9  Publication Figures

The sa-publication-figures module assembles individual analysis plots into multi-panel figures suitable for journal submission. All figures meet standard publication requirements: 300 DPI resolution, colorblind-safe palettes, and consistent typography.

9.1 Figure Standards

Parameter	Value
Resolution	300 DPI (minimum for print)
Colour palette	ggsci::scale_color_lancet() (colorblind-safe)
Font	Arial or Helvetica, 8–12 pt
Line width	0.5–1.0 pt
Panel labels	Uppercase letters (A, B, C, …)
Export formats	PNG, PDF, TIFF

9.2 Theme Setup

The pipeline uses a consistent ggplot2 theme across all figures:

library(ggplot2)

theme_publication <- theme_bw(base_size = 11) +
  theme(
    panel.grid.minor = element_blank(),
    strip.background = element_rect(fill = "grey95"),
    legend.position = "bottom",
    plot.title = element_text(size = 12, face = "bold")
  )

theme_set(theme_publication)

9.3 Multi-Panel Assembly with patchwork

Individual plots are combined into composite figures using the patchwork package:

library(patchwork)

figure1 <- (km_plot | forest_plot) /
            (residual_plot | calibration_plot) +
  plot_annotation(tag_levels = "A") +
  plot_layout(heights = c(1, 1))

ggsave("figure1.png", figure1,
       width = 180, height = 160, units = "mm", dpi = 300)

TipJournal Width Guidelines

Most journals accept figures at 85 mm (single column) or 180 mm (double column) width. The pipeline defaults to 180 mm for multi-panel figures.

9.4 Export Formats

Each figure is saved in three formats:

# PNG for screen/web
ggsave("figure1.png", figure1, width = 180, height = 160, units = "mm", dpi = 300)

# PDF for vector graphics
ggsave("figure1.pdf", figure1, width = 180, height = 160, units = "mm")

# TIFF for some journal requirements
ggsave("figure1.tiff", figure1, width = 180, height = 160, units = "mm",
       dpi = 300, compression = "lzw")

NoteOutput Location

All figures are written to projects/<name>/04_figures/. The manuscript module references them from this directory during Quarto rendering.

9.5 Running the Module

make figures PROJECT=my-study

This executes all scripts in sa-publication-figures/scripts/ in order.

9.6 Demo: Publication Figures (Scenario 1)

The demo-standard project generated the following publication-ready figures. Each was exported at 300 DPI in PNG, PDF, and TIFF formats.

9.6.1 Figure Inventory

Table 9.1: Figure inventory from demo-standard/04_figures/

Figure	PNG	PDF	TIFF	DPI	Description
Figure1_km_survival	Y	Y	Y	300	Kaplan-Meier survival curves with risk table and median annotation
Figure2_forest_plot	Y	Y	Y	300	Forest plot of hazard ratios from Cox regression
Figure_combined_panels	Y	Y	Y	300	Multi-panel composite figure combining all main analyses
FigureS1_diagnostics	Y	Y	Y	300	Supplementary: Schoenfeld and Martingale residual diagnostics

9.6.2 KM Survival Figure

Figure 9.1: Publication-ready KM curves (Figure 1)

9.6.3 Forest Plot

Figure 9.2: Adjusted HR forest plot (Figure 2)

9.6.4 Multi-Panel Assembly

Figure 9.3: Combined panels assembled with patchwork

Tip

All figures are exported at 300 DPI in PNG, PDF, and TIFF formats — ready for journal submission.