Multi-Panel Figure Assembly

patchwork Basics

library(patchwork)

p1 <- ggplot(df, aes(x, y)) + geom_point() p2 <- ggplot(df, aes(group, value)) + geom_boxplot() p3 <- ggplot(df, aes(x)) + geom_histogram()

Horizontal

p1 + p2 + p3

Vertical

p1 / p2 / p3

Mixed layouts

(p1 | p2) / p3 (p1 + p2) / (p3 + p4)

Panel Labels

Automatic labels

(p1 + p2 + p3) + plot_annotation(tag_levels = 'A')

Custom labels

(p1 + p2 + p3) + plot_annotation(tag_levels = list(c('A', 'B', 'C')))

Label styling

(p1 + p2) + plot_annotation( tag_levels = 'A', tag_prefix = '(', tag_suffix = ')', theme = theme(plot.tag = element_text(face = 'bold', size = 14)) )

Layout Control

Width ratios

p1 + p2 + plot_layout(widths = c(2, 1))

Height ratios

p1 / p2 + plot_layout(heights = c(1, 2))

Complex grid

layout <- " AAB AAB CCC " p1 + p2 + p3 + plot_layout(design = layout)

Fixed dimensions

p1 + p2 + plot_layout(widths = unit(c(5, 3), 'cm'))

Shared Legends

Collect legends

(p1 + p2 + p3) + plot_layout(guides = 'collect')

Position at bottom

(p1 + p2) + plot_layout(guides = 'collect') & theme(legend.position = 'bottom')

Keep individual legends

(p1 + p2) + plot_layout(guides = 'keep')

Inset Plots

Add inset

p1 + inset_element(p2, left = 0.6, bottom = 0.6, right = 1, top = 1)

Multiple insets

p1 + inset_element(p2, 0.6, 0.6, 1, 1) + inset_element(p3, 0.02, 0.6, 0.4, 1)

cowplot Alternative

library(cowplot)

Simple grid

plot_grid(p1, p2, p3, ncol = 3, labels = 'AUTO')

With labels

plot_grid(p1, p2, labels = c('A', 'B'), label_size = 14)

Relative widths

plot_grid(p1, p2, rel_widths = c(2, 1))

Nested grids

top_row <- plot_grid(p1, p2, ncol = 2) bottom_row <- p3 plot_grid(top_row, bottom_row, nrow = 2, labels = c('', 'C'))

Shared Axes

library(patchwork)

Same axis limits

(p1 + p2) & xlim(0, 10) & ylim(0, 100)

Same theme

(p1 + p2 + p3) & theme_minimal()

Same color scale

(p1 + p2) & scale_color_viridis_d()

Empty Spaces

Add blank panel

p1 + plot_spacer() + p2

With layout

layout <- " AB# CCC " p1 + p2 + p3 + plot_layout(design = layout)

Titles and Captions

(p1 + p2 + p3) + plot_annotation( title = 'Main Title', subtitle = 'Subtitle text', caption = 'Data source: ...', theme = theme( plot.title = element_text(face = 'bold', size = 16), plot.subtitle = element_text(size = 12, color = 'grey40') ) )

Saving Multi-Panel Figures

Combine and save

combined <- (p1 | p2) / (p3 | p4) + plot_annotation(tag_levels = 'A') & theme(plot.tag = element_text(face = 'bold'))

ggsave('figure.pdf', combined, width = 10, height = 8) ggsave('figure.png', combined, width = 10, height = 8, dpi = 300)

For specific journal dimensions

ggsave('figure.pdf', combined, width = 180, height = 150, units = 'mm')

Complex Publication Figure

Create themed plots

theme_pub <- theme_bw(base_size = 10) + theme( panel.grid = element_blank(), legend.position = 'none' )

p_volcano <- create_volcano(res) + theme_pub + ggtitle('Volcano Plot') p_pca <- create_pca(vsd) + theme_pub + ggtitle('PCA') p_heatmap <- wrap_elements(pheatmap_grob) p_boxplot <- create_boxplot(expr_df) + theme_pub + ggtitle('Expression')

Assemble

figure <- (p_volcano | p_pca) / (p_heatmap | p_boxplot) + plot_annotation(tag_levels = 'A') + plot_layout(guides = 'collect') & theme( plot.tag = element_text(face = 'bold', size = 12), legend.position = 'bottom' )

ggsave('Figure1.pdf', figure, width = 180, height = 160, units = 'mm')

matplotlib GridSpec (Python)

import matplotlib.pyplot as plt from matplotlib.gridspec import GridSpec

fig = plt.figure(figsize=(12, 8)) gs = GridSpec(2, 3, figure=fig)

ax1 = fig.add_subplot(gs[0, 0]) # Top left ax2 = fig.add_subplot(gs[0, 1:]) # Top right, spans 2 columns ax3 = fig.add_subplot(gs[1, :]) # Bottom, spans all columns

Add plots to each axis

ax1.plot(x, y) ax2.scatter(x, y) ax3.bar(x, y)

plt.tight_layout()

matplotlib Panel Labels

Add panel labels

for ax, label in zip([ax1, ax2, ax3], ['A', 'B', 'C']): ax.text(-0.1, 1.1, label, transform=ax.transAxes, fontsize=14, fontweight='bold', va='top')

matplotlib Subfigures

matplotlib 3.4+ subfigures for complex layouts

fig = plt.figure(figsize=(12, 8)) subfigs = fig.subfigures(1, 2, width_ratios=[2, 1])

axs_left = subfigs[0].subplots(2, 1) ax_right = subfigs[1].subplots(1, 1)

Publication Export

Python

fig.savefig('figure1.pdf', bbox_inches='tight') fig.savefig('figure1.png', dpi=300, bbox_inches='tight')

Related Skills

• data-visualization/ggplot2-fundamentals - Individual plots

• reporting/rmarkdown-reports - Figures in documents

• differential-expression/de-visualization - DE-specific plots