ModDotPlot 0.9.0__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.
- ModDotPlot-0.9.0.dist-info/LICENSE +21 -0
- ModDotPlot-0.9.0.dist-info/METADATA +421 -0
- ModDotPlot-0.9.0.dist-info/RECORD +14 -0
- ModDotPlot-0.9.0.dist-info/WHEEL +5 -0
- ModDotPlot-0.9.0.dist-info/entry_points.txt +2 -0
- ModDotPlot-0.9.0.dist-info/top_level.txt +1 -0
- moddotplot/__init__.py +1 -0
- moddotplot/__main__.py +11 -0
- moddotplot/const.py +293 -0
- moddotplot/estimate_identity.py +537 -0
- moddotplot/interactive.py +1755 -0
- moddotplot/moddotplot.py +1127 -0
- moddotplot/parse_fasta.py +156 -0
- moddotplot/static_plots.py +1264 -0
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import plotly.express as px
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from moddotplot.estimate_identity import (
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getInteractiveColor,
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getMatchingColors,
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makeDifferencesEqual,
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generateDictionaryFromList,
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findValueInRange,
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convertMatrixToBed,
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)
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import numpy as np
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import dash
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from dash import Input, Output, html, dcc, State
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import math
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import plotly.graph_objs as go
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import logging
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import os
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# Prevent HTTP protocol requests from showing up in terminal
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log = logging.getLogger("werkzeug")
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log.setLevel(logging.ERROR)
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def find_closest_elements(value, sorted_list):
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# Initialize variables to store the indices of the closest elements
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closest_index1 = None
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closest_index2 = None
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# Initialize a variable to store the minimum difference
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min_difference = float("inf")
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# Iterate through the sorted list
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for i in range(len(sorted_list)):
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# Calculate the absolute difference between the current element and the target value
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current_difference = abs(sorted_list[i] - value)
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# Update indices and minimum difference if a closer element is found
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if current_difference < min_difference:
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min_difference = current_difference
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closest_index1 = i
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# Check if there is a previous element to avoid index out of range
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if i > 0:
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closest_index2 = i - 1
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if closest_index1 == None:
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return closest_index2, closest_index2
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elif closest_index2 == None:
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return closest_index1, closest_index1
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if closest_index1 > closest_index2:
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return closest_index2, closest_index1
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else:
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return closest_index1, closest_index2
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def run_dash(matrices, metadata, axes, sparsity, identity, port_number, output_dir):
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# Run Dash app
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app = dash.Dash(__name__, prevent_initial_callbacks="initial_duplicate")
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app.title = "ModDotPlot"
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print(
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f"{app.title} interactive mode is successfully running on http://127.0.0.1:{port_number}/ \n"
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)
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# Initialize first sequence
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image_pyramid = matrices[0]
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current_metadata = metadata[0]
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x_name = metadata[0]["x_name"]
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y_name = metadata[0]["y_name"]
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# Initialize color palette
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palette = "Spectral_11"
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palette_orientation = "+"
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current_color = getInteractiveColor(palette, palette_orientation)
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# Initialize axes and titles for all images
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titles = []
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for i in range(len(metadata)):
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titles.append(metadata[i]["title"])
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# Get zooming thresholds, adjust sparsity respectively.
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def halving_sequence(size, start):
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sequence = [start]
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for _ in range(1, size):
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start /= 2
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sequence.append(start)
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return sequence
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# print(current_metadata)
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mod_thresholds_list = halving_sequence(
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len(current_metadata["sparsities"]), current_metadata["x_size"]
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)
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# print(mod_thresholds_list)
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# print(current_metadata["min_window_size"]* current_metadata["resolution"])
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# print(current_metadata["max_window_size"])
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numo = round(
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math.log2(
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current_metadata["max_window_size"] / current_metadata["min_window_size"]
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)
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+ 1
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)
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# print(numo)
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important = generateDictionaryFromList(mod_thresholds_list)
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# print(f"this is imprtant: {important}")
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main_level = image_pyramid[0]
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main_x_axis = axes[0][0]
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main_y_axis = axes[0][1]
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main_x_axis_np = np.array(main_x_axis)
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# TODO: modify value here
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main_x_axis_np += 3000
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# Modify text so that hover shows interval format
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# TODO: Add intervals in a way that's speedy
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'''X, Y = np.meshgrid(main_x_axis, main_y_axis)
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X = np.delete(X, -1, axis=1)
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X, Y = np.meshgrid(main_x_axis, main_y_axis)
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X = np.delete(X, -1, axis=1)
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X_str = np.array([[f"{str(val)}-{str(val + current_metadata['max_window_size'])}" for val in row] for row in X])
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Y = np.delete(Y, -1, axis=1)
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Y_str = np.array([[f"{str(val)}-{str(val + current_metadata['max_window_size'])}" for val in row] for row in Y])
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hover_template_text = "%{text}<br>%{customdata}<br>Identity: %{z:.1f}"'''
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hover_template_text = "Identity: %{z:.2f}"
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# Create initial heatmap
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heatmap = go.Heatmap(
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z=main_level,
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zmin=identity,
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zmax=100,
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colorscale=current_color,
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x=main_x_axis,
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y=main_y_axis,
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showscale=True,
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colorbar=dict(title="Identity"),
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hoverinfo="all",
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hovertemplate=hover_template_text,
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name="",
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x0=0,
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dx=current_metadata["max_window_size"],
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xtype="scaled",
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y0=0,
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dy=current_metadata["max_window_size"],
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ytype="scaled",
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)
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fig = go.Figure(data=[heatmap])
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fig.update_xaxes(
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showspikes=True,
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spikemode="across",
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ticks="outside",
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showline=True,
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linewidth=2,
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linecolor="black",
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mirror=True,
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)
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fig.update_xaxes(
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nticks=10, title_text=metadata[0]["x_name"], title_font=dict(size=18)
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)
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# Update y-axis properties directly within the heatmap trace
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fig.update_yaxes(
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showspikes=True,
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spikemode="across",
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ticks="outside",
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showline=True,
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linewidth=2,
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linecolor="black",
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mirror=True,
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)
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fig.update_yaxes(title_text=metadata[0]["y_name"], title_font=dict(size=18))
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fig_title = ""
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# TODO: Fine tuning on the names
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title_size = 28
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if metadata[0]["self"]:
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fig_title = f"Self-Identity Plot: {x_name}"
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if len(x_name) > 22:
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title_size = 20
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else:
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fig_title = f"Comparative Plot: {x_name} vs. {y_name}"
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if len(x_name) + len(y_name) > 22:
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title_size = 18
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# Set layout properties
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fig.update_layout(
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height=800,
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width=800,
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hoverlabel=dict(bgcolor="white", font_size=16, font_family="Helvetica"),
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yaxis_scaleanchor="x",
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title=fig_title,
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title_font=dict(size=title_size, family="Helvetica, Arial, sans-serif"),
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title_x=0.5,
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title_y=0.95,
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)
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colorscales = px.colors.named_colorscales()
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colornames = px.colors.named_colorscales()
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colorscales.insert(0, current_color)
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colornames.insert(0, palette)
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# HTML for plot webpage
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app.layout = html.Div(
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id="main_color",
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style={
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"alignItems": "center",
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"backgroundColor": "white",
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"color": "black",
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"height": "100vh",
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},
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children=[
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html.Link(rel="icon", href="/assets/favicon.png"),
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html.Div(
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[
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dcc.Graph(id="dotplot", figure=fig),
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html.Div(
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dcc.RangeSlider(
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id="threshold-slider",
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min=identity,
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max=100,
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step=0.1,
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value=[identity, 100],
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marks=None,
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vertical=True,
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verticalHeight=580,
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allowCross=False,
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pushable=0.1,
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tooltip={"placement": "bottom", "always_visible": False},
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className="custom-slider",
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),
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style={
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"display": "flex",
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"justifyContent": "center",
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"paddingTop": "110px",
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},
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),
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html.Div(
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[
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html.Div(
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[
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dcc.Loading(
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id="loading-2",
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children=[html.Div(id="loading-output-2")],
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type="circle",
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)
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],
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style={
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"paddingBottom": "40px",
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"paddingLeft": "40px",
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"width": "100px",
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"fontFamily": "Helvetica, Arial, sans-serif",
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}, # Added padding to separate the content
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),
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html.Div(
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id="invisible-div",
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children=0,
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style={"display": "none"},
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),
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html.Div(
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[
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html.Label(
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"Currently shown plot:",
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style={
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"marginRight": "10px",
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"padding-left": "20px",
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},
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),
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dcc.Dropdown(
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id="matrix-dropdown",
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options=[
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{"label": f"{title}", "value": f"{title}"}
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for title in titles # Iterate over each title
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],
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value=(
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titles[0] if titles else None
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), # Set default value based on the length of matrices
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clearable=False, # Prevent dropdown from clearing values,
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style={"width": "300px"},
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),
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html.Div(id="output-container"),
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dcc.Store(id="matrices-store", data=len(matrices)),
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],
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style={
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"display": "none" if len(titles) < 2 else "block",
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"width": "fit-content"
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* 2, # Set width to fit content
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"fontFamily": "Helvetica, Arial, sans-serif",
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"paddingTop": "10px",
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"paddingLeft": "25px",
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"paddingBottom": "30px",
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"textAlign": "left",
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},
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),
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html.Div(
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html.Button(
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"Save Matrix to Bed File",
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id="save-bed",
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n_clicks=0,
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disabled=False,
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style={
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"marginLeft": "45px",
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},
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),
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),
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html.Div(
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children=[
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f"Current Window Size: {current_metadata['max_window_size']}"
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],
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id="window-div",
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style={
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"fontFamily": "Helvetica, Arial, sans-serif",
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"paddingTop": "10px",
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"paddingLeft": "45px",
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"paddingBot": "30px",
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"width": "220px",
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"textAlign": "left",
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},
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),
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html.Div(
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f"Minimum Window Size: {current_metadata['min_window_size']}",
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style={
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"fontFamily": "Helvetica, Arial, sans-serif",
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"paddingTop": "10px",
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"paddingLeft": "45px",
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"paddingBot": "30px",
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+
"width": "220px",
|
|
324
|
+
"textAlign": "left",
|
|
325
|
+
},
|
|
326
|
+
),
|
|
327
|
+
dcc.Checklist(
|
|
328
|
+
id="gradient-toggle",
|
|
329
|
+
options=[
|
|
330
|
+
{
|
|
331
|
+
"label": " Readjust Gradient",
|
|
332
|
+
"value": "keep-original",
|
|
333
|
+
}
|
|
334
|
+
],
|
|
335
|
+
value=[],
|
|
336
|
+
style={
|
|
337
|
+
"paddingTop": "10px",
|
|
338
|
+
"paddingLeft": "24px",
|
|
339
|
+
"paddingBottom": "30px",
|
|
340
|
+
"width": "260px",
|
|
341
|
+
"textAlign": "left",
|
|
342
|
+
"fontFamily": "Helvetica, Arial, sans-serif",
|
|
343
|
+
},
|
|
344
|
+
),
|
|
345
|
+
html.Div(id="content"),
|
|
346
|
+
html.Div(
|
|
347
|
+
"Color Palette",
|
|
348
|
+
id="color-palette-text",
|
|
349
|
+
style={
|
|
350
|
+
"fontFamily": "Helvetica, Arial, sans-serif",
|
|
351
|
+
"paddingLeft": "45px", # Added padding to separate the content
|
|
352
|
+
},
|
|
353
|
+
),
|
|
354
|
+
html.Div(
|
|
355
|
+
style={"display": "flex", "height": "10vh"},
|
|
356
|
+
children=[
|
|
357
|
+
html.Div(
|
|
358
|
+
[
|
|
359
|
+
dcc.Dropdown(
|
|
360
|
+
[
|
|
361
|
+
{
|
|
362
|
+
"label": html.Span(
|
|
363
|
+
[
|
|
364
|
+
html.Img(
|
|
365
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/diverging/img/Spectral_11_discrete.png",
|
|
366
|
+
height=10,
|
|
367
|
+
width=100,
|
|
368
|
+
),
|
|
369
|
+
html.Span(
|
|
370
|
+
"Spectral",
|
|
371
|
+
style={
|
|
372
|
+
"fontSize": 15,
|
|
373
|
+
"paddingLeft": 10,
|
|
374
|
+
},
|
|
375
|
+
),
|
|
376
|
+
],
|
|
377
|
+
style={
|
|
378
|
+
"alignItems": "center",
|
|
379
|
+
"justifyContent": "center",
|
|
380
|
+
},
|
|
381
|
+
),
|
|
382
|
+
"value": "Spectral",
|
|
383
|
+
},
|
|
384
|
+
{
|
|
385
|
+
"label": html.Span(
|
|
386
|
+
[
|
|
387
|
+
html.Span(
|
|
388
|
+
"Sequential Color Palettes",
|
|
389
|
+
style={
|
|
390
|
+
"fontSize": 15,
|
|
391
|
+
"paddingLeft": 10,
|
|
392
|
+
},
|
|
393
|
+
),
|
|
394
|
+
],
|
|
395
|
+
style={
|
|
396
|
+
"alignItems": "center",
|
|
397
|
+
"justifyContent": "center",
|
|
398
|
+
},
|
|
399
|
+
),
|
|
400
|
+
"value": "Sequential",
|
|
401
|
+
"disabled": True,
|
|
402
|
+
},
|
|
403
|
+
{
|
|
404
|
+
"label": html.Span(
|
|
405
|
+
[
|
|
406
|
+
html.Img(
|
|
407
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/sequential/img/Blues_9_discrete.png",
|
|
408
|
+
height=10,
|
|
409
|
+
width=100,
|
|
410
|
+
),
|
|
411
|
+
html.Span(
|
|
412
|
+
"Blues",
|
|
413
|
+
style={
|
|
414
|
+
"fontSize": 15,
|
|
415
|
+
"paddingLeft": 10,
|
|
416
|
+
},
|
|
417
|
+
),
|
|
418
|
+
],
|
|
419
|
+
style={
|
|
420
|
+
"alignItems": "center",
|
|
421
|
+
"justifyContent": "center",
|
|
422
|
+
},
|
|
423
|
+
),
|
|
424
|
+
"value": "Blues",
|
|
425
|
+
},
|
|
426
|
+
{
|
|
427
|
+
"label": html.Span(
|
|
428
|
+
[
|
|
429
|
+
html.Img(
|
|
430
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/sequential/img/BuGn_9_discrete.png",
|
|
431
|
+
height=10,
|
|
432
|
+
width=100,
|
|
433
|
+
),
|
|
434
|
+
html.Span(
|
|
435
|
+
"BuGn",
|
|
436
|
+
style={
|
|
437
|
+
"fontSize": 15,
|
|
438
|
+
"paddingLeft": 10,
|
|
439
|
+
},
|
|
440
|
+
),
|
|
441
|
+
],
|
|
442
|
+
style={
|
|
443
|
+
"alignItems": "center",
|
|
444
|
+
"justifyContent": "center",
|
|
445
|
+
},
|
|
446
|
+
),
|
|
447
|
+
"value": "BuGn",
|
|
448
|
+
},
|
|
449
|
+
{
|
|
450
|
+
"label": html.Span(
|
|
451
|
+
[
|
|
452
|
+
html.Img(
|
|
453
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/sequential/img/BuPu_9_discrete.png",
|
|
454
|
+
height=10,
|
|
455
|
+
width=100,
|
|
456
|
+
),
|
|
457
|
+
html.Span(
|
|
458
|
+
"BuPu",
|
|
459
|
+
style={
|
|
460
|
+
"fontSize": 15,
|
|
461
|
+
"paddingLeft": 10,
|
|
462
|
+
},
|
|
463
|
+
),
|
|
464
|
+
],
|
|
465
|
+
style={
|
|
466
|
+
"alignItems": "center",
|
|
467
|
+
"justifyContent": "center",
|
|
468
|
+
},
|
|
469
|
+
),
|
|
470
|
+
"value": "BuPu",
|
|
471
|
+
},
|
|
472
|
+
{
|
|
473
|
+
"label": html.Span(
|
|
474
|
+
[
|
|
475
|
+
html.Img(
|
|
476
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/sequential/img/GnBu_9_discrete.png",
|
|
477
|
+
height=10,
|
|
478
|
+
width=100,
|
|
479
|
+
),
|
|
480
|
+
html.Span(
|
|
481
|
+
"GnBu",
|
|
482
|
+
style={
|
|
483
|
+
"fontSize": 15,
|
|
484
|
+
"paddingLeft": 10,
|
|
485
|
+
},
|
|
486
|
+
),
|
|
487
|
+
],
|
|
488
|
+
style={
|
|
489
|
+
"alignItems": "center",
|
|
490
|
+
"justifyContent": "center",
|
|
491
|
+
},
|
|
492
|
+
),
|
|
493
|
+
"value": "GnBu",
|
|
494
|
+
},
|
|
495
|
+
{
|
|
496
|
+
"label": html.Span(
|
|
497
|
+
[
|
|
498
|
+
html.Img(
|
|
499
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/sequential/img/Greens_9_discrete.png",
|
|
500
|
+
height=10,
|
|
501
|
+
width=100,
|
|
502
|
+
),
|
|
503
|
+
html.Span(
|
|
504
|
+
"Greens",
|
|
505
|
+
style={
|
|
506
|
+
"fontSize": 15,
|
|
507
|
+
"paddingLeft": 10,
|
|
508
|
+
},
|
|
509
|
+
),
|
|
510
|
+
],
|
|
511
|
+
style={
|
|
512
|
+
"alignItems": "center",
|
|
513
|
+
"justifyContent": "center",
|
|
514
|
+
},
|
|
515
|
+
),
|
|
516
|
+
"value": "Green",
|
|
517
|
+
},
|
|
518
|
+
{
|
|
519
|
+
"label": html.Span(
|
|
520
|
+
[
|
|
521
|
+
html.Img(
|
|
522
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/sequential/img/Greys_9_discrete.png",
|
|
523
|
+
height=10,
|
|
524
|
+
width=100,
|
|
525
|
+
),
|
|
526
|
+
html.Span(
|
|
527
|
+
"Greys",
|
|
528
|
+
style={
|
|
529
|
+
"fontSize": 15,
|
|
530
|
+
"paddingLeft": 10,
|
|
531
|
+
},
|
|
532
|
+
),
|
|
533
|
+
],
|
|
534
|
+
style={
|
|
535
|
+
"alignItems": "center",
|
|
536
|
+
"justifyContent": "center",
|
|
537
|
+
},
|
|
538
|
+
),
|
|
539
|
+
"value": "Greys",
|
|
540
|
+
},
|
|
541
|
+
{
|
|
542
|
+
"label": html.Span(
|
|
543
|
+
[
|
|
544
|
+
html.Img(
|
|
545
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/sequential/img/OrRd_9_discrete.png",
|
|
546
|
+
height=10,
|
|
547
|
+
width=100,
|
|
548
|
+
),
|
|
549
|
+
html.Span(
|
|
550
|
+
"OrRd",
|
|
551
|
+
style={
|
|
552
|
+
"fontSize": 15,
|
|
553
|
+
"paddingLeft": 10,
|
|
554
|
+
},
|
|
555
|
+
),
|
|
556
|
+
],
|
|
557
|
+
style={
|
|
558
|
+
"alignItems": "center",
|
|
559
|
+
"justifyContent": "center",
|
|
560
|
+
},
|
|
561
|
+
),
|
|
562
|
+
"value": "OrRd",
|
|
563
|
+
},
|
|
564
|
+
{
|
|
565
|
+
"label": html.Span(
|
|
566
|
+
[
|
|
567
|
+
html.Img(
|
|
568
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/sequential/img/Oranges_9_discrete.png",
|
|
569
|
+
height=10,
|
|
570
|
+
width=100,
|
|
571
|
+
),
|
|
572
|
+
html.Span(
|
|
573
|
+
"Oranges",
|
|
574
|
+
style={
|
|
575
|
+
"fontSize": 15,
|
|
576
|
+
"paddingLeft": 10,
|
|
577
|
+
},
|
|
578
|
+
),
|
|
579
|
+
],
|
|
580
|
+
style={
|
|
581
|
+
"alignItems": "center",
|
|
582
|
+
"justifyContent": "center",
|
|
583
|
+
},
|
|
584
|
+
),
|
|
585
|
+
"value": "Oranges",
|
|
586
|
+
},
|
|
587
|
+
{
|
|
588
|
+
"label": html.Span(
|
|
589
|
+
[
|
|
590
|
+
html.Img(
|
|
591
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/sequential/img/PuBu_9_discrete.png",
|
|
592
|
+
height=10,
|
|
593
|
+
width=100,
|
|
594
|
+
),
|
|
595
|
+
html.Span(
|
|
596
|
+
"PuBu",
|
|
597
|
+
style={
|
|
598
|
+
"fontSize": 15,
|
|
599
|
+
"paddingLeft": 10,
|
|
600
|
+
},
|
|
601
|
+
),
|
|
602
|
+
],
|
|
603
|
+
style={
|
|
604
|
+
"alignItems": "center",
|
|
605
|
+
"justifyContent": "center",
|
|
606
|
+
},
|
|
607
|
+
),
|
|
608
|
+
"value": "PuBu",
|
|
609
|
+
},
|
|
610
|
+
{
|
|
611
|
+
"label": html.Span(
|
|
612
|
+
[
|
|
613
|
+
html.Img(
|
|
614
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/sequential/img/PuBuGn_9_discrete.png",
|
|
615
|
+
height=10,
|
|
616
|
+
width=100,
|
|
617
|
+
),
|
|
618
|
+
html.Span(
|
|
619
|
+
"PuBuGn",
|
|
620
|
+
style={
|
|
621
|
+
"fontSize": 15,
|
|
622
|
+
"paddingLeft": 10,
|
|
623
|
+
},
|
|
624
|
+
),
|
|
625
|
+
],
|
|
626
|
+
style={
|
|
627
|
+
"alignItems": "center",
|
|
628
|
+
"justifyContent": "center",
|
|
629
|
+
},
|
|
630
|
+
),
|
|
631
|
+
"value": "PuBuGn",
|
|
632
|
+
},
|
|
633
|
+
{
|
|
634
|
+
"label": html.Span(
|
|
635
|
+
[
|
|
636
|
+
html.Img(
|
|
637
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/sequential/img/PuRd_9_discrete.png",
|
|
638
|
+
height=10,
|
|
639
|
+
width=100,
|
|
640
|
+
),
|
|
641
|
+
html.Span(
|
|
642
|
+
"PuRd",
|
|
643
|
+
style={
|
|
644
|
+
"fontSize": 15,
|
|
645
|
+
"paddingLeft": 10,
|
|
646
|
+
},
|
|
647
|
+
),
|
|
648
|
+
],
|
|
649
|
+
style={
|
|
650
|
+
"alignItems": "center",
|
|
651
|
+
"justifyContent": "center",
|
|
652
|
+
},
|
|
653
|
+
),
|
|
654
|
+
"value": "PuRd",
|
|
655
|
+
},
|
|
656
|
+
{
|
|
657
|
+
"label": html.Span(
|
|
658
|
+
[
|
|
659
|
+
html.Img(
|
|
660
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/sequential/img/Purples_9_discrete.png",
|
|
661
|
+
height=10,
|
|
662
|
+
width=100,
|
|
663
|
+
),
|
|
664
|
+
html.Span(
|
|
665
|
+
"Purples",
|
|
666
|
+
style={
|
|
667
|
+
"fontSize": 15,
|
|
668
|
+
"paddingLeft": 10,
|
|
669
|
+
},
|
|
670
|
+
),
|
|
671
|
+
],
|
|
672
|
+
style={
|
|
673
|
+
"alignItems": "center",
|
|
674
|
+
"justifyContent": "center",
|
|
675
|
+
},
|
|
676
|
+
),
|
|
677
|
+
"value": "Purples",
|
|
678
|
+
},
|
|
679
|
+
{
|
|
680
|
+
"label": html.Span(
|
|
681
|
+
[
|
|
682
|
+
html.Img(
|
|
683
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/sequential/img/RdPu_9_discrete.png",
|
|
684
|
+
height=10,
|
|
685
|
+
width=100,
|
|
686
|
+
),
|
|
687
|
+
html.Span(
|
|
688
|
+
"RdPu",
|
|
689
|
+
style={
|
|
690
|
+
"fontSize": 15,
|
|
691
|
+
"paddingLeft": 10,
|
|
692
|
+
},
|
|
693
|
+
),
|
|
694
|
+
],
|
|
695
|
+
style={
|
|
696
|
+
"alignItems": "center",
|
|
697
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|
+
[
|
|
1065
|
+
html.Img(
|
|
1066
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/qualitative/img/Dark2_8_discrete.png",
|
|
1067
|
+
height=10,
|
|
1068
|
+
width=100,
|
|
1069
|
+
),
|
|
1070
|
+
html.Span(
|
|
1071
|
+
"Dark2",
|
|
1072
|
+
style={
|
|
1073
|
+
"fontSize": 15,
|
|
1074
|
+
"paddingLeft": 10,
|
|
1075
|
+
},
|
|
1076
|
+
),
|
|
1077
|
+
],
|
|
1078
|
+
style={
|
|
1079
|
+
"alignItems": "center",
|
|
1080
|
+
"justifyContent": "center",
|
|
1081
|
+
},
|
|
1082
|
+
),
|
|
1083
|
+
"value": "Dark2",
|
|
1084
|
+
},
|
|
1085
|
+
{
|
|
1086
|
+
"label": html.Span(
|
|
1087
|
+
[
|
|
1088
|
+
html.Img(
|
|
1089
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/qualitative/img/Paired_12_discrete.png",
|
|
1090
|
+
height=10,
|
|
1091
|
+
width=100,
|
|
1092
|
+
),
|
|
1093
|
+
html.Span(
|
|
1094
|
+
"Paired",
|
|
1095
|
+
style={
|
|
1096
|
+
"fontSize": 15,
|
|
1097
|
+
"paddingLeft": 10,
|
|
1098
|
+
},
|
|
1099
|
+
),
|
|
1100
|
+
],
|
|
1101
|
+
style={
|
|
1102
|
+
"alignItems": "center",
|
|
1103
|
+
"justifyContent": "center",
|
|
1104
|
+
},
|
|
1105
|
+
),
|
|
1106
|
+
"value": "Paired",
|
|
1107
|
+
},
|
|
1108
|
+
{
|
|
1109
|
+
"label": html.Span(
|
|
1110
|
+
[
|
|
1111
|
+
html.Img(
|
|
1112
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/qualitative/img/Pastel1_8_discrete.png",
|
|
1113
|
+
height=10,
|
|
1114
|
+
width=100,
|
|
1115
|
+
),
|
|
1116
|
+
html.Span(
|
|
1117
|
+
"Pastel1",
|
|
1118
|
+
style={
|
|
1119
|
+
"fontSize": 15,
|
|
1120
|
+
"paddingLeft": 10,
|
|
1121
|
+
},
|
|
1122
|
+
),
|
|
1123
|
+
],
|
|
1124
|
+
style={
|
|
1125
|
+
"alignItems": "center",
|
|
1126
|
+
"justifyContent": "center",
|
|
1127
|
+
},
|
|
1128
|
+
),
|
|
1129
|
+
"value": "Pastel1",
|
|
1130
|
+
},
|
|
1131
|
+
{
|
|
1132
|
+
"label": html.Span(
|
|
1133
|
+
[
|
|
1134
|
+
html.Img(
|
|
1135
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/qualitative/img/Pastel2_8_discrete.png",
|
|
1136
|
+
height=10,
|
|
1137
|
+
width=100,
|
|
1138
|
+
),
|
|
1139
|
+
html.Span(
|
|
1140
|
+
"Pastel2",
|
|
1141
|
+
style={
|
|
1142
|
+
"fontSize": 15,
|
|
1143
|
+
"paddingLeft": 10,
|
|
1144
|
+
},
|
|
1145
|
+
),
|
|
1146
|
+
],
|
|
1147
|
+
style={
|
|
1148
|
+
"alignItems": "center",
|
|
1149
|
+
"justifyContent": "center",
|
|
1150
|
+
},
|
|
1151
|
+
),
|
|
1152
|
+
"value": "Pastel2",
|
|
1153
|
+
},
|
|
1154
|
+
{
|
|
1155
|
+
"label": html.Span(
|
|
1156
|
+
[
|
|
1157
|
+
html.Img(
|
|
1158
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/qualitative/img/Set1_8_discrete.png",
|
|
1159
|
+
height=10,
|
|
1160
|
+
width=100,
|
|
1161
|
+
),
|
|
1162
|
+
html.Span(
|
|
1163
|
+
"Set1",
|
|
1164
|
+
style={
|
|
1165
|
+
"fontSize": 15,
|
|
1166
|
+
"paddingLeft": 10,
|
|
1167
|
+
},
|
|
1168
|
+
),
|
|
1169
|
+
],
|
|
1170
|
+
style={
|
|
1171
|
+
"alignItems": "center",
|
|
1172
|
+
"justifyContent": "center",
|
|
1173
|
+
},
|
|
1174
|
+
),
|
|
1175
|
+
"value": "Set1",
|
|
1176
|
+
},
|
|
1177
|
+
{
|
|
1178
|
+
"label": html.Span(
|
|
1179
|
+
[
|
|
1180
|
+
html.Img(
|
|
1181
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/qualitative/img/Set2_8_discrete.png",
|
|
1182
|
+
height=10,
|
|
1183
|
+
width=100,
|
|
1184
|
+
),
|
|
1185
|
+
html.Span(
|
|
1186
|
+
"Set2",
|
|
1187
|
+
style={
|
|
1188
|
+
"fontSize": 15,
|
|
1189
|
+
"paddingLeft": 10,
|
|
1190
|
+
},
|
|
1191
|
+
),
|
|
1192
|
+
],
|
|
1193
|
+
style={
|
|
1194
|
+
"alignItems": "center",
|
|
1195
|
+
"justifyContent": "center",
|
|
1196
|
+
},
|
|
1197
|
+
),
|
|
1198
|
+
"value": "Set2",
|
|
1199
|
+
},
|
|
1200
|
+
{
|
|
1201
|
+
"label": html.Span(
|
|
1202
|
+
[
|
|
1203
|
+
html.Img(
|
|
1204
|
+
src="https://jiffyclub.github.io/palettable/colorbrewer/qualitative/img/Set3_8_discrete.png",
|
|
1205
|
+
height=10,
|
|
1206
|
+
width=100,
|
|
1207
|
+
),
|
|
1208
|
+
html.Span(
|
|
1209
|
+
"Set3",
|
|
1210
|
+
style={
|
|
1211
|
+
"fontSize": 15,
|
|
1212
|
+
"paddingLeft": 10,
|
|
1213
|
+
},
|
|
1214
|
+
),
|
|
1215
|
+
],
|
|
1216
|
+
style={
|
|
1217
|
+
"alignItems": "center",
|
|
1218
|
+
"justifyContent": "center",
|
|
1219
|
+
},
|
|
1220
|
+
),
|
|
1221
|
+
"value": "Set3",
|
|
1222
|
+
},
|
|
1223
|
+
],
|
|
1224
|
+
value=palette.split("_")[0],
|
|
1225
|
+
id="color-options",
|
|
1226
|
+
),
|
|
1227
|
+
html.Div(id="output-div"),
|
|
1228
|
+
],
|
|
1229
|
+
style={
|
|
1230
|
+
"paddingTop": "10px",
|
|
1231
|
+
"paddingLeft": "20px",
|
|
1232
|
+
"width": "250px",
|
|
1233
|
+
"fontFamily": "Helvetica, Arial, sans-serif",
|
|
1234
|
+
}, # Added padding to separate the content
|
|
1235
|
+
)
|
|
1236
|
+
],
|
|
1237
|
+
),
|
|
1238
|
+
html.Div(
|
|
1239
|
+
[
|
|
1240
|
+
html.Div(
|
|
1241
|
+
"Coordinate Log:",
|
|
1242
|
+
id="coordinate-text",
|
|
1243
|
+
style={
|
|
1244
|
+
"fontFamily": "Helvetica, Arial, sans-serif",
|
|
1245
|
+
"paddingLeft": "45px", # Added padding to separate the content
|
|
1246
|
+
"paddingBottom": "10px",
|
|
1247
|
+
},
|
|
1248
|
+
),
|
|
1249
|
+
dcc.Loading(
|
|
1250
|
+
id="loading",
|
|
1251
|
+
type="default",
|
|
1252
|
+
children=[
|
|
1253
|
+
dcc.Textarea(
|
|
1254
|
+
id="text-input",
|
|
1255
|
+
value="",
|
|
1256
|
+
style={
|
|
1257
|
+
"padding": "10px",
|
|
1258
|
+
"height": "40px",
|
|
1259
|
+
"width": "62%",
|
|
1260
|
+
"margin-left": "22px",
|
|
1261
|
+
"fontFamily": "Helvetica, Arial, sans-serif",
|
|
1262
|
+
},
|
|
1263
|
+
),
|
|
1264
|
+
html.Button(
|
|
1265
|
+
"Save Coordinates to Bed File",
|
|
1266
|
+
id="save-button",
|
|
1267
|
+
n_clicks=0,
|
|
1268
|
+
disabled=True,
|
|
1269
|
+
style={"margin": "20px"},
|
|
1270
|
+
),
|
|
1271
|
+
dcc.Download(id="download"),
|
|
1272
|
+
],
|
|
1273
|
+
),
|
|
1274
|
+
],
|
|
1275
|
+
style={
|
|
1276
|
+
"fontFamily": "Helvetica, Arial, sans-serif",
|
|
1277
|
+
},
|
|
1278
|
+
),
|
|
1279
|
+
],
|
|
1280
|
+
style={
|
|
1281
|
+
"paddingTop": "110px",
|
|
1282
|
+
"paddingLeft": "20px",
|
|
1283
|
+
"textAlign": "left",
|
|
1284
|
+
}, # Added paddingTop for the text and centered the text
|
|
1285
|
+
),
|
|
1286
|
+
],
|
|
1287
|
+
style={
|
|
1288
|
+
"display": "flex",
|
|
1289
|
+
"justifyContent": "center",
|
|
1290
|
+
"flex-wrap": "wrap",
|
|
1291
|
+
},
|
|
1292
|
+
),
|
|
1293
|
+
],
|
|
1294
|
+
)
|
|
1295
|
+
|
|
1296
|
+
@app.callback(
|
|
1297
|
+
Output("text-input", "value"),
|
|
1298
|
+
Input("dotplot", "clickData"),
|
|
1299
|
+
Input("invisible-div", "children"),
|
|
1300
|
+
Input("matrix-dropdown", "value"),
|
|
1301
|
+
)
|
|
1302
|
+
def update_text(click_data, zoom_level, timothy):
|
|
1303
|
+
updated_info = ""
|
|
1304
|
+
for i in range(len(titles)):
|
|
1305
|
+
if timothy == titles[i]:
|
|
1306
|
+
updated_info = metadata[i]
|
|
1307
|
+
global clicked_values
|
|
1308
|
+
tmp = updated_info["max_window_size"] // (2**zoom_level)
|
|
1309
|
+
if click_data:
|
|
1310
|
+
x_val = (
|
|
1311
|
+
click_data["points"][0]["x"] if "x" in click_data["points"][0] else ""
|
|
1312
|
+
)
|
|
1313
|
+
y_val = (
|
|
1314
|
+
click_data["points"][0]["y"] if "y" in click_data["points"][0] else ""
|
|
1315
|
+
)
|
|
1316
|
+
z_val = (
|
|
1317
|
+
click_data["points"][0]["z"] if "z" in click_data["points"][0] else ""
|
|
1318
|
+
)
|
|
1319
|
+
|
|
1320
|
+
# Create clicked_values list if it doesn't exist in the global scope
|
|
1321
|
+
if "clicked_values" not in globals():
|
|
1322
|
+
globals()["clicked_values"] = []
|
|
1323
|
+
|
|
1324
|
+
# Append x and y values to the list and keep only the last 5 values
|
|
1325
|
+
# TODO: I shouldn't have to round, but I do :/
|
|
1326
|
+
clicked_values.insert(
|
|
1327
|
+
0,
|
|
1328
|
+
f'{updated_info["x_name"]}: {round(x_val)}-{round(x_val + tmp)}\n{updated_info["y_name"]}: {round(y_val)}-{round(y_val + tmp)}\nIdentity: {round(z_val,2)}\n~',
|
|
1329
|
+
)
|
|
1330
|
+
clicked_values = clicked_values[-100:]
|
|
1331
|
+
return "\n".join((clicked_values))
|
|
1332
|
+
else:
|
|
1333
|
+
return ""
|
|
1334
|
+
|
|
1335
|
+
@app.callback(Output("save-button", "disabled"), Input("text-input", "value"))
|
|
1336
|
+
def update_button_state(text_value):
|
|
1337
|
+
return text_value == ""
|
|
1338
|
+
|
|
1339
|
+
@app.callback(
|
|
1340
|
+
Output("text-input", "value", allow_duplicate=True),
|
|
1341
|
+
Output("save-bed", "n_clicks"),
|
|
1342
|
+
Input("save-bed", "n_clicks"),
|
|
1343
|
+
Input("dotplot", "figure"),
|
|
1344
|
+
)
|
|
1345
|
+
def save_bed(n_clicks, figure):
|
|
1346
|
+
global clicked_values
|
|
1347
|
+
if n_clicks > 0:
|
|
1348
|
+
window_size = figure["data"][0]["x"][1] - figure["data"][0]["x"][0]
|
|
1349
|
+
try:
|
|
1350
|
+
identity = round(
|
|
1351
|
+
min([val for val in figure["data"][0]["z"][0] if val > 0])
|
|
1352
|
+
)
|
|
1353
|
+
x_axis_name = figure["layout"]["xaxis"]["title"]["text"]
|
|
1354
|
+
y_axis_name = figure["layout"]["yaxis"]["title"]["text"]
|
|
1355
|
+
if x_axis_name == y_axis_name:
|
|
1356
|
+
selfy = True
|
|
1357
|
+
title_hi = x_axis_name + ".bed"
|
|
1358
|
+
else:
|
|
1359
|
+
selfy = False
|
|
1360
|
+
title_hi = x_axis_name + "-" + y_axis_name + ".bed"
|
|
1361
|
+
except:
|
|
1362
|
+
identity = 86
|
|
1363
|
+
x_axis_name = "x"
|
|
1364
|
+
y_axis_name = "y"
|
|
1365
|
+
selfy = False
|
|
1366
|
+
title_hi = "x-y.bed"
|
|
1367
|
+
pls = np.array(figure["data"][0]["z"])
|
|
1368
|
+
tr = convertMatrixToBed(
|
|
1369
|
+
pls, window_size, identity, x_axis_name, y_axis_name, selfy
|
|
1370
|
+
)
|
|
1371
|
+
if not output_dir:
|
|
1372
|
+
bedfile_output = os.path.join("./", title_hi)
|
|
1373
|
+
else:
|
|
1374
|
+
bedfile_output = os.path.join(output_dir, title_hi)
|
|
1375
|
+
if (output_dir) and not os.path.exists(output_dir):
|
|
1376
|
+
os.makedirs(output_dir)
|
|
1377
|
+
with open(bedfile_output, "w") as bedfile:
|
|
1378
|
+
for row in tr:
|
|
1379
|
+
bedfile.write("\t".join(map(str, row)) + "\n")
|
|
1380
|
+
msg = f"Saved bed file to {bedfile_output}\n"
|
|
1381
|
+
return msg, 0 # Make sure to return a tuple of values for the outputs
|
|
1382
|
+
else:
|
|
1383
|
+
return (
|
|
1384
|
+
dash.no_update,
|
|
1385
|
+
dash.no_update,
|
|
1386
|
+
) # Return dash.no_update for outputs not being updated
|
|
1387
|
+
|
|
1388
|
+
@app.callback(
|
|
1389
|
+
Output("text-input", "value", allow_duplicate=True),
|
|
1390
|
+
Input("save-button", "n_clicks"),
|
|
1391
|
+
State("text-input", "value"),
|
|
1392
|
+
)
|
|
1393
|
+
def save_to_file(n_clicks, content):
|
|
1394
|
+
global clicked_values
|
|
1395
|
+
if n_clicks > 0 and content:
|
|
1396
|
+
content = content.replace("\n", ",")
|
|
1397
|
+
content = content.replace(": ", ", ")
|
|
1398
|
+
content = content.replace("~,", "\n")
|
|
1399
|
+
content = content.replace(" Identity,", "")
|
|
1400
|
+
content = content.replace("~", "")
|
|
1401
|
+
content = content.replace(",\n", "\n")
|
|
1402
|
+
msg = f"Saved coordinate history to coordinate_log.txt!"
|
|
1403
|
+
with open("coordinate_log.txt", "w") as file:
|
|
1404
|
+
file.write(str(content))
|
|
1405
|
+
return msg
|
|
1406
|
+
|
|
1407
|
+
# Callback activates when panning, zooming, or changing color
|
|
1408
|
+
@app.callback(
|
|
1409
|
+
Output("dotplot", "figure", allow_duplicate=True),
|
|
1410
|
+
Output("loading-output-2", "children"),
|
|
1411
|
+
Output("window-div", "children"),
|
|
1412
|
+
Output("invisible-div", "children"),
|
|
1413
|
+
Input("dotplot", "relayoutData"),
|
|
1414
|
+
Input("dotplot", "figure"),
|
|
1415
|
+
Input("color-options", "value"),
|
|
1416
|
+
Input("threshold-slider", "value"),
|
|
1417
|
+
Input("gradient-toggle", "value"),
|
|
1418
|
+
Input("matrix-dropdown", "value"),
|
|
1419
|
+
Input("invisible-div", "children"),
|
|
1420
|
+
prevent_initial_call=True,
|
|
1421
|
+
)
|
|
1422
|
+
def update_dotplot(
|
|
1423
|
+
relayoutData,
|
|
1424
|
+
figure,
|
|
1425
|
+
color,
|
|
1426
|
+
threshold_range,
|
|
1427
|
+
button_states,
|
|
1428
|
+
timothy,
|
|
1429
|
+
current_zoom,
|
|
1430
|
+
):
|
|
1431
|
+
updated_info = ""
|
|
1432
|
+
updated_title = ""
|
|
1433
|
+
title_size = 28
|
|
1434
|
+
image_axes = []
|
|
1435
|
+
# Matrix dropdown value = Timothy
|
|
1436
|
+
for i in range(len(titles)):
|
|
1437
|
+
if timothy == titles[i]:
|
|
1438
|
+
image_pyramid = matrices[i]
|
|
1439
|
+
image_axes = axes[i]
|
|
1440
|
+
updated_info = metadata[i]
|
|
1441
|
+
if updated_info["self"]:
|
|
1442
|
+
updated_title = f"Self-Identity Plot: {updated_info['x_name']}"
|
|
1443
|
+
if len(updated_info["x_name"]) > 22:
|
|
1444
|
+
title_size = 20
|
|
1445
|
+
else:
|
|
1446
|
+
updated_title = f"Comparative Plot: {updated_info['x_name']} vs. {updated_info['y_name']}"
|
|
1447
|
+
if len(updated_info["x_name"]) + len(updated_info["y_name"]) > 22:
|
|
1448
|
+
title_size = 16
|
|
1449
|
+
new_main_level = image_pyramid[0]
|
|
1450
|
+
fig = go.Figure(data=[heatmap])
|
|
1451
|
+
current_color = getInteractiveColor(getMatchingColors(color), "+")
|
|
1452
|
+
new_heatmap = heatmap
|
|
1453
|
+
new_heatmap.update(dict(colorscale=current_color, z=new_main_level))
|
|
1454
|
+
|
|
1455
|
+
masked_data = np.where(
|
|
1456
|
+
(new_heatmap["z"] < threshold_range[0])
|
|
1457
|
+
| (new_heatmap["z"] > threshold_range[1]),
|
|
1458
|
+
0,
|
|
1459
|
+
new_heatmap["z"],
|
|
1460
|
+
)
|
|
1461
|
+
fig = go.Figure(data=[new_heatmap])
|
|
1462
|
+
fig.update_traces(z=masked_data)
|
|
1463
|
+
|
|
1464
|
+
if "keep-original" in button_states:
|
|
1465
|
+
fig.update_traces(zmin=threshold_range[0])
|
|
1466
|
+
fig.update_traces(zmax=threshold_range[1])
|
|
1467
|
+
else:
|
|
1468
|
+
fig.update_traces(zmin=identity)
|
|
1469
|
+
fig.update_traces(zmax=100)
|
|
1470
|
+
|
|
1471
|
+
fig.update_xaxes(
|
|
1472
|
+
showspikes=True,
|
|
1473
|
+
spikemode="across",
|
|
1474
|
+
ticks="outside",
|
|
1475
|
+
showline=True,
|
|
1476
|
+
linewidth=2,
|
|
1477
|
+
linecolor="black",
|
|
1478
|
+
mirror=True,
|
|
1479
|
+
)
|
|
1480
|
+
# TODO: nticks not working
|
|
1481
|
+
fig.update_xaxes(
|
|
1482
|
+
nticks=10, title_text=updated_info["x_name"], title_font=dict(size=18)
|
|
1483
|
+
)
|
|
1484
|
+
|
|
1485
|
+
# Update y-axis properties directly within the heatmap trace
|
|
1486
|
+
fig.update_yaxes(
|
|
1487
|
+
showspikes=True,
|
|
1488
|
+
spikemode="across",
|
|
1489
|
+
ticks="outside",
|
|
1490
|
+
showline=True,
|
|
1491
|
+
linewidth=2,
|
|
1492
|
+
linecolor="black",
|
|
1493
|
+
mirror=True,
|
|
1494
|
+
)
|
|
1495
|
+
fig.update_yaxes(title_text=updated_info["y_name"], title_font=dict(size=18))
|
|
1496
|
+
|
|
1497
|
+
fig.update_layout(
|
|
1498
|
+
hoverlabel=dict(bgcolor="white", font_size=16, font_family="Helvetica"),
|
|
1499
|
+
title=updated_title, # Add your title here
|
|
1500
|
+
title_font=dict(
|
|
1501
|
+
size=title_size, family="Helvetica"
|
|
1502
|
+
), # Adjust the title font size if needed
|
|
1503
|
+
title_x=0.5,
|
|
1504
|
+
title_y=0.95,
|
|
1505
|
+
)
|
|
1506
|
+
|
|
1507
|
+
fig.update_layout(yaxis_scaleanchor="x")
|
|
1508
|
+
if relayoutData is not None:
|
|
1509
|
+
# TODO: Pan mode should stay in pan mode
|
|
1510
|
+
|
|
1511
|
+
if "xaxis.range[0]" in relayoutData:
|
|
1512
|
+
x_start_range = relayoutData.get("xaxis.range[0]")
|
|
1513
|
+
y_start_range = relayoutData.get("yaxis.range[0]")
|
|
1514
|
+
x_end_range = relayoutData.get("xaxis.range[1]")
|
|
1515
|
+
y_end_range = relayoutData.get("yaxis.range[1]")
|
|
1516
|
+
|
|
1517
|
+
# Check that selected range is in bounds, snap to boundary otherwise
|
|
1518
|
+
# TODO: still broken here
|
|
1519
|
+
if x_start_range is not None:
|
|
1520
|
+
if x_start_range < 0:
|
|
1521
|
+
print("x axis out of bounds! Shifting to x=0")
|
|
1522
|
+
relayoutData["xaxis.range[0]"] = 0
|
|
1523
|
+
x_start_range = 0
|
|
1524
|
+
if y_start_range < 0:
|
|
1525
|
+
print("y axis out of bounds! Shifting to y=0")
|
|
1526
|
+
relayoutData["yaxis.range[0]"] = 0
|
|
1527
|
+
y_start_range = 0
|
|
1528
|
+
if x_end_range > updated_info["x_size"]:
|
|
1529
|
+
print(
|
|
1530
|
+
f"x axis out of bounds! Shifting to x={updated_info['x_size']}"
|
|
1531
|
+
)
|
|
1532
|
+
relayoutData["xaxis.range[1]"] = updated_info["x_size"]
|
|
1533
|
+
x_end_range = updated_info["x_size"]
|
|
1534
|
+
if y_end_range > updated_info["y_size"]:
|
|
1535
|
+
print(
|
|
1536
|
+
f"y axis out of bounds! Shifting to y={updated_info['y_size']}"
|
|
1537
|
+
)
|
|
1538
|
+
relayoutData["yaxis.range[1]"] = updated_info["y_size"]
|
|
1539
|
+
y_end_range = updated_info["y_size"]
|
|
1540
|
+
|
|
1541
|
+
if x_start_range >= 0 and y_start_range >= 0:
|
|
1542
|
+
x_begin = round(relayoutData["xaxis.range[0]"])
|
|
1543
|
+
x_end = round(relayoutData["xaxis.range[1]"])
|
|
1544
|
+
|
|
1545
|
+
y_begin = round(relayoutData["yaxis.range[0]"])
|
|
1546
|
+
y_end = round(relayoutData["yaxis.range[1]"])
|
|
1547
|
+
|
|
1548
|
+
amount = x_end - x_begin
|
|
1549
|
+
|
|
1550
|
+
# This function finds the correct level in the image pyramid
|
|
1551
|
+
try:
|
|
1552
|
+
zoom_factor = findValueInRange(amount, important)
|
|
1553
|
+
except ValueError as err:
|
|
1554
|
+
zoom_factor = 0
|
|
1555
|
+
# If zoom_factor is less than current_zoom, base tmp factors on the older amount
|
|
1556
|
+
|
|
1557
|
+
if zoom_factor > len(image_pyramid) - 1:
|
|
1558
|
+
zoom_factor = len(image_pyramid) - 1
|
|
1559
|
+
if (zoom_factor != 0) or (zoom_factor != current_zoom):
|
|
1560
|
+
using_matrix = image_pyramid[zoom_factor]
|
|
1561
|
+
# Get the coordinates for the better matrix
|
|
1562
|
+
tmp1 = find_closest_elements(
|
|
1563
|
+
x_start_range, image_axes[2 * zoom_factor]
|
|
1564
|
+
)[0]
|
|
1565
|
+
tmp2 = find_closest_elements(
|
|
1566
|
+
x_end_range, image_axes[2 * zoom_factor]
|
|
1567
|
+
)[1]
|
|
1568
|
+
tmp3 = find_closest_elements(
|
|
1569
|
+
y_start_range, image_axes[(2 * zoom_factor) + 1]
|
|
1570
|
+
)[0]
|
|
1571
|
+
tmp4 = find_closest_elements(
|
|
1572
|
+
y_end_range, image_axes[(2 * zoom_factor) + 1]
|
|
1573
|
+
)[1]
|
|
1574
|
+
x_start_updated = math.floor(tmp1)
|
|
1575
|
+
x_end_updated = math.ceil(tmp2)
|
|
1576
|
+
y_start_updated = math.floor(tmp3)
|
|
1577
|
+
y_end_updated = math.ceil(tmp4)
|
|
1578
|
+
|
|
1579
|
+
x_equi, y_equi = makeDifferencesEqual(
|
|
1580
|
+
x_start_updated,
|
|
1581
|
+
x_end_updated,
|
|
1582
|
+
y_start_updated,
|
|
1583
|
+
y_end_updated,
|
|
1584
|
+
)
|
|
1585
|
+
# TODO: flip axes here
|
|
1586
|
+
using_matrix = np.copy(
|
|
1587
|
+
using_matrix[y_start_updated:y_equi, x_start_updated:x_equi]
|
|
1588
|
+
)
|
|
1589
|
+
masked_matrix = np.where(
|
|
1590
|
+
(using_matrix < threshold_range[0])
|
|
1591
|
+
| (using_matrix > threshold_range[1]),
|
|
1592
|
+
0,
|
|
1593
|
+
using_matrix,
|
|
1594
|
+
)
|
|
1595
|
+
|
|
1596
|
+
x_ax = image_axes[2 * zoom_factor][x_start_updated:x_equi]
|
|
1597
|
+
y_ax = image_axes[(2 * zoom_factor) + 1][y_start_updated:y_equi]
|
|
1598
|
+
|
|
1599
|
+
new_hover_template_text = "Identity: %{z:.1f}"
|
|
1600
|
+
|
|
1601
|
+
# Create figure
|
|
1602
|
+
new_heatmap = go.Heatmap(
|
|
1603
|
+
z=masked_matrix,
|
|
1604
|
+
zmin=identity,
|
|
1605
|
+
zmax=100,
|
|
1606
|
+
colorscale=current_color,
|
|
1607
|
+
x=x_ax,
|
|
1608
|
+
y=y_ax,
|
|
1609
|
+
showscale=True, # Shows color scale bar
|
|
1610
|
+
colorbar=dict(title="Identity"), # Color bar title
|
|
1611
|
+
hoverinfo="z", # Hover info to display
|
|
1612
|
+
hovertemplate=new_hover_template_text,
|
|
1613
|
+
name="",
|
|
1614
|
+
x0=x_ax[0],
|
|
1615
|
+
dx=updated_info["max_window_size"] // (2**zoom_factor),
|
|
1616
|
+
xtype="scaled",
|
|
1617
|
+
y0=y_ax[0],
|
|
1618
|
+
dy=updated_info["max_window_size"] // (2**zoom_factor),
|
|
1619
|
+
ytype="scaled",
|
|
1620
|
+
)
|
|
1621
|
+
|
|
1622
|
+
# Create the figure
|
|
1623
|
+
current_fig = go.Figure(data=[new_heatmap])
|
|
1624
|
+
current_fig.update_xaxes(
|
|
1625
|
+
showspikes=True,
|
|
1626
|
+
spikemode="across",
|
|
1627
|
+
ticks="outside",
|
|
1628
|
+
showline=True,
|
|
1629
|
+
linewidth=2,
|
|
1630
|
+
linecolor="black",
|
|
1631
|
+
mirror=True,
|
|
1632
|
+
)
|
|
1633
|
+
current_fig.update_xaxes(
|
|
1634
|
+
nticks=10,
|
|
1635
|
+
title_text=updated_info["x_name"],
|
|
1636
|
+
title_font=dict(size=18),
|
|
1637
|
+
)
|
|
1638
|
+
|
|
1639
|
+
# Update y-axis properties directly within the heatmap trace
|
|
1640
|
+
current_fig.update_yaxes(
|
|
1641
|
+
showspikes=True,
|
|
1642
|
+
spikemode="across",
|
|
1643
|
+
ticks="outside",
|
|
1644
|
+
showline=True,
|
|
1645
|
+
linewidth=2,
|
|
1646
|
+
linecolor="black",
|
|
1647
|
+
mirror=True,
|
|
1648
|
+
)
|
|
1649
|
+
|
|
1650
|
+
current_fig.update_yaxes(
|
|
1651
|
+
title_text=updated_info["y_name"], title_font=dict(size=18)
|
|
1652
|
+
)
|
|
1653
|
+
current_fig.update_layout(
|
|
1654
|
+
hoverlabel=dict(
|
|
1655
|
+
bgcolor="white", font_size=16, font_family="Helvetica"
|
|
1656
|
+
),
|
|
1657
|
+
title=fig_title, # Add your title here
|
|
1658
|
+
title_font=dict(size=28, family="Helvetica"),
|
|
1659
|
+
title_x=0.5, # Center horizontally
|
|
1660
|
+
title_y=0.95, # Center vertically
|
|
1661
|
+
)
|
|
1662
|
+
current_fig.update_layout(yaxis_scaleanchor="x")
|
|
1663
|
+
return (
|
|
1664
|
+
current_fig,
|
|
1665
|
+
"",
|
|
1666
|
+
f"Current Window Size: {updated_info['max_window_size']//(2**zoom_factor)}",
|
|
1667
|
+
zoom_factor,
|
|
1668
|
+
)
|
|
1669
|
+
else:
|
|
1670
|
+
# Happens when panning or zooming in/out within threshold
|
|
1671
|
+
return (
|
|
1672
|
+
figure,
|
|
1673
|
+
"",
|
|
1674
|
+
f"Current Window Size: {updated_info['max_window_size']//(2**current_zoom)}",
|
|
1675
|
+
current_zoom,
|
|
1676
|
+
)
|
|
1677
|
+
|
|
1678
|
+
elif "xaxis.autorange" in relayoutData:
|
|
1679
|
+
# Triggers when double-clicked or reset axes
|
|
1680
|
+
return (
|
|
1681
|
+
fig,
|
|
1682
|
+
"",
|
|
1683
|
+
f"Current Window Size: {updated_info['max_window_size']}",
|
|
1684
|
+
0,
|
|
1685
|
+
)
|
|
1686
|
+
|
|
1687
|
+
# TODO: disable Autosizing
|
|
1688
|
+
elif "autosize" in relayoutData:
|
|
1689
|
+
# Autosize should be disabled: if not it gets handled here
|
|
1690
|
+
return (
|
|
1691
|
+
figure,
|
|
1692
|
+
"",
|
|
1693
|
+
f"Current Window Size: {updated_info['max_window_size']}",
|
|
1694
|
+
zoom_factor,
|
|
1695
|
+
)
|
|
1696
|
+
|
|
1697
|
+
else:
|
|
1698
|
+
# Happens when user selects pan mode.
|
|
1699
|
+
# TODO: get correct window size
|
|
1700
|
+
return (
|
|
1701
|
+
figure,
|
|
1702
|
+
"",
|
|
1703
|
+
f"Current Window Size: {updated_info['max_window_size']//(2**current_zoom)}",
|
|
1704
|
+
current_zoom,
|
|
1705
|
+
)
|
|
1706
|
+
else:
|
|
1707
|
+
# This occurs at startup and when selecting color. Return the base figure with color
|
|
1708
|
+
# fig.update_layout(coloraxis=dict(colorscale=current_color))
|
|
1709
|
+
return (
|
|
1710
|
+
fig,
|
|
1711
|
+
"",
|
|
1712
|
+
f"Current Window Size: {updated_info['max_window_size']}",
|
|
1713
|
+
current_zoom,
|
|
1714
|
+
)
|
|
1715
|
+
|
|
1716
|
+
# -------DO NOT DELETE! CUSTOM CSS FOR IDENTITY THRESHOLD SLIDER--------
|
|
1717
|
+
app.index_string = """
|
|
1718
|
+
<!DOCTYPE html>
|
|
1719
|
+
<html>
|
|
1720
|
+
<head>
|
|
1721
|
+
{%metas%}
|
|
1722
|
+
<title>{%title%}</title>
|
|
1723
|
+
{%favicon%}
|
|
1724
|
+
{%css%}
|
|
1725
|
+
<style>
|
|
1726
|
+
/* Custom CSS for the RangeSlider */
|
|
1727
|
+
.custom-slider .rc-slider-track {
|
|
1728
|
+
background-color: gray; /* Change the highlight color to gray */
|
|
1729
|
+
}
|
|
1730
|
+
|
|
1731
|
+
.custom-slider .rc-slider-dot {
|
|
1732
|
+
display: none; /* Hide the dots */
|
|
1733
|
+
}
|
|
1734
|
+
|
|
1735
|
+
.custom-slider .rc-slider-handle {
|
|
1736
|
+
border: 2px solid black; /* Change the handle border color to gray */
|
|
1737
|
+
font-family: Helvetica, Arial, sans-serif;
|
|
1738
|
+
}
|
|
1739
|
+
#main_color {
|
|
1740
|
+
justify-content:center;
|
|
1741
|
+
}
|
|
1742
|
+
</style>
|
|
1743
|
+
</head>
|
|
1744
|
+
<body>
|
|
1745
|
+
{%app_entry%}
|
|
1746
|
+
<footer>
|
|
1747
|
+
{%config%}
|
|
1748
|
+
{%scripts%}
|
|
1749
|
+
{%renderer%}
|
|
1750
|
+
</footer>
|
|
1751
|
+
</body>
|
|
1752
|
+
</html>
|
|
1753
|
+
"""
|
|
1754
|
+
# TODO: Change debug to False for production
|
|
1755
|
+
app.run(debug=False, use_reloader=False, port=port_number)
|