R Plotting Conventions

Default Theme

Always use theme_classic() as the base for plots. This provides a clean, minimal style without grid lines.

# Standard theme_clean function for all projects
theme_clean <- function(base_size = 12) {
  theme_classic(base_size = base_size) +
    theme(
      plot.title = element_text(face = "bold", size = base_size * 1.1),
      plot.subtitle = element_text(size = base_size * 0.9, color = "grey40"),
      plot.title.position = "plot",
      plot.caption.position = "plot",
      plot.margin = margin(12, 12, 12, 12),
      axis.line = element_line(linewidth = 0.4, color = "grey30"),
      axis.ticks = element_line(linewidth = 0.3, color = "grey30"),
      axis.text = element_text(size = base_size * 0.9, color = "grey20"),
      axis.title = element_text(size = base_size, color = "grey20"),
      legend.title = element_text(size = base_size * 0.9),
      legend.text = element_text(size = base_size * 0.85),
      strip.text = element_text(face = "bold", size = base_size),
      strip.background = element_blank()
    )
}

Style Preferences

• No grid lines — use theme_classic() not theme_bw()
• No stacked bar charts — use grouped/dodged bars instead
• Clean axis labels — avoid special characters that may not render (use "3 to 15 min" not "3→15 min")
• Legends at top — left-justified when possible
• Minimal borders and boxes — keep visual clutter low

Text Legibility

Ensure text never overlaps or falls off the plot edge:

• Use ggrepel for data labels — geom_text_repel() and geom_label_repel() prevent overlap
• Rotate long axis labels — axis.text.x = element_text(angle = 45, hjust = 1)
• Sufficient margins — increase plot.margin if labels are clipped
• Check rendered output — labels that fit in RStudio may clip in saved PDFs
• Wrap long text — use str_wrap() for titles or labels exceeding plot width

# Example: repel labels to avoid overlap
library(ggrepel)
ggplot(data, aes(x, y, label = gene)) +

  geom_point() +
  geom_text_repel(max.overlaps = 20, size = 3)

Consistency Across Related Plots

When creating multiple plots of the same type (e.g., per-module heatmaps, cluster markers), keep dimensions and styling consistent so they can be combined in a figure:

• Fixed dimensions — use the same width and height in ggsave() for all plots of a type
• Fixed text sizes — don't let base_size vary between related plots
• Fixed color scales — define shared scale_fill_* / scale_color_* once and reuse
• Fixed axis ranges — consider shared limits when comparing across plots
• Consistent aspect ratio — use coord_fixed() or consistent width/height ratios

# Example: define shared parameters for a set of heatmaps
HEATMAP_WIDTH <- 8
HEATMAP_HEIGHT <- 6
HEATMAP_BASE_SIZE <- 10
HEATMAP_COLORS <- scale_fill_gradient2(low = "blue", mid = "white", high = "red", midpoint = 0)

# Apply consistently to each plot
ggsave(filename, plot, width = HEATMAP_WIDTH, height = HEATMAP_HEIGHT)