Generating Publication Ready Figures In R

--- name: generating-publication-ready-figures-in-r description: Transform standard ggplot2 figures into publication-quality visualizations matching Nature, Science, and other top journal styles with proper themes, colors, fonts, and export settings. --- # Generating Publication-Ready Figures in R This skill specializes in transforming ordinary ggplot2 plots into professional, publication-ready figures that meet the strict standards of top-tier journals like Nature, Science, Cell, and others. Use this skill when the user wants to: - Convert ggplot plots to journal-style figures - Apply Nature/Science publication themes to existing plots - Create multi-panel figures with consistent styling - Export figures with proper DPI, dimensions, and formats - Match specific journal submission guidelines - Create colorblind-safe and publication-quality color schemes --- ## What This Skill Does When activated, this skill will: 1. **Analyze existing ggplot code** - Read and understand the current plot structure 2. **Apply journal themes** - Add publication-quality themes including: - Proper font sizes and families - Clean axis lines and backgrounds - Journal-specific color palettes - Legend positioning and styling 3. **Optimize for submission** - Ensure figures meet: - DPI requirements (typically 300-600 DPI) - Width/height specifications (single vs double column) - File format requirements (TIFF, PDF, EPS) - Color space requirements (CMYK vs RGB) 4. **Create multi-panel figures** - Combine plots using: - `patchwork` for simple layouts - `cowplot` for complex compositions - Custom annotation and labeling 5. **Export properly** - Save with correct: - Resolution (DPI) - Dimensions (inches/cm) - File format - Color profile --- ## Example User Requests That Should Trigger This Skill - "Transform this ggplot to Nature journal style" - "Make this figure publication-ready for Science" - "Create a two-column figure matching Cell format" - "Export these plots at 600 DPI for submission" - "Apply a colorblind-safe palette to my plots" - "Combine these four plots into one publication figure" - "Format my scatter plot for PNAS submission" --- ## Journal Style Guidelines ### Nature Style - Font: Arial or Helvetica - Font sizes: Axis titles 7-9 pt, axis labels 6-8 pt - Single column: 89 mm (3.5 in) width - Double column: 183 mm (7.2 in) width - Max height: 234 mm (9.2 in) - Resolution: 300-600 DPI - Formats: TIFF, PDF, EPS (vector preferred) ### Science Style - Font: Arial - Font sizes: Title 9 pt, labels 7 pt - Single column: 57 mm (2.25 in) width - Double column: 114 mm (4.5 in) width - Resolution: 300-600 DPI - Formats: TIFF, PDF, EPS ### Cell Press Style - Font: Arial or Helvetica - Single column: 85 mm (3.3 in) width - Double column: 178 mm (7 in) width - Resolution: 300 DPI minimum - Formats: TIFF, EPS, PDF --- ## Theme Templates Available ### `theme_nature()` Clean, minimalist theme matching Nature journals: - No gray backgrounds - Minimal grid lines - Arial font family - Proper axis sizing ### `theme_science()` Theme for Science journal submissions: - Compact layout - Clean typography - Optimized for smaller widths ### `theme_cellpress()` Cell Press journal theme: - Professional appearance - Flexible legend placement - Publication-ready defaults ### `theme_colorblind()` Colorblind-safe palette with: - Viridis/Colorbrewer schemes - High contrast ratios - Print-friendly colors --- ## Color Palettes ### Nature-Approved Colors ```r # Primary colors nature_colors <- c( blue = "#3B4992", red = "#EE0000", green = "#008B45", purple = "#631879" ) ``` ### Colorblind-Safe Scales - `scale_fill_viridis()` - `scale_color_okabe_ito()` (Okabe-Ito palette) - `scale_color_viridis()` --- ## Example Workflow **User:** Here's my ggplot code, make it Nature-style. ```r # Original plot p <- ggplot(mtcars, aes(x = wt, y = mpg, color = factor(cyl))) + geom_point(size = 3) ``` **Skill transforms to:** ```r # Publication-ready version p <- ggplot(mtcars, aes(x = "Weight (tons)", y = "Fuel Efficiency (mpg)", color = "Cylinders")) + geom_point(size = 2.5, shape = 16, alpha = 0.8) + scale_color_nature() + theme_nature(base_size = 8) + labs(title = NULL) # Export at correct size ggsave("figure1.pdf", p, width = 3.5, height = 3, dpi = 300, device = "pdf") ``` --- ## Multi-Panel Figures ```r # Combine plots with patchwork library(patchwork) figure1 <- (panel_a | panel_b) / (panel_c | panel_d) # Add panel labels figure1 <- figure1 + plot_annotation(tag_levels = "A", tag_suffix = ")") # Export ggsave("figure1.pdf", figure1, width = 7, height = 6, dpi = 300) ``` --- ## Tools & Packages Commonly Used | Purpose | R Packages | |--------|------------| | Base plotting | ggplot2 | | Themes | ggplot2, cowplot, hrbrthemes | | Color palettes | viridis, RColorBrewer, scales, ggsci | | Multi-panel | patchwork, cowplot, ggpubr | | Export | ggplot2, ragg | | Fonts | extrafont, showtext | | Annotations | ggrepel, ggpp | --- ## Common Journal Requirements | Journal | Width (single) | Width (double) | Max Height | Min DPI | |---------|---------------|----------------|------------|---------| | Nature | 89 mm | 183 mm | 234 mm | 300 | | Science | 57 mm | 114 mm | 229 mm | 300 | | Cell | 85 mm | 178 mm | 229 mm | 300 | | PNAS | 87 mm | 178 mm | 227 mm | 300 | | PLOS ONE | 170 mm | - | 230 mm | 300 | | eLife | 183 mm | - | 244 mm | 300 | --- ## Quick Reference ### Applying a theme ```r p + theme_nature() # Nature style p + theme_science() # Science style p + theme_cellpress() # Cell Press style p + theme_colorblind() # Colorblind-safe ``` ### Export formats ```r # Vector (preferred) ggsave("figure.pdf", ... device = "pdf") ggsave("figure.eps", ... device = "eps") # Raster (high DPI) ggsave("figure.tiff", ... device = "tiff", dpi = 600) ggsave("figure.png", ... device = "png", dpi = 300) ``` ### Common fixes - **Text too small**: Increase `base_size` in theme - **Legend overlap**: Use `theme(legend.position = "bottom")` - **Colors not distinct**: Use `scale_fill_viridis()` - **Fonts not rendering**: Use `extrafont::font_import()` --- ## Notes - Always check specific journal guidelines before submission - Vector formats (PDF/EPS) are preferred over raster - Use consistent styling across all figures in a paper - Test colorblind accessibility with `colorblindr` package - Keep axis labels clear and concise - Avoid redundant chart junk (backgrounds, grid lines)

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