@wentorai/research-plugins 1.0.0

package/skills/analysis/dataviz/color-accessibility-guide/SKILL.md

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+---
+name: color-accessibility-guide
+description: "Colorblind-friendly palettes and accessible visualization design"
+metadata:
+  openclaw:
+    emoji: "palette"
+    category: "analysis"
+    subcategory: "dataviz"
+    keywords: ["colorblind-friendly palette", "accessible color scheme", "visualization principles", "data-ink ratio"]
+    source: "wentor-research-plugins"
+---
+
+# Color Accessibility Guide
+
+Design data visualizations that are accessible to colorblind readers and follow best practices for clarity, using tested palettes and encoding principles.
+
+## Color Vision Deficiency Overview
+
+Approximately 8% of males and 0.5% of females have some form of color vision deficiency (CVD). The most common types:
+
+| Type | Prevalence (Male) | Affected Colors | Commonly Confused |
+|------|-------------------|-----------------|-------------------|
+| Deuteranomaly (green-weak) | 5% | Green | Red and green |
+| Protanomaly (red-weak) | 1% | Red | Red and green |
+| Deuteranopia (no green) | 1% | Green | Red and green |
+| Protanopia (no red) | 1% | Red | Red and green |
+| Tritanopia (no blue) | 0.003% | Blue | Blue and yellow |
+| Monochromacy | Very rare | All | All colors |
+
+**Key takeaway**: Never rely solely on a red-green distinction to convey information. About 1 in 12 male readers cannot distinguish them.
+
+## Recommended Colorblind-Safe Palettes
+
+### Qualitative Palettes (Categorical Data)
+
+#### Wong (2011) Nature Palette (8 colors)
+
+Widely recommended for scientific publications:
+
+```python
+# Wong's colorblind-friendly palette
+wong_palette = {
+    "black":       "#000000",
+    "orange":      "#E69F00",
+    "sky_blue":    "#56B4E9",
+    "bluish_green":"#009E73",
+    "yellow":      "#F0E442",
+    "blue":        "#0072B2",
+    "vermillion":  "#D55E00",
+    "reddish_purple":"#CC79A7"
+}
+```
+
+#### Okabe-Ito Palette
+
+```python
+okabe_ito = ["#E69F00", "#56B4E9", "#009E73", "#F0E442",
+             "#0072B2", "#D55E00", "#CC79A7", "#000000"]
+```
+
+#### Tol's Qualitative Palette
+
+```python
+# Paul Tol's qualitative palette (up to 12 distinct colors)
+tol_qualitative = ["#332288", "#88CCEE", "#44AA99", "#117733",
+                   "#999933", "#DDCC77", "#CC6677", "#882255",
+                   "#AA4499", "#661100", "#6699CC", "#888888"]
+```
+
+### Sequential Palettes (Ordered Data)
+
+For continuous data, use perceptually uniform colormaps:
+
+```python
+import matplotlib.pyplot as plt
+
+# Recommended sequential colormaps
+# These are perceptually uniform and colorblind-safe:
+good_cmaps = ["viridis", "plasma", "inferno", "magma", "cividis"]
+
+# Avoid these (not perceptually uniform, not colorblind-safe):
+bad_cmaps = ["jet", "rainbow", "hsv"]  # NEVER use these
+
+# Example usage
+import numpy as np
+data = np.random.randn(10, 10)
+fig, ax = plt.subplots(figsize=(8, 6))
+im = ax.imshow(data, cmap="viridis")
+plt.colorbar(im)
+plt.title("Use viridis, not jet")
+plt.savefig("heatmap.pdf", dpi=300, bbox_inches="tight")
+```
+
+### Diverging Palettes (Data with Meaningful Center)
+
+```python
+# Colorblind-safe diverging palettes
+# Blue-to-Red via white (good for temperature, correlation)
+import matplotlib.colors as mcolors
+
+# Built-in matplotlib options:
+diverging_safe = ["RdBu_r", "PuOr_r", "BrBG"]
+
+# Custom two-color diverging (Tol):
+tol_diverging = ["#364B9A", "#4A7BB7", "#6EA6CD", "#98CAE1", "#C2E4EF",
+                 "#EAECCC", "#FEDA8B", "#FDB366", "#F67E4B", "#DD3D2D", "#A50026"]
+```
+
+## Design Principles for Accessible Visualization
+
+### 1. Data-Ink Ratio
+
+Edward Tufte's principle: maximize the proportion of ink used to display actual data.
+
+```python
+import matplotlib.pyplot as plt
+
+fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(12, 5))
+
+# BAD: Low data-ink ratio (chartjunk)
+ax1.bar(range(5), [3, 7, 2, 5, 8], color="blue", edgecolor="black",
+        linewidth=2)
+ax1.set_facecolor("#EEEEEE")
+ax1.grid(True, color="white", linewidth=2)
+ax1.set_title("Before: Low Data-Ink Ratio")
+
+# GOOD: High data-ink ratio
+ax2.bar(range(5), [3, 7, 2, 5, 8], color="#0072B2", edgecolor="none")
+ax2.spines["top"].set_visible(False)
+ax2.spines["right"].set_visible(False)
+ax2.set_title("After: High Data-Ink Ratio")
+
+plt.tight_layout()
+plt.savefig("data_ink_ratio.pdf", dpi=300)
+```
+
+### 2. Redundant Encoding
+
+Never use color as the sole channel for conveying information. Combine color with at least one other visual channel:
+
+| Channel | Examples |
+|---------|----------|
+| Shape | Circles, squares, triangles for different groups |
+| Pattern | Solid, dashed, dotted lines |
+| Fill pattern | Hatching, cross-hatching for bar charts |
+| Label | Direct text labels on or near data points |
+| Position | Separate panels (facets) for each group |
+| Size | Varying point sizes |
+
+```python
+import matplotlib.pyplot as plt
+
+markers = ['o', 's', '^', 'D']  # Different shapes
+colors = ['#0072B2', '#D55E00', '#009E73', '#CC79A7']
+labels = ['Group A', 'Group B', 'Group C', 'Group D']
+
+fig, ax = plt.subplots(figsize=(8, 6))
+for i in range(4):
+    ax.scatter(x[i], y[i], c=colors[i], marker=markers[i],
+               s=80, label=labels[i], edgecolors='black', linewidth=0.5)
+
+ax.legend()
+ax.set_xlabel("X Variable")
+ax.set_ylabel("Y Variable")
+plt.savefig("redundant_encoding.pdf", dpi=300)
+```
+
+### 3. Line Style Differentiation
+
+```python
+line_styles = ['-', '--', '-.', ':', (0, (3, 1, 1, 1))]
+colors = ['#0072B2', '#D55E00', '#009E73', '#CC79A7', '#E69F00']
+
+fig, ax = plt.subplots(figsize=(8, 5))
+for i in range(5):
+    ax.plot(x, data[i], color=colors[i], linestyle=line_styles[i],
+            linewidth=2, label=f"Method {i+1}")
+
+ax.legend()
+```
+
+## Checking Your Visualizations
+
+### Simulation Tools
+
+| Tool | Platform | URL |
+|------|----------|-----|
+| Coblis | Web | color-blindness.com/coblis |
+| Color Oracle | Desktop (Win/Mac/Linux) | colororacle.org |
+| Sim Daltonism | macOS | michelf.ca/projects/sim-daltonism |
+| Colorblindly | Chrome extension | Chrome Web Store |
+| Matplotlib CVD simulation | Python | See code below |
+
+### Programmatic CVD Simulation
+
+```python
+from colorspacious import cspace_convert
+import numpy as np
+
+def simulate_cvd(rgb_hex, deficiency="deuteranomaly", severity=100):
+    """Simulate how a color appears to someone with CVD."""
+    # Convert hex to RGB [0,1]
+    rgb = np.array([int(rgb_hex[i:i+2], 16)/255 for i in (1, 3, 5)])
+
+    # Convert using colorspacious
+    cvd_space = {"name": "sRGB1+CVD",
+                 "cvd_type": deficiency,
+                 "severity": severity}
+    rgb_cvd = cspace_convert(rgb, cvd_space, "sRGB1")
+    rgb_cvd = np.clip(rgb_cvd, 0, 1)
+
+    return "#{:02x}{:02x}{:02x}".format(*[int(c*255) for c in rgb_cvd])
+
+# Test your palette
+for color in ["#FF0000", "#00FF00", "#0072B2", "#D55E00"]:
+    sim = simulate_cvd(color)
+    print(f"{color} -> {sim} (deuteranomaly)")
+```
+
+## Quick Reference: Do's and Don'ts
+
+| Do | Don't |
+|----|-------|
+| Use Wong or Okabe-Ito palettes | Use red vs. green to distinguish categories |
+| Use viridis/cividis colormaps | Use jet/rainbow colormaps |
+| Add shape/pattern as redundant encoding | Rely on color alone |
+| Use direct labels when possible | Force readers to match colors to legend repeatedly |
+| Test with CVD simulators | Assume your color choices work for everyone |
+| Use high contrast (WCAG AA: 4.5:1 ratio) | Use light colors on white backgrounds |
+| Keep maximum 7-8 colors in categorical charts | Use 15+ colors that are impossible to distinguish |

package/skills/analysis/dataviz/geospatial-viz-guide/SKILL.md

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+---
+name: geospatial-viz-guide
+description: "Create maps, choropleths, and spatial data visualizations for research"
+metadata:
+  openclaw:
+    emoji: "world_map"
+    category: "analysis"
+    subcategory: "dataviz"
+    keywords: ["geospatial", "choropleth", "maps", "GIS", "spatial visualization", "geopandas"]
+    source: "wentor-research-plugins"
+---
+
+# Geospatial Visualization Guide
+
+A skill for creating maps, choropleths, and spatial data visualizations for research publications. Covers coordinate systems, choropleth maps, point maps, Python geospatial libraries, and cartographic best practices for academic papers.
+
+## Geospatial Data Fundamentals
+
+### Common Spatial Data Formats
+
+```
+Vector data (discrete features):
+  - Shapefile (.shp): Legacy standard, multi-file
+  - GeoJSON (.geojson): Web-friendly, single file
+  - GeoPackage (.gpkg): Modern SQLite-based, recommended
+  - KML (.kml): Google Earth format
+
+Raster data (continuous surfaces):
+  - GeoTIFF (.tif): Georeferenced image
+  - NetCDF (.nc): Climate and atmospheric data
+  - HDF5 (.h5): Satellite and remote sensing data
+
+Key concepts:
+  - CRS (Coordinate Reference System): How 3D Earth maps to 2D
+  - EPSG:4326 (WGS84): Latitude/longitude (most GPS data)
+  - EPSG:3857: Web Mercator (Google Maps, web tiles)
+  - Always check and document your CRS
+```
+
+## Choropleth Maps
+
+### Building a Choropleth with GeoPandas
+
+```python
+import geopandas as gpd
+import matplotlib.pyplot as plt
+
+
+def create_choropleth(shapefile_path: str, data_column: str,
+                      title: str, cmap: str = "YlOrRd") -> None:
+    """
+    Create a choropleth map from a shapefile.
+
+    Args:
+        shapefile_path: Path to shapefile or GeoPackage
+        data_column: Column name to visualize
+        title: Map title
+        cmap: Matplotlib colormap name
+    """
+    gdf = gpd.read_file(shapefile_path)
+
+    fig, ax = plt.subplots(1, 1, figsize=(12, 8))
+
+    gdf.plot(
+        column=data_column,
+        cmap=cmap,
+        linewidth=0.5,
+        edgecolor="0.5",
+        legend=True,
+        legend_kwds={
+            "label": data_column,
+            "orientation": "horizontal",
+            "shrink": 0.6,
+            "pad": 0.05
+        },
+        ax=ax
+    )
+
+    ax.set_title(title, fontsize=14, fontweight="bold")
+    ax.axis("off")
+    plt.tight_layout()
+    plt.savefig("choropleth.pdf", bbox_inches="tight", dpi=300)
+```
+
+### Joining Data to Geometries
+
+```python
+import pandas as pd
+
+
+def join_data_to_map(gdf: gpd.GeoDataFrame,
+                     data: pd.DataFrame,
+                     geo_key: str,
+                     data_key: str) -> gpd.GeoDataFrame:
+    """
+    Join tabular data to geographic features.
+
+    Args:
+        gdf: GeoDataFrame with polygons (e.g., country boundaries)
+        data: DataFrame with your research data
+        geo_key: Column in gdf to join on (e.g., 'ISO_A3')
+        data_key: Column in data to join on (e.g., 'country_code')
+    """
+    merged = gdf.merge(data, left_on=geo_key, right_on=data_key, how="left")
+
+    missing = merged[merged[data.columns[1]].isna()]
+    if len(missing) > 0:
+        print(f"Warning: {len(missing)} regions have no data (will appear blank)")
+
+    return merged
+```
+
+## Point Maps and Proportional Symbols
+
+### Mapping Research Sites or Events
+
+```python
+def create_point_map(gdf_base: gpd.GeoDataFrame,
+                     points: gpd.GeoDataFrame,
+                     size_column: str = None,
+                     color_column: str = None) -> None:
+    """
+    Create a point map with proportional symbols.
+
+    Args:
+        gdf_base: Base map (country or region polygons)
+        points: GeoDataFrame with point geometries
+        size_column: Column to scale point sizes
+        color_column: Column to color points
+    """
+    fig, ax = plt.subplots(figsize=(12, 8))
+
+    # Base map
+    gdf_base.plot(ax=ax, color="lightgray", edgecolor="white", linewidth=0.5)
+
+    # Points
+    sizes = points[size_column] * 2 if size_column else 30
+    colors = points[color_column] if color_column else "red"
+
+    points.plot(
+        ax=ax,
+        markersize=sizes,
+        color=colors,
+        alpha=0.6,
+        edgecolor="black",
+        linewidth=0.3
+    )
+
+    ax.axis("off")
+    plt.tight_layout()
+    plt.savefig("point_map.pdf", bbox_inches="tight", dpi=300)
+```
+
+## Interactive Maps with Folium
+
+```python
+import folium
+
+
+def create_interactive_map(center: tuple = (20, 0),
+                            zoom: int = 2) -> folium.Map:
+    """
+    Create an interactive web map (useful for supplementary materials).
+
+    Args:
+        center: (latitude, longitude) center point
+        zoom: Initial zoom level
+    """
+    m = folium.Map(location=center, zoom_start=zoom,
+                   tiles="CartoDB positron")
+
+    # Add markers, choropleth layers, or heatmaps as needed
+    # folium.Marker([lat, lon], popup="Label").add_to(m)
+
+    return m
+```
+
+## Cartographic Best Practices
+
+### Publication Standards
+
+```
+1. Projection choice:
+   - Global maps: Robinson or Equal Earth (not Mercator for thematic maps)
+   - Country/region: Appropriate local projection
+   - Mercator distorts area -- misleading for choropleths
+
+2. Color schemes:
+   - Sequential: Low-to-high values (YlOrRd, Blues, Viridis)
+   - Diverging: Values around a midpoint (RdBu, BrBG)
+   - Qualitative: Categorical data (Set2, Paired)
+   - Use colorbrewer2.org for perceptually uniform palettes
+   - Test for colorblind accessibility
+
+3. Required map elements:
+   - Title
+   - Legend with units
+   - Scale bar
+   - North arrow (if orientation is non-standard)
+   - Data source attribution
+   - CRS/projection information
+
+4. Ethical considerations:
+   - Disputed borders: Use dashed lines or note in caption
+   - Data gaps: Show "no data" regions explicitly (do not leave blank)
+   - Privacy: Aggregate point data to protect individual locations
+```
+
+## Free Data Sources
+
+| Source | Data | Format |
+|--------|------|--------|
+| Natural Earth | Country/region boundaries, physical features | Shapefile, GeoJSON |
+| GADM | Administrative boundaries (all countries, all levels) | GeoPackage, Shapefile |
+| OpenStreetMap | Roads, buildings, land use | PBF, Shapefile |
+| WorldPop | Population density grids | GeoTIFF |
+| NASA SEDAC | Socioeconomic and environmental data | GeoTIFF, Shapefile |
+| USGS Earth Explorer | Satellite imagery, elevation | GeoTIFF |