml_dropdown", "value"), State("design_dropdown", "value")],
|
|
610
|
+
# )
|
|
611
|
+
# def show_pca(n_clicks, features, algo, design_name):
|
|
612
|
+
# if n_clicks >= 1:
|
|
613
|
+
# df = self.r[design_name][algo].results["features_table"]
|
|
614
|
+
# classes = self.r[design_name][algo].results["classes"]
|
|
615
|
+
# return self._plots.show_two_most_important_feature(df[pca_value], classes, pca_value, algo)
|
|
616
|
+
# else:
|
|
617
|
+
# return dash.no_update
|
|
618
|
+
|
|
619
|
+
@self.app.callback(
|
|
620
|
+
[
|
|
621
|
+
Output("cooc_matrix_graph", "elements"),
|
|
622
|
+
Output("cooc_matrix_graph", "style"),
|
|
623
|
+
Output("cooc_matrix_graph_error", "children")
|
|
624
|
+
],
|
|
625
|
+
[
|
|
626
|
+
Input("load_ML_results_button", "n_clicks")
|
|
627
|
+
],
|
|
628
|
+
[
|
|
629
|
+
State("ml_dropdown", "value"),
|
|
630
|
+
State("design_dropdown", "value")
|
|
631
|
+
]
|
|
632
|
+
)
|
|
633
|
+
@log_exceptions(self._logger)
|
|
634
|
+
def show_cooc_matrix(_, algo, design_name):
|
|
635
|
+
if algo == "None" or design_name == "None":
|
|
636
|
+
return [dash.no_update] * 3
|
|
637
|
+
|
|
638
|
+
(
|
|
639
|
+
counter,
|
|
640
|
+
mean_importance,
|
|
641
|
+
number_of_split,
|
|
642
|
+
cardinality
|
|
643
|
+
) = self.r[design_name][algo].results["coocurence_matrix"]
|
|
644
|
+
|
|
645
|
+
if counter is None:
|
|
646
|
+
msg = "Due to the high cardinality of the features, " \
|
|
647
|
+
"the co-occurrence graph cannot be displayed. " \
|
|
648
|
+
"The estimated cardinality is " + str(int(cardinality)) + \
|
|
649
|
+
" and exceed the 1000 links limit."
|
|
650
|
+
return dash.no_update, {'display': 'none'}, msg
|
|
651
|
+
|
|
652
|
+
parameters = self._plots.create_coocurence_graph(counter, mean_importance, number_of_split)
|
|
653
|
+
return parameters, {'display': 'block', "width": "100%", "height": "800px"}, ""
|
|
654
|
+
|
|
655
|
+
@self.app.callback(Output('cooc_matrix_graph', 'stylesheet'),
|
|
656
|
+
[Input('cooc_matrix_graph', 'selectedNodeData')])
|
|
657
|
+
@log_exceptions(self._logger)
|
|
658
|
+
def update_stylesheet(nodes):
|
|
659
|
+
default_stylesheet = self._plots.get_default_stylesheet_for_cooc_graph()
|
|
660
|
+
if nodes is None:
|
|
661
|
+
return default_stylesheet
|
|
662
|
+
else:
|
|
663
|
+
updated_stylesheet = default_stylesheet.copy()
|
|
664
|
+
self._logger.info(f"nodes:\n{nodes}")
|
|
665
|
+
for node in nodes:
|
|
666
|
+
updated_stylesheet.append(self._plots.format_style_for_selected_node(node))
|
|
667
|
+
return updated_stylesheet
|
|
668
|
+
|
|
669
|
+
@self.app.callback(
|
|
670
|
+
[
|
|
671
|
+
Output("pca_slider", "marks"),
|
|
672
|
+
Output("umap_slider", "marks"),
|
|
673
|
+
Output("strip_chart_slider", "marks"),
|
|
674
|
+
Output("pca_slider", "value"),
|
|
675
|
+
Output("umap_slider", "value"),
|
|
676
|
+
Output("strip_chart_slider", "value"),
|
|
677
|
+
],
|
|
678
|
+
[
|
|
679
|
+
Input("load_ML_results_button", "n_clicks")
|
|
680
|
+
],
|
|
681
|
+
[
|
|
682
|
+
State("ml_dropdown", "value"), State("design_dropdown", "value")
|
|
683
|
+
]
|
|
684
|
+
)
|
|
685
|
+
@log_exceptions(self._logger)
|
|
686
|
+
def update_sliders_with_used(_, algo, design_name):
|
|
687
|
+
"""Update PCA, UMAP and Strip chart sliders marks and triggers each plots by updating there values"""
|
|
688
|
+
if algo == "None" or design_name == "None":
|
|
689
|
+
return [dash.no_update] * 6
|
|
690
|
+
|
|
691
|
+
feature_df = self.r[design_name][algo].results["features_table"]
|
|
692
|
+
number_of_used_feature = len(feature_df[feature_df["times_used"] > 0])
|
|
693
|
+
|
|
694
|
+
marks_container = []
|
|
695
|
+
locations_container = []
|
|
696
|
+
|
|
697
|
+
marks, used_location = utils.update_marks(
|
|
698
|
+
custom_value=number_of_used_feature,
|
|
699
|
+
add_all_value=True
|
|
700
|
+
)
|
|
701
|
+
pca_marks, umap_marks = marks, marks
|
|
702
|
+
pca_location, umap_location = used_location, used_location
|
|
703
|
+
marks_container.extend([pca_marks, umap_marks])
|
|
704
|
+
locations_container.extend([pca_location, umap_location])
|
|
705
|
+
|
|
706
|
+
strip_chart_marks, strip_location = utils.update_marks(
|
|
707
|
+
custom_value=number_of_used_feature,
|
|
708
|
+
add_all_value=False
|
|
709
|
+
)
|
|
710
|
+
marks_container.append(strip_chart_marks)
|
|
711
|
+
locations_container.append(strip_location)
|
|
712
|
+
|
|
713
|
+
return (*marks_container, *locations_container)
|
|
714
|
+
|
|
715
|
+
|
|
716
|
+
@self.app.callback(
|
|
717
|
+
[
|
|
718
|
+
Output("PCA", "figure")
|
|
719
|
+
],
|
|
720
|
+
[
|
|
721
|
+
Input("pca_slider", "value"),
|
|
722
|
+
Input("pca_dimensions", "value")
|
|
723
|
+
],
|
|
724
|
+
[
|
|
725
|
+
State("ml_dropdown", "value"),
|
|
726
|
+
State("design_dropdown", "value"),
|
|
727
|
+
State("pca_slider", "marks")
|
|
728
|
+
],
|
|
729
|
+
prevent_initial_call=True
|
|
730
|
+
)
|
|
731
|
+
@log_exceptions(self._logger)
|
|
732
|
+
def show_pca(pca_value, dimensions, algo, design_name, marks):
|
|
733
|
+
"""
|
|
734
|
+
pca_value : represent the number of feature selected by the slider, but is given as indexes
|
|
735
|
+
"""
|
|
736
|
+
if algo == "None" or design_name == "None":
|
|
737
|
+
return dash.no_update
|
|
738
|
+
|
|
739
|
+
classes = self.r[design_name][algo].results["classes"]
|
|
740
|
+
|
|
741
|
+
index = utils.get_index_from_marks(pca_value, marks)
|
|
742
|
+
|
|
743
|
+
if dimensions == "2d":
|
|
744
|
+
data_list, labels_list = self.r[design_name][algo].results["pca_data"]
|
|
745
|
+
fig = self._plots.show_PCA(
|
|
746
|
+
data_list[index], labels_list[index], classes, index, algo,
|
|
747
|
+
self.r[design_name][algo].results["samples_id"]
|
|
748
|
+
)
|
|
749
|
+
elif dimensions == "3d":
|
|
750
|
+
data_list, labels_list = self.r[design_name][algo].results["3d_pca_data"]
|
|
751
|
+
fig = self._plots.show_3D_PCA(
|
|
752
|
+
data_list[index], labels_list[index], classes, index, algo,
|
|
753
|
+
self.r[design_name][algo].results["samples_id"]
|
|
754
|
+
)
|
|
755
|
+
|
|
756
|
+
return [fig]
|
|
757
|
+
|
|
758
|
+
@self.app.callback(
|
|
759
|
+
[
|
|
760
|
+
Output("umap_overview", "figure")
|
|
761
|
+
],
|
|
762
|
+
[
|
|
763
|
+
Input("load_ML_results_button", "n_clicks"),
|
|
764
|
+
Input("umap_slider", "value"),
|
|
765
|
+
Input("umap_dimensions", "value"),
|
|
766
|
+
],
|
|
767
|
+
[
|
|
768
|
+
State("ml_dropdown", "value"),
|
|
769
|
+
State("design_dropdown", "value"),
|
|
770
|
+
State("umap_slider", "marks")
|
|
771
|
+
],
|
|
772
|
+
)
|
|
773
|
+
@log_exceptions(self._logger)
|
|
774
|
+
def show_umap(_, slider_value, dimensions, algo, design_name, marks):
|
|
775
|
+
if algo == "None" or design_name == "None":
|
|
776
|
+
return dash.no_update
|
|
777
|
+
|
|
778
|
+
classes = self.r[design_name][algo].results["classes"]
|
|
779
|
+
|
|
780
|
+
index = utils.get_index_from_marks(slider_value, marks)
|
|
781
|
+
|
|
782
|
+
if dimensions == "2d":
|
|
783
|
+
df = self.r[design_name][algo].results["umap_data"]
|
|
784
|
+
fig = self._plots.show_umap(
|
|
785
|
+
df[index], classes, algo, index,
|
|
786
|
+
self.r[design_name][algo].results["samples_id"]
|
|
787
|
+
)
|
|
788
|
+
elif dimensions == "3d":
|
|
789
|
+
df = self.r[design_name][algo].results["3d_umap_data"]
|
|
790
|
+
fig = self._plots.show_3D_umap(
|
|
791
|
+
df[index], classes, algo, index,
|
|
792
|
+
self.r[design_name][algo].results["samples_id"]
|
|
793
|
+
)
|
|
794
|
+
|
|
795
|
+
return [fig]
|
|
796
|
+
|
|
797
|
+
|
|
798
|
+
@self.app.callback(
|
|
799
|
+
[
|
|
800
|
+
Output("2d_overview", "figure")
|
|
801
|
+
],
|
|
802
|
+
[
|
|
803
|
+
Input("load_ML_results_button", "n_clicks")
|
|
804
|
+
],
|
|
805
|
+
[
|
|
806
|
+
State("ml_dropdown", "value"),
|
|
807
|
+
State("design_dropdown", "value")
|
|
808
|
+
],
|
|
809
|
+
)
|
|
810
|
+
@log_exceptions(self._logger)
|
|
811
|
+
def show_2d(_, algo, design_name):
|
|
812
|
+
if algo == "None" or design_name == "None":
|
|
813
|
+
return dash.no_update
|
|
814
|
+
|
|
815
|
+
df = (
|
|
816
|
+
self.r[design_name][algo].results["features_2d_and_3d"].iloc[:, :-1]
|
|
817
|
+
)
|
|
818
|
+
classes = self.r[design_name][algo].results["classes"]
|
|
819
|
+
fig = self._plots.show_2d(
|
|
820
|
+
df, classes,
|
|
821
|
+
self.r[design_name][algo].results["samples_id"]
|
|
822
|
+
)
|
|
823
|
+
return [fig]
|
|
824
|
+
|
|
825
|
+
|
|
826
|
+
@self.app.callback(
|
|
827
|
+
[
|
|
828
|
+
Output("3d_overview", "figure")
|
|
829
|
+
],
|
|
830
|
+
[
|
|
831
|
+
Input("load_ML_results_button", "n_clicks")
|
|
832
|
+
],
|
|
833
|
+
[
|
|
834
|
+
State("ml_dropdown", "value"),
|
|
835
|
+
State("design_dropdown", "value")
|
|
836
|
+
],
|
|
837
|
+
)
|
|
838
|
+
@log_exceptions(self._logger)
|
|
839
|
+
def show_3d(_, algo, design_name):
|
|
840
|
+
if algo == "None" or design_name == "None":
|
|
841
|
+
return dash.no_update
|
|
842
|
+
|
|
843
|
+
df = self.r[design_name][algo].results["features_2d_and_3d"]
|
|
844
|
+
classes = self.r[design_name][algo].results["classes"]
|
|
845
|
+
fig = self._plots.show_3d(
|
|
846
|
+
df, classes,
|
|
847
|
+
self.r[design_name][algo].results["samples_id"]
|
|
848
|
+
)
|
|
849
|
+
return [fig]
|
|
850
|
+
|
|
851
|
+
@self.app.callback(
|
|
852
|
+
[
|
|
853
|
+
Output("expe_table", "children")
|
|
854
|
+
],
|
|
855
|
+
[
|
|
856
|
+
Input("load_ML_results_button", "n_clicks")
|
|
857
|
+
],
|
|
858
|
+
[
|
|
859
|
+
State("ml_dropdown", "value"),
|
|
860
|
+
State("design_dropdown", "value")
|
|
861
|
+
],
|
|
862
|
+
)
|
|
863
|
+
@log_exceptions(self._logger)
|
|
864
|
+
def get_experiment_statistics(_, algo, design_name):
|
|
865
|
+
if algo == "None" or design_name == "None":
|
|
866
|
+
return dash.no_update
|
|
867
|
+
|
|
868
|
+
df = self.r[design_name][algo].results["info_expe"]
|
|
869
|
+
table_body = self._plots.show_exp_info_all(df)
|
|
870
|
+
table = dbc.Table(
|
|
871
|
+
table_body, id="table_exp_info", borderless=True, hover=True
|
|
872
|
+
) # dbc.Table.from_dataframe(df, borderless=True)
|
|
873
|
+
return [table]
|
|
874
|
+
|
|
875
|
+
|
|
876
|
+
@self.app.callback(
|
|
877
|
+
[
|
|
878
|
+
Output("accuracy_overview", "figure")
|
|
879
|
+
],
|
|
880
|
+
[
|
|
881
|
+
Input("load_ML_results_button", "n_clicks")
|
|
882
|
+
],
|
|
883
|
+
[
|
|
884
|
+
State("ml_dropdown", "value"),
|
|
885
|
+
State("design_dropdown", "value")
|
|
886
|
+
],
|
|
887
|
+
)
|
|
888
|
+
@log_exceptions(self._logger)
|
|
889
|
+
def generates_accuracyPlot_global(_, algo, design_name):
|
|
890
|
+
if algo == "None" or design_name == "None":
|
|
891
|
+
return dash.no_update
|
|
892
|
+
|
|
893
|
+
df = self.r[design_name][algo].results["accuracies_table"]
|
|
894
|
+
fig = self._plots.show_accuracy_all(df, algo)
|
|
895
|
+
return [fig]
|
|
896
|
+
|
|
897
|
+
@self.app.callback(
|
|
898
|
+
[
|
|
899
|
+
Output("metrics_score_table", "children")
|
|
900
|
+
],
|
|
901
|
+
[
|
|
902
|
+
Input("load_ML_results_button", "n_clicks")
|
|
903
|
+
],
|
|
904
|
+
[
|
|
905
|
+
State("ml_dropdown", "value"),
|
|
906
|
+
State("design_dropdown", "value")
|
|
907
|
+
],
|
|
908
|
+
)
|
|
909
|
+
@log_exceptions(self._logger)
|
|
910
|
+
def show_metrics(_, algo, design_name):
|
|
911
|
+
if algo == "None" or design_name == "None":
|
|
912
|
+
return dash.no_update
|
|
913
|
+
|
|
914
|
+
df = self.r[design_name][algo].results["metrics_table"]
|
|
915
|
+
table = dbc.Table.from_dataframe(df, borderless=True)
|
|
916
|
+
return [table]
|
|
917
|
+
|
|
918
|
+
|
|
919
|
+
@self.app.callback(
|
|
920
|
+
[
|
|
921
|
+
Output("split_conf_matrix", "figure"),
|
|
922
|
+
Output("hyperparam_table", "children")
|
|
923
|
+
],
|
|
924
|
+
[
|
|
925
|
+
Input("update_specific_results_button", "n_clicks")],
|
|
926
|
+
[
|
|
927
|
+
State("ml_dropdown", "value"),
|
|
928
|
+
State("design_dropdown", "value"),
|
|
929
|
+
State("splits_dropdown", "value"),
|
|
930
|
+
],
|
|
931
|
+
)
|
|
932
|
+
@log_exceptions(self._logger)
|
|
933
|
+
def compute_split_conf_matrix(_, algo, design_name, split):
|
|
934
|
+
if algo == "None" or design_name == "None":
|
|
935
|
+
return dash.no_update, dash.no_update
|
|
936
|
+
|
|
937
|
+
cm = self.r[design_name][algo].results[split]["Confusion_matrix"][1]
|
|
938
|
+
labels = self.r[design_name][algo].results[split]["Confusion_matrix"][0]
|
|
939
|
+
|
|
940
|
+
text_mat = []
|
|
941
|
+
for i, line in enumerate(cm):
|
|
942
|
+
text_mat.append([])
|
|
943
|
+
for j, col in enumerate(line):
|
|
944
|
+
text_mat[i].append(str(col))
|
|
945
|
+
|
|
946
|
+
hps = self.r[design_name][algo].results[split]["hyperparameters"]
|
|
947
|
+
|
|
948
|
+
hps_df = pd.DataFrame.from_dict({"Hyperparameters": hps.keys(), "Values": hps.values()})
|
|
949
|
+
|
|
950
|
+
dash_table_element = dbc.Table.from_dataframe(hps_df, borderless=True)
|
|
951
|
+
fig = self._plots.show_general_confusion_matrix(
|
|
952
|
+
cm, labels, text_mat, algo, split
|
|
953
|
+
)
|
|
954
|
+
|
|
955
|
+
return fig, dash_table_element
|
|
956
|
+
|
|
957
|
+
|
|
958
|
+
@self.app.callback(
|
|
959
|
+
Output("features_table", "children"),
|
|
960
|
+
Input("load_ML_results_button", "n_clicks"),
|
|
961
|
+
[
|
|
962
|
+
State("ml_dropdown", "value"),
|
|
963
|
+
State("design_dropdown", "value")
|
|
964
|
+
],
|
|
965
|
+
)
|
|
966
|
+
@log_exceptions(self._logger)
|
|
967
|
+
def show_features(_, algo, design_name):
|
|
968
|
+
if algo == "None" or design_name == "None":
|
|
969
|
+
return dash.no_update
|
|
970
|
+
|
|
971
|
+
df = self.r[design_name][algo].results["features_table"].copy()
|
|
972
|
+
df = df.sort_values(by="importance_usage", ascending=False)
|
|
973
|
+
df = df.round(4)
|
|
974
|
+
|
|
975
|
+
return dbc.Table.from_dataframe(df.iloc[:10, :], borderless=True)
|
|
976
|
+
|
|
977
|
+
|
|
978
|
+
@self.app.callback(
|
|
979
|
+
Output("download_dataframe_csv", "data"),
|
|
980
|
+
[Input("export_features", "n_clicks")],
|
|
981
|
+
[State("ml_dropdown", "value"), State("design_dropdown", "value")],
|
|
982
|
+
prevent_initial_call=True,
|
|
983
|
+
)
|
|
984
|
+
@log_exceptions(self._logger)
|
|
985
|
+
def export_download_features_table(n_click, algo, design_name):
|
|
986
|
+
if n_click >= 1:
|
|
987
|
+
df = self.r[design_name][algo].results["features_table"]
|
|
988
|
+
return dcc.send_data_frame(
|
|
989
|
+
df.to_csv, "featuresImportancesTable" + algo + ".csv"
|
|
990
|
+
)
|
|
991
|
+
else:
|
|
992
|
+
return dash.no_update
|
|
993
|
+
|
|
994
|
+
|
|
995
|
+
@self.app.callback(
|
|
996
|
+
[
|
|
997
|
+
Output("features_stripChart", "figure")
|
|
998
|
+
],
|
|
999
|
+
[
|
|
1000
|
+
Input("strip_chart_slider", "value")
|
|
1001
|
+
],
|
|
1002
|
+
[
|
|
1003
|
+
State("ml_dropdown", "value"),
|
|
1004
|
+
State("design_dropdown", "value"),
|
|
1005
|
+
State("strip_chart_slider", "marks")
|
|
1006
|
+
],
|
|
1007
|
+
)
|
|
1008
|
+
@log_exceptions(self._logger)
|
|
1009
|
+
def show_stripChart_features(slider_value, algo, design_name, marks):
|
|
1010
|
+
if algo == "None" or design_name == "None":
|
|
1011
|
+
return dash.no_update
|
|
1012
|
+
|
|
1013
|
+
try:
|
|
1014
|
+
real_value = utils.get_index_from_marks(slider_value, marks)
|
|
1015
|
+
strip_chart_data = self.r[design_name][algo].results["features_stripchart"][real_value]
|
|
1016
|
+
fig = self._plots.show_metabolite_levels(
|
|
1017
|
+
strip_chart_data, algo,
|
|
1018
|
+
self.r[design_name][algo].results["samples_id"]
|
|
1019
|
+
)
|
|
1020
|
+
return [fig]
|
|
1021
|
+
except IndexError:
|
|
1022
|
+
return dash.no_update
|
|
1023
|
+
|
|
1024
|
+
@self.app.callback(
|
|
1025
|
+
[
|
|
1026
|
+
Output("DTTT", "disabled"),
|
|
1027
|
+
Output("DTTT_graph", "dot_source")
|
|
1028
|
+
],
|
|
1029
|
+
[
|
|
1030
|
+
Input("load_ML_results_button", "n_clicks")
|
|
1031
|
+
],
|
|
1032
|
+
[
|
|
1033
|
+
State("ml_dropdown", "value"),
|
|
1034
|
+
State("design_dropdown", "value")
|
|
1035
|
+
],
|
|
1036
|
+
)
|
|
1037
|
+
@log_exceptions(self._logger)
|
|
1038
|
+
def disable_DTTT(_, algo, design_name):
|
|
1039
|
+
if algo == "None" or design_name == "None":
|
|
1040
|
+
return dash.no_update, dash.no_update
|
|
1041
|
+
|
|
1042
|
+
if algo == "DecisionTree":
|
|
1043
|
+
model = self.r[design_name][algo].results["best_model"]
|
|
1044
|
+
classes = list(set(self.r[design_name][algo].results["classes"]))
|
|
1045
|
+
plt.margins(0.05)
|
|
1046
|
+
df = self.r[design_name][algo].results["features_table"]
|
|
1047
|
+
df.sort_index(inplace=True)
|
|
1048
|
+
features_name = list(df["features"])
|
|
1049
|
+
dot_data = tree.export_graphviz(
|
|
1050
|
+
model,
|
|
1051
|
+
out_file=None,
|
|
1052
|
+
class_names=classes,
|
|
1053
|
+
feature_names=features_name,
|
|
1054
|
+
proportion=True,
|
|
1055
|
+
filled=True,
|
|
1056
|
+
rounded=True,
|
|
1057
|
+
special_characters=True,
|
|
1058
|
+
)
|
|
1059
|
+
|
|
1060
|
+
return False, dot_data
|
|
1061
|
+
|
|
1062
|
+
return True, ""
|