datavis

# Scientific Data Visualization Create publication-quality scientific plots and visualizations using matplotlib and seaborn. ## Overview This skill provides data visualization capabilities for scientific data: - Line plots, scatter plots, bar charts - Heatmaps and clustermaps - Box plots and violin plots - Histograms and density plots - Sequence logos (for bioinformatics) - Multiple subplot layouts ## Usage ### Create a line plot from CSV: ```bash python3 {baseDir}/scripts/plot_data.py line --data data.csv --x time --y value --output plot.png ``` ### Create a scatter plot: ```bash python3 {baseDir}/scripts/plot_data.py scatter --data data.csv --x x_col --y y_col --hue group ``` ### Create a heatmap: ```bash python3 {baseDir}/scripts/plot_data.py heatmap --data matrix.csv --output heatmap.png ``` ### Create a bar chart: ```bash python3 {baseDir}/scripts/plot_data.py bar --data data.csv --x category --y value ``` ### Plot from JSON data: ```bash python3 {baseDir}/scripts/plot_data.py line --json '{"x": [1,2,3], "y": [4,5,6]}' ``` ## Plot Types ### line Line plot for continuous data. | Parameter | Description | Default | |-----------|-------------|---------| | `--data` | CSV file path | - | | `--json` | JSON data string | - | | `--x` | X-axis column | Required | | `--y` | Y-axis column(s), comma-separated | Required | | `--hue` | Color grouping column | - | | `--style` | Line style column | - | | `--markers` | Add markers | False | ### scatter Scatter plot for showing relationships. | Parameter | Description | Default | |-----------|-------------|---------| | `--data` | CSV file path | - | | `--x` | X-axis column | Required | | `--y` | Y-axis column | Required | | `--hue` | Color grouping column | - | | `--size` | Size column | - | | `--alpha` | Point transparency | 0.7 | ### bar Bar chart for categorical data. | Parameter | Description | Default | |-----------|-------------|---------| | `--data` | CSV file path | - | | `--x` | Category column | Required | | `--y` | Value column | Required | | `--hue` | Color grouping column | - | | `--horizontal` | Horizontal bars | False | | `--error` | Error bar column | - | ### heatmap Heatmap for matrix data. | Parameter | Description | Default | |-----------|-------------|---------| | `--data` | CSV file path | Required | | `--cmap` | Color map | viridis | | `--annotate` | Show values | False | | `--cluster` | Cluster rows/columns | False | ### box Box plot for distributions. | Parameter | Description | Default | |-----------|-------------|---------| | `--data` | CSV file path | - | | `--x` | Grouping column | - | | `--y` | Value column | Required | | `--hue` | Color grouping column | - | ### violin Violin plot for distributions. | Parameter | Description | Default | |-----------|-------------|---------| | `--data` | CSV file path | - | | `--x` | Grouping column | - | | `--y` | Value column | Required | | `--hue` | Color grouping column | - | | `--split` | Split violins by hue | False | ### histogram Histogram for distributions. | Parameter | Description | Default | |-----------|-------------|---------| | `--data` | CSV file path | - | | `--x` | Value column | Required | | `--bins` | Number of bins | auto | | `--kde` | Add KDE line | False | | `--hue` | Color grouping column | - | ## Common Options | Option | Description | Default | |--------|-------------|---------| | `--output` | Output file path | plot.png | | `--format` | Output format: png, svg, pdf | png | | `--title` | Plot title | - | | `--xlabel` | X-axis label | column name | | `--ylabel` | Y-axis label | column name | | `--figsize` | Figure size (width,height) | 10,6 | | `--style` | Seaborn style | whitegrid | | `--palette` | Color palette | deep | | `--dpi` | Output resolution | 150 | | `--legend` | Legend position | auto | | `--logx` | Log scale X-axis | False | | `--logy` | Log scale Y-axis | False | ## Examples ### Multi-line plot with legend: ```bash python3 {baseDir}/scripts/plot_data.py line --data timeseries.csv --x date --y "temp,humidity" --title "Weather Data" --output weather.png ``` ### Scatter plot with regression line: ```bash python3 {baseDir}/scripts/plot_data.py scatter --data experiment.csv --x dose --y response --hue treatment --title "Dose Response" --output dose_response.png ``` ### Clustered heatmap: ```bash python3 {baseDir}/scripts/plot_data.py heatmap --data expression.csv --cluster --cmap RdBu_r --title "Gene Expression" --output heatmap.svg --format svg ``` ### Box plot with multiple groups: ```bash python3 {baseDir}/scripts/plot_data.py box --data measurements.csv --x condition --y value --hue treatment --title "Treatment Effects" ``` ### Histogram with KDE: ```bash python3 {baseDir}/scripts/plot_data.py histogram --data samples.csv --x measurement --bins 30 --kde --title "Distribution" ``` ### Publication-quality figure: ```bash python3 {baseDir}/scripts/plot_data.py scatter --data results.csv --x x --y y --figsize 8,6 --dpi 300 --format svg --style white --output figure1.svg ``` ## Color Palettes - **deep**: Default seaborn palette - **muted**: Muted colors - **bright**: Bright colors - **pastel**: Pastel colors - **dark**: Dark colors - **colorblind**: Colorblind-friendly - **viridis**: Perceptually uniform - **plasma**: Perceptually uniform - **RdBu**: Red-Blue diverging - **coolwarm**: Cool-Warm diverging ## Notes - Data can be provided as CSV files or JSON strings - SVG output is recommended for publications - Use `--dpi 300` for high-resolution figures - Column names with spaces should be quoted