Plotly

Plotly

Python graphing library for creating interactive, publication-quality visualizations with 40+ chart types.

For paper-facing palette choices, do not maintain a separate Plotly-only palette policy. Use the shared palette API: python scripts/palette.py recommend ... and python scripts/palette.py snippet <palette-id> --target plotly. Keep journal-inspired, cols4all, and Notion-derived disclaimers visible when turning palette metadata into Plotly code.

Quick Start

Install Plotly:

uv pip install plotly

Basic usage with Plotly Express (high-level API):

import plotly.express as px
import pandas as pd

df = pd.DataFrame({
    'x': [1, 2, 3, 4],
    'y': [10, 11, 12, 13]
})

fig = px.scatter(df, x='x', y='y', title='My First Plot')
fig.show()

Choosing Between APIs

Use Plotly Express (px)

For quick, standard visualizations with sensible defaults:

• Working with pandas DataFrames
• Creating common chart types (scatter, line, bar, histogram, etc.)
• Need automatic color encoding and legends
• Want minimal code (1-5 lines)

See reference/plotly-express.md for complete guide.

Use Graph Objects (go)

For fine-grained control and custom visualizations:

• Chart types not in Plotly Express (3D mesh, isosurface, complex financial charts)
• Building complex multi-trace figures from scratch
• Need precise control over individual components
• Creating specialized visualizations with custom shapes and annotations

See reference/graph-objects.md for complete guide.

Note: Plotly Express returns graph objects Figure, so you can combine approaches:

fig = px.scatter(df, x='x', y='y')
fig.update_layout(title='Custom Title')  # Use go methods on px figure
fig.add_hline(y=10)                     # Add shapes

Core Capabilities

1. Chart Types

Plotly supports 40+ chart types organized into categories:

Basic Charts: scatter, line, bar, pie, area, bubble

Statistical Charts: histogram, box plot, violin, distribution, error bars

Scientific Charts: heatmap, contour, ternary, image display

Financial Charts: candlestick, OHLC, waterfall, funnel, time series

Maps: scatter maps, choropleth, density maps (geographic visualization)

3D Charts: scatter3d, surface, mesh, cone, volume

Specialized: sunburst, treemap, sankey, parallel coordinates, gauge

For detailed examples and usage of all chart types, see reference/chart-types.md.

Canonical Scientific Palettes

For interactive paper supplements, exploratory dashboards tied to manuscript figures, or static Plotly export, use the canonical scientific palette library instead of ad hoc Plotly defaults. In this repo, generate snippets with python scripts/palette.py snippet <palette-id> --target plotly; inside the scientific-visualization plugin, read ../../shared/palette/scientific-figure-palettes.json.

2. Layouts and Styling

Subplots: Create multi-plot figures with shared axes:

from plotly.subplots import make_subplots
import plotly.graph_objects as go

fig = make_subplots(rows=2, cols=2, subplot_titles=('A', 'B', 'C', 'D'))
fig.add_trace(go.Scatter(x=[1, 2], y=[3, 4]), row=1, col=1)

Templates: Apply coordinated styling:

fig = px.scatter(df, x='x', y='y', template='plotly_dark')
# Built-in: plotly_white, plotly_dark, ggplot2, seaborn, simple_white

Customization: Control every aspect of appearance:

• Colors (discrete sequences, continuous scales)
• Fonts and text
• Axes (ranges, ticks, grids)
• Legends
• Margins and sizing
• Annotations and shapes

For complete layout and styling options, see reference/layouts-styling.md.

3. Interactivity

Built-in interactive features:

• Hover tooltips with customizable data
• Pan and zoom
• Legend toggling
• Box/lasso selection
• Rangesliders for time series
• Buttons and dropdowns
• Animations

# Custom hover template
fig.update_traces(
    hovertemplate='<b>%{x}</b><br>Value: %{y:.2f}<extra></extra>'
)

# Add rangeslider
fig.update_xaxes(rangeslider_visible=True)

# Animations
fig = px.scatter(df, x='x', y='y', animation_frame='year')

For complete interactivity guide, see reference/export-interactivity.md.

4. Export Options

Interactive HTML:

fig.write_html('chart.html')                       # Full standalone
fig.write_html('chart.html', include_plotlyjs='cdn')  # Smaller file

Static Images (requires kaleido):

uv pip install kaleido

fig.write_image('chart.png')   # PNG
fig.write_image('chart.pdf')   # PDF
fig.write_image('chart.svg')   # SVG

For complete export options, see reference/export-interactivity.md.

Common Workflows

Scientific Data Visualization

import plotly.express as px

# Scatter plot with trendline
fig = px.scatter(df, x='temperature', y='yield', trendline='ols')

# Heatmap from matrix
fig = px.imshow(correlation_matrix, text_auto=True, color_continuous_scale='RdBu')

# 3D surface plot
import plotly.graph_objects as go
fig = go.Figure(data=[go.Surface(z=z_data, x=x_data, y=y_data)])

Statistical Analysis

# Distribution comparison
fig = px.histogram(df, x='values', color='group', marginal='box', nbins=30)

# Box plot with all points
fig = px.box(df, x='category', y='value', points='all')

# Violin plot
fig = px.violin(df, x='group', y='measurement', box=True)

Time Series and Financial

# Time series with rangeslider
fig = px.line(df, x='date', y='price')
fig.update_xaxes(rangeslider_visible=True)

# Candlestick chart
import plotly.graph_objects as go
fig = go.Figure(data=[go.Candlestick(
    x=df['date'],
    open=df['open'],
    high=df['high'],
    low=df['low'],
    close=df['close']
)])

Multi-Plot Dashboards

from plotly.subplots import make_subplots
import plotly.graph_objects as go

fig = make_subplots(
    rows=2, cols=2,
    subplot_titles=('Scatter', 'Bar', 'Histogram', 'Box'),
    specs=[[{'type': 'scatter'}, {'type': 'bar'}],
           [{'type': 'histogram'}, {'type': 'box'}]]
)

fig.add_trace(go.Scatter(x=[1, 2, 3], y=[4, 5, 6]), row=1, col=1)
fig.add_trace(go.Bar(x=['A', 'B'], y=[1, 2]), row=1, col=2)
fig.add_trace(go.Histogram(x=data), row=2, col=1)
fig.add_trace(go.Box(y=data), row=2, col=2)

fig.update_layout(height=800, showlegend=False)

Integration with Dash

For interactive web applications, use Dash (Plotly's web app framework):

uv pip install dash

import dash
from dash import dcc, html
import plotly.express as px

app = dash.Dash(__name__)

fig = px.scatter(df, x='x', y='y')

app.layout = html.Div([
    html.H1('Dashboard'),
    dcc.Graph(figure=fig)
])

app.run_server(debug=True)

Reference Files

• plotly-express.md - High-level API for quick visualizations
• graph-objects.md - Low-level API for fine-grained control
• chart-types.md - Complete catalog of 40+ chart types with examples
• layouts-styling.md - Subplots, templates, colors, customization
• export-interactivity.md - Export options and interactive features

Additional Resources

• Official documentation: https://plotly.com/python/
• API reference: https://plotly.com/python-api-reference/
• Community forum: https://community.plotly.com/