Arrange_plots_patchwork.R

## Arranging plots with patchwork. For details see this manual page: https://ggplot2-book.org/arranging-plots.html

## Load libraries and create some sample data
library(ggplot2); library(reshape2); library(patchwork)
iris_mean <- aggregate(iris[,1:4], by=list(Species=iris$Species), FUN=mean)                                                                                  
df_mean <- melt(iris_mean, id.vars=c("Species"), variable.name = "Samples", value.name="Values")                                                             

## Create lots of plots
p1 <- ggplot(cbind(iris, Samples="Sepal.Length"), aes(Species, Sepal.Length)) + geom_boxplot(aes(fill = Species)) + ylim(4, 8) + theme(axis.title.x=element_blank(), axis.title.y=element_blank(), legend.position = "none") + facet_grid(rows = ~Samples) + ggtitle("(A)") + theme(plot.title = element_text(hjust=-0.3)) 
p2 <- ggplot(df_mean[df_mean$Samples=="Sepal.Width",], aes(Species, Values)) + geom_bar(position="dodge", aes(fill = Species), stat="identity") + ylim(0, 20) + theme(axis.title.x=element_blank(), axis.title.y=element_blank(), axis.text.y=element_blank(), axis.ticks.y=element_blank(), legend.position = "none") + facet_grid(rows = ~Samples)
p3 <- ggplot(df_mean[df_mean$Samples=="Petal.Length",], aes(Species, Values)) + geom_bar(position="dodge", aes(fill = Species), stat="identity") + ylim(0, 6) + theme(axis.title.y=element_blank(), axis.text.y=element_blank(), axis.ticks.y=element_blank(), legend.position = "none") + facet_grid(rows = ~Samples) + theme(axis.title.x = element_text(hjust=-0.2))
p4 <- ggplot(df_mean[df_mean$Samples=="Petal.Width",], aes(Species, Values)) + geom_bar(position="dodge", aes(fill = Species), stat="identity") + theme(axis.title.x=element_blank(), axis.title.y=element_blank(), axis.text.y=element_blank(), axis.ticks.y=element_blank(), legend.position = "none") + facet_grid(rows = ~Samples)

p5 <- ggplot(df_mean[df_mean$Samples=="Sepal.Length",], aes(Species, Values)) + geom_bar(position="dodge", aes(fill = Species), stat="identity") + ylim(0, 15) + theme(axis.title.x=element_blank(), axis.title.y=element_blank(), legend.position = "none") + facet_grid(rows = ~Samples) + ggtitle("(B)") + theme(plot.title = element_text(hjust=-0.9)) 
p6 <- ggplot(df_mean[df_mean$Samples=="Sepal.Width",], aes(Species, Values)) + geom_bar(position="dodge", aes(fill = Species), stat="identity") + ylim(0, 20) + theme(axis.title.x=element_blank(), axis.title.y=element_blank(), axis.text.y=element_blank(), axis.ticks.y=element_blank(), legend.position = "none") + facet_grid(rows = ~Samples)
p7 <- ggplot(df_mean[df_mean$Samples=="Petal.Length",], aes(Species, Values)) + geom_bar(position="dodge", aes(fill = Species), stat="identity") + ylim(0, 6) + theme(axis.title.y=element_blank(), axis.text.y=element_blank(), axis.ticks.y=element_blank(), legend.position = "none") + facet_grid(rows = ~Samples) + theme(axis.title.x = element_text(hjust=-0.3))
p8 <- ggplot(df_mean[df_mean$Samples=="Petal.Width",], aes(Species, Values)) + geom_bar(position="dodge", aes(fill = Species), stat="identity") + theme(axis.title.x=element_blank(), axis.title.y=element_blank(), axis.text.y=element_blank(), axis.ticks.y=element_blank(), legend.position = "none") + facet_grid(rows = ~Samples)

p9 <- ggplot(df_mean[df_mean$Samples=="Sepal.Length",], aes(Species, Values)) + geom_bar(position="dodge", aes(fill = Species), stat="identity") + ylim(0, 15) + theme(axis.title.x=element_blank(), axis.title.y=element_blank(), legend.position = "none") + facet_grid(rows = ~Samples) + ggtitle("(C)") + theme(plot.title = element_text(hjust=-0.9))
p10 <- ggplot(df_mean[df_mean$Samples=="Sepal.Width",], aes(Species, Values)) + geom_bar(position="dodge", aes(fill = Species), stat="identity") + ylim(0, 20) + theme(axis.title.x=element_blank(), axis.title.y=element_blank(), axis.text.y=element_blank(), axis.ticks.y=element_blank(), legend.position = "none") + facet_grid(rows = ~Samples)
p11 <- ggplot(df_mean[df_mean$Samples=="Petal.Length",], aes(Species, Values)) + geom_bar(position="dodge", aes(fill = Species), stat="identity") + ylim(0, 6) + theme(axis.title.y=element_blank(), axis.text.y=element_blank(), axis.ticks.y=element_blank(), legend.position = "none") + facet_grid(rows = ~Samples) + theme(axis.title.x = element_text(hjust=-0.3))
p12 <- ggplot(df_mean[df_mean$Samples=="Petal.Width",], aes(Species, Values)) + geom_bar(position="dodge", aes(fill = Species), stat="identity") + theme(axis.title.x=element_blank(), axis.title.y=element_blank(), axis.text.y=element_blank(), axis.ticks.y=element_blank(), legend.position = "none") + facet_grid(rows = ~Samples)

## Lay them out with patchwork
( p1 + p2 + p3 + p4 + plot_layout(ncol = 4) & coord_flip() ) /
( ( p5 + p6 + p7 + p8 + plot_layout(ncol = 4) & coord_flip() ) |
( p9 + p10 + p11 + p12 + plot_layout(ncol = 4) & coord_flip() ) )