Install and load the package gridExtra

install.packages("gridExtra")
library("gridExtra")

Install and load the package cowplot

cowplot can be installed as follow:

install.packages("cowplot")

OR

as follow using devtools package (devtools should be installed before using the code below):

devtools::install_github("wilkelab/cowplot")

Load cowplot:

library("cowplot")

Basic plots

library(cowplot)
# Default plot
bp <- ggplot(df, aes(x=dose, y=len, color=dose)) +
  geom_boxplot() + 
  theme(legend.position = "none")
bp

# Add gridlines
bp + background_grid(major = "xy", minor = "none")

Recall that, the function ggsave()[in ggplot2 package] can be used to save ggplots. However, when working with cowplot, the function save_plot() [in cowplot package] is preferred. It’s an alternative to ggsave with a better support for multi-figure plots.

save_plot("mpg.pdf", plot.mpg,
          base_aspect_ratio = 1.3 # make room for figure legend
          )

Arranging multiple graphs using cowplot

# Scatter plot
sp <- ggplot(mpg, aes(x = cty, y = hwy, colour = factor(cyl)))+ 
  geom_point(size=2.5)
sp

# Bar plot
bp <- ggplot(diamonds, aes(clarity, fill = cut)) +
  geom_bar() +
  theme(axis.text.x = element_text(angle=70, vjust=0.5))
bp

Combine the two plots (the scatter plot and the bar plot):

plot_grid(sp, bp, labels=c("A", "B"), ncol = 2, nrow = 1)

The function draw_plot() can be used to place graphs at particular locations with a particular sizes. The format of the function is:

draw_plot(plot, x = 0, y = 0, width = 1, height = 1)

• plot: the plot to place (ggplot2 or a gtable)
• x: The x location of the lower left corner of the plot.
• y: The y location of the lower left corner of the plot.
• width, height: the width and the height of the plot

The function ggdraw() is used to initialize an empty drawing canvas.

plot.iris <- ggplot(iris, aes(Sepal.Length, Sepal.Width)) + 
  geom_point() + facet_grid(. ~ Species) + stat_smooth(method = "lm") +
  background_grid(major = 'y', minor = "none") + # add thin horizontal lines 
  panel_border() # and a border around each panel
# plot.mpt and plot.diamonds were defined earlier
ggdraw() +
  draw_plot(plot.iris, 0, .5, 1, .5) +
  draw_plot(sp, 0, 0, .5, .5) +
  draw_plot(bp, .5, 0, .5, .5) +
  draw_plot_label(c("A", "B", "C"), c(0, 0, 0.5), c(1, 0.5, 0.5), size = 15)

grid.arrange() and arrangeGrob(): Change column/row span of a plot

Using the R code below:

• The box plot will live in the first column
• The dot plot and the strip chart will live in the second column

grid.arrange(bp, arrangeGrob(dp, sc), ncol = 2)

It’s also possible to use the argument layout_matrix in grid.arrange(). In the R code below layout_matrix is a 2X3 matrix (2 columns and three rows). The first column is all 1s, that’s where the first plot lives, spanning the three rows; second column contains plots 2, 3, 4, each occupying one row.

grid.arrange(bp, dp, sc, vp, ncol = 2, 
             layout_matrix = cbind(c(1,1,1), c(2,3,4)))

Add a common legend for multiple ggplot2 graphs

This can be done in four simple steps :

1. Create the plots : p1, p2, ….
2. Save the legend of the plot p1 as an external graphical element (called a “grob” in Grid terminology)
3. Remove the legends from all plots
4. Draw all the plots with only one legend in the right panel

To save the legend of a ggplot, the helper function below can be used :

library(gridExtra)
get_legend<-function(myggplot){
  tmp <- ggplot_gtable(ggplot_build(myggplot))
  leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
  legend <- tmp$grobs[[leg]]
  return(legend)
}

(The function above is derived from this forum. )

# 1. Create the plots
#++++++++++++++++++++++++++++++++++
# Create a box plot
bp <- ggplot(df, aes(x=dose, y=len, color=dose)) +
  geom_boxplot()

# Create a violin plot
vp <- ggplot(df, aes(x=dose, y=len, color=dose)) +
  geom_violin()+
  geom_boxplot(width=0.1)+
  theme(legend.position="none")

# 2. Save the legend
#+++++++++++++++++++++++
legend <- get_legend(bp)

# 3. Remove the legend from the box plot
#+++++++++++++++++++++++
bp <- bp + theme(legend.position="none")

# 4. Arrange ggplot2 graphs with a specific width
grid.arrange(bp, vp, legend, ncol=3, widths=c(2.3, 2.3, 0.8))

Change legend position

# 1. Create the plots
#++++++++++++++++++++++++++++++++++
# Create a box plot with a top legend position
bp <- ggplot(df, aes(x=dose, y=len, color=dose)) +
  geom_boxplot()+theme(legend.position = "top")

# Create a violin plot
vp <- ggplot(df, aes(x=dose, y=len, color=dose)) +
  geom_violin()+
  geom_boxplot(width=0.1)+
  theme(legend.position="none")

# 2. Save the legend
#+++++++++++++++++++++++
legend <- get_legend(bp)

# 3. Remove the legend from the box plot
#+++++++++++++++++++++++
bp <- bp + theme(legend.position="none")

# 4. Create a blank plot
blankPlot <- ggplot()+geom_blank(aes(1,1)) + 
  cowplot::theme_nothing()

Change legend position by changing the order of plots using the following R code. Grids with four cells are created (2X2). The height of the legend zone is set to 0.2.

Top-left legend:

# Top-left legend
grid.arrange(legend, blankPlot,  bp, vp,
             ncol=2, nrow = 2, 
             widths = c(2.7, 2.7), heights = c(0.2, 2.5))

Top-right legend:

# Top-right
grid.arrange(blankPlot, legend,  bp, vp,
             ncol=2, nrow = 2, 
             widths = c(2.7, 2.7), heights = c(0.2, 2.5))

Bottom-right and bottom-left legend can be drawn as follow:

# Bottom-left legend
grid.arrange(bp, vp, legend, blankPlot,
             ncol=2, nrow = 2, 
             widths = c(2.7, 2.7), heights = c(2.5, 0.2))
# Bottom-right
grid.arrange( bp, vp, blankPlot, legend, 
             ncol=2, nrow = 2, 
             widths = c(2.7, 2.7), heights = c( 2.5, 0.2))

It’s also possible to use the argument layout_matrix to customize legend position. In the R code below, layout_matrix is a 2X2 matrix:

• The first row (height = 2.5) is where the first plot (bp) and the second plot (vp) live
• The second row (height = 0.2) is where the legend lives spanning 2 columns

Bottom-center legend:

grid.arrange(bp, vp, legend, ncol=2, nrow = 2, 
             layout_matrix = rbind(c(1,2), c(3,3)),
             widths = c(2.7, 2.7), heights = c(2.5, 0.2))

Top-center legend:

• The legend (plot 1) lives in the first row (height = 0.2) spanning two columns
• bp (plot 2) and vp (plot 3) live in the second row (height = 2.5)

grid.arrange(legend, bp, vp,  ncol=2, nrow = 2, 
             layout_matrix = rbind(c(1,1), c(2,3)),
             widths = c(2.7, 2.7), heights = c(0.2, 2.5))

Scatter plot with marginal density plots

Step 1/3. Create some data :

set.seed(1234)
x <- c(rnorm(500, mean = -1), rnorm(500, mean = 1.5))
y <- c(rnorm(500, mean = 1), rnorm(500, mean = 1.7))
group <- as.factor(rep(c(1,2), each=500))
df2 <- data.frame(x, y, group)
head(df2)

##             x          y group
## 1 -2.20706575 -0.2053334     1
## 2 -0.72257076  1.3014667     1
## 3  0.08444118 -0.5391452     1
## 4 -3.34569770  1.6353707     1
## 5 -0.57087531  1.7029518     1
## 6 -0.49394411 -0.9058829     1

Step 2/3. Create the plots :

# Scatter plot of x and y variables and color by groups
scatterPlot <- ggplot(df2,aes(x, y, color=group)) + 
  geom_point() + 
  scale_color_manual(values = c('#999999','#E69F00')) + 
  theme(legend.position=c(0,1), legend.justification=c(0,1))


# Marginal density plot of x (top panel)
xdensity <- ggplot(df2, aes(x, fill=group)) + 
  geom_density(alpha=.5) + 
  scale_fill_manual(values = c('#999999','#E69F00')) + 
  theme(legend.position = "none")

# Marginal density plot of y (right panel)
ydensity <- ggplot(df2, aes(y, fill=group)) + 
  geom_density(alpha=.5) + 
  scale_fill_manual(values = c('#999999','#E69F00')) + 
  theme(legend.position = "none")

Create a blank placeholder plot :

blankPlot <- ggplot()+geom_blank(aes(1,1))+
  theme(
    plot.background = element_blank(), 
   panel.grid.major = element_blank(),
   panel.grid.minor = element_blank(), 
   panel.border = element_blank(),
   panel.background = element_blank(),
   axis.title.x = element_blank(),
   axis.title.y = element_blank(),
   axis.text.x = element_blank(), 
   axis.text.y = element_blank(),
   axis.ticks = element_blank(),
   axis.line = element_blank()
     )

Step 3/3. Put the plots together:

Arrange ggplot2 with adapted height and width for each row and column :

library("gridExtra")
grid.arrange(xdensity, blankPlot, scatterPlot, ydensity, 
        ncol=2, nrow=2, widths=c(4, 1.4), heights=c(1.4, 4))

Create a complex layout using the function viewport()

The different steps are :

1. Create plots : p1, p2, p3, ….
2. Move to a new page on a grid device using the function grid.newpage()
3. Create a layout 2X2 - number of columns = 2; number of rows = 2
4. Define a grid viewport : a rectangular region on a graphics device
5. Print a plot into the viewport

# Move to a new page
grid.newpage()

# Create layout : nrow = 2, ncol = 2
pushViewport(viewport(layout = grid.layout(2, 2)))

# A helper function to define a region on the layout
define_region <- function(row, col){
  viewport(layout.pos.row = row, layout.pos.col = col)
} 

# Arrange the plots
print(scatterPlot, vp=define_region(1, 1:2))
print(xdensity, vp = define_region(2, 1))
print(ydensity, vp = define_region(2, 2))