opencode-skills-collection 4.0.53 → 4.0.55

package/bundled-skills/seaborn/SKILL.md

@@ -6,676 +6,20 @@ metadata:
     skill-author: K-Dense Inc.
 risk: critical
 source: community
+date_added: "2026-09-04"
 ---
 
 # Seaborn Statistical Visualization
 
+## Detailed Guide
+
+Read [the detailed guide](references/detailed-guide.md) before executing this skill. It retains the complete procedure and reference material. Treat its safety, prerequisites, and validation requirements as mandatory. For focused work, load the relevant sections; for end-to-end work, read the guide completely.
+
 ## When to Use
 - You need publication-quality statistical graphics directly from tabular datasets.
 - You are exploring multivariate relationships, distributions, or grouped comparisons with minimal plotting code.
 - You want seaborn's dataset-oriented API and statistical defaults on top of matplotlib.
 
-## Overview
-
-Seaborn is a Python visualization library for creating publication-quality statistical graphics. Use this skill for dataset-oriented plotting, multivariate analysis, automatic statistical estimation, and complex multi-panel figures with minimal code.
-
-## Design Philosophy
-
-Seaborn follows these core principles:
-
-1. **Dataset-oriented**: Work directly with DataFrames and named variables rather than abstract coordinates
-2. **Semantic mapping**: Automatically translate data values into visual properties (colors, sizes, styles)
-3. **Statistical awareness**: Built-in aggregation, error estimation, and confidence intervals
-4. **Aesthetic defaults**: Publication-ready themes and color palettes out of the box
-5. **Matplotlib integration**: Full compatibility with matplotlib customization when needed
-
-## Quick Start
-
-```python
-import seaborn as sns
-import matplotlib.pyplot as plt
-import pandas as pd
-
-# Load example dataset
-df = sns.load_dataset('tips')
-
-# Create a simple visualization
-sns.scatterplot(data=df, x='total_bill', y='tip', hue='day')
-plt.show()
-```
-
-## Core Plotting Interfaces
-
-### Function Interface (Traditional)
-
-The function interface provides specialized plotting functions organized by visualization type. Each category has **axes-level** functions (plot to single axes) and **figure-level** functions (manage entire figure with faceting).
-
-**When to use:**
-- Quick exploratory analysis
-- Single-purpose visualizations
-- When you need a specific plot type
-
-### Objects Interface (Modern)
-
-The `seaborn.objects` interface provides a declarative, composable API similar to ggplot2. Build visualizations by chaining methods to specify data mappings, marks, transformations, and scales.
-
-**When to use:**
-- Complex layered visualizations
-- When you need fine-grained control over transformations
-- Building custom plot types
-- Programmatic plot generation
-
-```python
-from seaborn import objects as so
-
-# Declarative syntax
-(
-    so.Plot(data=df, x='total_bill', y='tip')
-    .add(so.Dot(), color='day')
-    .add(so.Line(), so.PolyFit())
-)
-```
-
-## Plotting Functions by Category
-
-### Relational Plots (Relationships Between Variables)
-
-**Use for:** Exploring how two or more variables relate to each other
-
-- `scatterplot()` - Display individual observations as points
-- `lineplot()` - Show trends and changes (automatically aggregates and computes CI)
-- `relplot()` - Figure-level interface with automatic faceting
-
-**Key parameters:**
-- `x`, `y` - Primary variables
-- `hue` - Color encoding for additional categorical/continuous variable
-- `size` - Point/line size encoding
-- `style` - Marker/line style encoding
-- `col`, `row` - Facet into multiple subplots (figure-level only)
-
-```python
-# Scatter with multiple semantic mappings
-sns.scatterplot(data=df, x='total_bill', y='tip',
-                hue='time', size='size', style='sex')
-
-# Line plot with confidence intervals
-sns.lineplot(data=timeseries, x='date', y='value', hue='category')
-
-# Faceted relational plot
-sns.relplot(data=df, x='total_bill', y='tip',
-            col='time', row='sex', hue='smoker', kind='scatter')
-```
-
-### Distribution Plots (Single and Bivariate Distributions)
-
-**Use for:** Understanding data spread, shape, and probability density
-
-- `histplot()` - Bar-based frequency distributions with flexible binning
-- `kdeplot()` - Smooth density estimates using Gaussian kernels
-- `ecdfplot()` - Empirical cumulative distribution (no parameters to tune)
-- `rugplot()` - Individual observation tick marks
-- `displot()` - Figure-level interface for univariate and bivariate distributions
-- `jointplot()` - Bivariate plot with marginal distributions
-- `pairplot()` - Matrix of pairwise relationships across dataset
-
-**Key parameters:**
-- `x`, `y` - Variables (y optional for univariate)
-- `hue` - Separate distributions by category
-- `stat` - Normalization: "count", "frequency", "probability", "density"
-- `bins` / `binwidth` - Histogram binning control
-- `bw_adjust` - KDE bandwidth multiplier (higher = smoother)
-- `fill` - Fill area under curve
-- `multiple` - How to handle hue: "layer", "stack", "dodge", "fill"
-
-```python
-# Histogram with density normalization
-sns.histplot(data=df, x='total_bill', hue='time',
-             stat='density', multiple='stack')
-
-# Bivariate KDE with contours
-sns.kdeplot(data=df, x='total_bill', y='tip',
-            fill=True, levels=5, thresh=0.1)
-
-# Joint plot with marginals
-sns.jointplot(data=df, x='total_bill', y='tip',
-              kind='scatter', hue='time')
-
-# Pairwise relationships
-sns.pairplot(data=df, hue='species', corner=True)
-```
-
-### Categorical Plots (Comparisons Across Categories)
-
-**Use for:** Comparing distributions or statistics across discrete categories
-
-**Categorical scatterplots:**
-- `stripplot()` - Points with jitter to show all observations
-- `swarmplot()` - Non-overlapping points (beeswarm algorithm)
-
-**Distribution comparisons:**
-- `boxplot()` - Quartiles and outliers
-- `violinplot()` - KDE + quartile information
-- `boxenplot()` - Enhanced boxplot for larger datasets
-
-**Statistical estimates:**
-- `barplot()` - Mean/aggregate with confidence intervals
-- `pointplot()` - Point estimates with connecting lines
-- `countplot()` - Count of observations per category
-
-**Figure-level:**
-- `catplot()` - Faceted categorical plots (set `kind` parameter)
-
-**Key parameters:**
-- `x`, `y` - Variables (one typically categorical)
-- `hue` - Additional categorical grouping
-- `order`, `hue_order` - Control category ordering
-- `dodge` - Separate hue levels side-by-side
-- `orient` - "v" (vertical) or "h" (horizontal)
-- `kind` - Plot type for catplot: "strip", "swarm", "box", "violin", "bar", "point"
-
-```python
-# Swarm plot showing all points
-sns.swarmplot(data=df, x='day', y='total_bill', hue='sex')
-
-# Violin plot with split for comparison
-sns.violinplot(data=df, x='day', y='total_bill',
-               hue='sex', split=True)
-
-# Bar plot with error bars
-sns.barplot(data=df, x='day', y='total_bill',
-            hue='sex', estimator='mean', errorbar='ci')
-
-# Faceted categorical plot
-sns.catplot(data=df, x='day', y='total_bill',
-            col='time', kind='box')
-```
-
-### Regression Plots (Linear Relationships)
-
-**Use for:** Visualizing linear regressions and residuals
-
-- `regplot()` - Axes-level regression plot with scatter + fit line
-- `lmplot()` - Figure-level with faceting support
-- `residplot()` - Residual plot for assessing model fit
-
-**Key parameters:**
-- `x`, `y` - Variables to regress
-- `order` - Polynomial regression order
-- `logistic` - Fit logistic regression
-- `robust` - Use robust regression (less sensitive to outliers)
-- `ci` - Confidence interval width (default 95)
-- `scatter_kws`, `line_kws` - Customize scatter and line properties
-
-```python
-# Simple linear regression
-sns.regplot(data=df, x='total_bill', y='tip')
-
-# Polynomial regression with faceting
-sns.lmplot(data=df, x='total_bill', y='tip',
-           col='time', order=2, ci=95)
-
-# Check residuals
-sns.residplot(data=df, x='total_bill', y='tip')
-```
-
-### Matrix Plots (Rectangular Data)
-
-**Use for:** Visualizing matrices, correlations, and grid-structured data
-
-- `heatmap()` - Color-encoded matrix with annotations
-- `clustermap()` - Hierarchically-clustered heatmap
-
-**Key parameters:**
-- `data` - 2D rectangular dataset (DataFrame or array)
-- `annot` - Display values in cells
-- `fmt` - Format string for annotations (e.g., ".2f")
-- `cmap` - Colormap name
-- `center` - Value at colormap center (for diverging colormaps)
-- `vmin`, `vmax` - Color scale limits
-- `square` - Force square cells
-- `linewidths` - Gap between cells
-
-```python
-# Correlation heatmap
-corr = df.corr()
-sns.heatmap(corr, annot=True, fmt='.2f',
-            cmap='coolwarm', center=0, square=True)
-
-# Clustered heatmap
-sns.clustermap(data, cmap='viridis',
-               standard_scale=1, figsize=(10, 10))
-```
-
-## Multi-Plot Grids
-
-Seaborn provides grid objects for creating complex multi-panel figures:
-
-### FacetGrid
-
-Create subplots based on categorical variables. Most useful when called through figure-level functions (`relplot`, `displot`, `catplot`), but can be used directly for custom plots.
-
-```python
-g = sns.FacetGrid(df, col='time', row='sex', hue='smoker')
-g.map(sns.scatterplot, 'total_bill', 'tip')
-g.add_legend()
-```
-
-### PairGrid
-
-Show pairwise relationships between all variables in a dataset.
-
-```python
-g = sns.PairGrid(df, hue='species')
-g.map_upper(sns.scatterplot)
-g.map_lower(sns.kdeplot)
-g.map_diag(sns.histplot)
-g.add_legend()
-```
-
-### JointGrid
-
-Combine bivariate plot with marginal distributions.
-
-```python
-g = sns.JointGrid(data=df, x='total_bill', y='tip')
-g.plot_joint(sns.scatterplot)
-g.plot_marginals(sns.histplot)
-```
-
-## Figure-Level vs Axes-Level Functions
-
-Understanding this distinction is crucial for effective seaborn usage:
-
-### Axes-Level Functions
-- Plot to a single matplotlib `Axes` object
-- Integrate easily into complex matplotlib figures
-- Accept `ax=` parameter for precise placement
-- Return `Axes` object
-- Examples: `scatterplot`, `histplot`, `boxplot`, `regplot`, `heatmap`
-
-**When to use:**
-- Building custom multi-plot layouts
-- Combining different plot types
-- Need matplotlib-level control
-- Integrating with existing matplotlib code
-
-```python
-fig, axes = plt.subplots(2, 2, figsize=(10, 10))
-sns.scatterplot(data=df, x='x', y='y', ax=axes[0, 0])
-sns.histplot(data=df, x='x', ax=axes[0, 1])
-sns.boxplot(data=df, x='cat', y='y', ax=axes[1, 0])
-sns.kdeplot(data=df, x='x', y='y', ax=axes[1, 1])
-```
-
-### Figure-Level Functions
-- Manage entire figure including all subplots
-- Built-in faceting via `col` and `row` parameters
-- Return `FacetGrid`, `JointGrid`, or `PairGrid` objects
-- Use `height` and `aspect` for sizing (per subplot)
-- Cannot be placed in existing figure
-- Examples: `relplot`, `displot`, `catplot`, `lmplot`, `jointplot`, `pairplot`
-
-**When to use:**
-- Faceted visualizations (small multiples)
-- Quick exploratory analysis
-- Consistent multi-panel layouts
-- Don't need to combine with other plot types
-
-```python
-# Automatic faceting
-sns.relplot(data=df, x='x', y='y', col='category', row='group',
-            hue='type', height=3, aspect=1.2)
-```
-
-## Data Structure Requirements
-
-### Long-Form Data (Preferred)
-
-Each variable is a column, each observation is a row. This "tidy" format provides maximum flexibility:
-
-```python
-# Long-form structure
-   subject  condition  measurement
-0        1    control         10.5
-1        1  treatment         12.3
-2        2    control          9.8
-3        2  treatment         13.1
-```
-
-**Advantages:**
-- Works with all seaborn functions
-- Easy to remap variables to visual properties
-- Supports arbitrary complexity
-- Natural for DataFrame operations
-
-### Wide-Form Data
-
-Variables are spread across columns. Useful for simple rectangular data:
-
-```python
-# Wide-form structure
-   control  treatment
-0     10.5       12.3
-1      9.8       13.1
-```
-
-**Use cases:**
-- Simple time series
-- Correlation matrices
-- Heatmaps
-- Quick plots of array data
-
-**Converting wide to long:**
-```python
-df_long = df.melt(var_name='condition', value_name='measurement')
-```
-
-## Color Palettes
-
-Seaborn provides carefully designed color palettes for different data types:
-
-### Qualitative Palettes (Categorical Data)
-
-Distinguish categories through hue variation:
-- `"deep"` - Default, vivid colors
-- `"muted"` - Softer, less saturated
-- `"pastel"` - Light, desaturated
-- `"bright"` - Highly saturated
-- `"dark"` - Dark values
-- `"colorblind"` - Safe for color vision deficiency
-
-```python
-sns.set_palette("colorblind")
-sns.color_palette("Set2")
-```
-
-### Sequential Palettes (Ordered Data)
-
-Show progression from low to high values:
-- `"rocket"`, `"mako"` - Wide luminance range (good for heatmaps)
-- `"flare"`, `"crest"` - Restricted luminance (good for points/lines)
-- `"viridis"`, `"magma"`, `"plasma"` - Matplotlib perceptually uniform
-
-```python
-sns.heatmap(data, cmap='rocket')
-sns.kdeplot(data=df, x='x', y='y', cmap='mako', fill=True)
-```
-
-### Diverging Palettes (Centered Data)
-
-Emphasize deviations from a midpoint:
-- `"vlag"` - Blue to red
-- `"icefire"` - Blue to orange
-- `"coolwarm"` - Cool to warm
-- `"Spectral"` - Rainbow diverging
-
-```python
-sns.heatmap(correlation_matrix, cmap='vlag', center=0)
-```
-
-### Custom Palettes
-
-```python
-# Create custom palette
-custom = sns.color_palette("husl", 8)
-
-# Light to dark gradient
-palette = sns.light_palette("seagreen", as_cmap=True)
-
-# Diverging palette from hues
-palette = sns.diverging_palette(250, 10, as_cmap=True)
-```
-
-## Theming and Aesthetics
-
-### Set Theme
-
-`set_theme()` controls overall appearance:
-
-```python
-# Set complete theme
-sns.set_theme(style='whitegrid', palette='pastel', font='sans-serif')
-
-# Reset to defaults
-sns.set_theme()
-```
-
-### Styles
-
-Control background and grid appearance:
-- `"darkgrid"` - Gray background with white grid (default)
-- `"whitegrid"` - White background with gray grid
-- `"dark"` - Gray background, no grid
-- `"white"` - White background, no grid
-- `"ticks"` - White background with axis ticks
-
-```python
-sns.set_style("whitegrid")
-
-# Remove spines
-sns.despine(left=False, bottom=False, offset=10, trim=True)
-
-# Temporary style
-with sns.axes_style("white"):
-    sns.scatterplot(data=df, x='x', y='y')
-```
-
-### Contexts
-
-Scale elements for different use cases:
-- `"paper"` - Smallest (default)
-- `"notebook"` - Slightly larger
-- `"talk"` - Presentation slides
-- `"poster"` - Large format
-
-```python
-sns.set_context("talk", font_scale=1.2)
-
-# Temporary context
-with sns.plotting_context("poster"):
-    sns.barplot(data=df, x='category', y='value')
-```
-
-## Best Practices
-
-### 1. Data Preparation
-
-Always use well-structured DataFrames with meaningful column names:
-
-```python
-# Good: Named columns in DataFrame
-df = pd.DataFrame({'bill': bills, 'tip': tips, 'day': days})
-sns.scatterplot(data=df, x='bill', y='tip', hue='day')
-
-# Avoid: Unnamed arrays
-sns.scatterplot(x=x_array, y=y_array)  # Loses axis labels
-```
-
-### 2. Choose the Right Plot Type
-
-**Continuous x, continuous y:** `scatterplot`, `lineplot`, `kdeplot`, `regplot`
-**Continuous x, categorical y:** `violinplot`, `boxplot`, `stripplot`, `swarmplot`
-**One continuous variable:** `histplot`, `kdeplot`, `ecdfplot`
-**Correlations/matrices:** `heatmap`, `clustermap`
-**Pairwise relationships:** `pairplot`, `jointplot`
-
-### 3. Use Figure-Level Functions for Faceting
-
-```python
-# Instead of manual subplot creation
-sns.relplot(data=df, x='x', y='y', col='category', col_wrap=3)
-
-# Not: Creating subplots manually for simple faceting
-```
-
-### 4. Leverage Semantic Mappings
-
-Use `hue`, `size`, and `style` to encode additional dimensions:
-
-```python
-sns.scatterplot(data=df, x='x', y='y',
-                hue='category',      # Color by category
-                size='importance',    # Size by continuous variable
-                style='type')         # Marker style by type
-```
-
-### 5. Control Statistical Estimation
-
-Many functions compute statistics automatically. Understand and customize:
-
-```python
-# Lineplot computes mean and 95% CI by default
-sns.lineplot(data=df, x='time', y='value',
-             errorbar='sd')  # Use standard deviation instead
-
-# Barplot computes mean by default
-sns.barplot(data=df, x='category', y='value',
-            estimator='median',  # Use median instead
-            errorbar=('ci', 95))  # Bootstrapped CI
-```
-
-### 6. Combine with Matplotlib
-
-Seaborn integrates seamlessly with matplotlib for fine-tuning:
-
-```python
-ax = sns.scatterplot(data=df, x='x', y='y')
-ax.set(xlabel='Custom X Label', ylabel='Custom Y Label',
-       title='Custom Title')
-ax.axhline(y=0, color='r', linestyle='--')
-plt.tight_layout()
-```
-
-### 7. Save High-Quality Figures
-
-```python
-fig = sns.relplot(data=df, x='x', y='y', col='group')
-fig.savefig('figure.png', dpi=300, bbox_inches='tight')
-fig.savefig('figure.pdf')  # Vector format for publications
-```
-
-## Common Patterns
-
-### Exploratory Data Analysis
-
-```python
-# Quick overview of all relationships
-sns.pairplot(data=df, hue='target', corner=True)
-
-# Distribution exploration
-sns.displot(data=df, x='variable', hue='group',
-            kind='kde', fill=True, col='category')
-
-# Correlation analysis
-corr = df.corr()
-sns.heatmap(corr, annot=True, cmap='coolwarm', center=0)
-```
-
-### Publication-Quality Figures
-
-```python
-sns.set_theme(style='ticks', context='paper', font_scale=1.1)
-
-g = sns.catplot(data=df, x='treatment', y='response',
-                col='cell_line', kind='box', height=3, aspect=1.2)
-g.set_axis_labels('Treatment Condition', 'Response (μM)')
-g.set_titles('{col_name}')
-sns.despine(trim=True)
-
-g.savefig('figure.pdf', dpi=300, bbox_inches='tight')
-```
-
-### Complex Multi-Panel Figures
-
-```python
-# Using matplotlib subplots with seaborn
-fig, axes = plt.subplots(2, 2, figsize=(12, 10))
-
-sns.scatterplot(data=df, x='x1', y='y', hue='group', ax=axes[0, 0])
-sns.histplot(data=df, x='x1', hue='group', ax=axes[0, 1])
-sns.violinplot(data=df, x='group', y='y', ax=axes[1, 0])
-sns.heatmap(df.pivot_table(values='y', index='x1', columns='x2'),
-            ax=axes[1, 1], cmap='viridis')
-
-plt.tight_layout()
-```
-
-### Time Series with Confidence Bands
-
-```python
-# Lineplot automatically aggregates and shows CI
-sns.lineplot(data=timeseries, x='date', y='measurement',
-             hue='sensor', style='location', errorbar='sd')
-
-# For more control
-g = sns.relplot(data=timeseries, x='date', y='measurement',
-                col='location', hue='sensor', kind='line',
-                height=4, aspect=1.5, errorbar=('ci', 95))
-g.set_axis_labels('Date', 'Measurement (units)')
-```
-
-## Troubleshooting
-
-### Issue: Legend Outside Plot Area
-
-Figure-level functions place legends outside by default. To move inside:
-
-```python
-g = sns.relplot(data=df, x='x', y='y', hue='category')
-g._legend.set_bbox_to_anchor((0.9, 0.5))  # Adjust position
-```
-
-### Issue: Overlapping Labels
-
-```python
-plt.xticks(rotation=45, ha='right')
-plt.tight_layout()
-```
-
-### Issue: Figure Too Small
-
-For figure-level functions:
-```python
-sns.relplot(data=df, x='x', y='y', height=6, aspect=1.5)
-```
-
-For axes-level functions:
-```python
-fig, ax = plt.subplots(figsize=(10, 6))
-sns.scatterplot(data=df, x='x', y='y', ax=ax)
-```
-
-### Issue: Colors Not Distinct Enough
-
-```python
-# Use a different palette
-sns.set_palette("bright")
-
-# Or specify number of colors
-palette = sns.color_palette("husl", n_colors=len(df['category'].unique()))
-sns.scatterplot(data=df, x='x', y='y', hue='category', palette=palette)
-```
-
-### Issue: KDE Too Smooth or Jagged
-
-```python
-# Adjust bandwidth
-sns.kdeplot(data=df, x='x', bw_adjust=0.5)  # Less smooth
-sns.kdeplot(data=df, x='x', bw_adjust=2)    # More smooth
-```
-
-## Resources
-
-This skill includes reference materials for deeper exploration:
-
-### references/
-
-- `function_reference.md` - Comprehensive listing of all seaborn functions with parameters and examples
-- `objects_interface.md` - Detailed guide to the modern seaborn.objects API
-- `examples.md` - Common use cases and code patterns for different analysis scenarios
-
-Load reference files as needed for detailed function signatures, advanced parameters, or specific examples.
-
 ## Limitations
 - Use this skill only when the task clearly matches the scope described above.
 - Do not treat the output as a substitute for environment-specific validation, testing, or expert review.