I would like to combine some graphs together using cowplot. But I cannot change the margin sizes. I want to use only one y-axes, but than the margin is still quite large, which I want to decrease. I have used the plot.margin code from ggplot, although that works when I look at the single plot, it doesn't seem to work when the plots are combined.
I have made some example code:
library(ggplot2)
library(cowplot)
x <- c("a", "b")
y1 <- c(3,6)
y2 <- c(10,15)
data1 <- data.frame(x,y1)
data2 <- data.frame(x, y2)
ylab1 <- ylab("Very nice y values")
xlab1 <- xlab("Very nice factors")
plot1 <- ggplot(data1, aes(x=x, y = y1)) +
geom_bar(stat ="identity", position=position_dodge(), fill = "grey")+
theme(plot.margin = unit(c(0.5,0.5,0.5,0.5), "cm")) + xlab1 + ylab1
plot1
ylab2 <- ylab("")
xlab2 <- xlab("Very nice factors")
plot2 <- ggplot(data2, aes(x=x, y = y2)) +
geom_bar(stat = "identity",position=position_dodge(), fill = "grey")+
theme(plot.margin = unit(c(0.5,0.5,0.5,-0.5), "cm")) + xlab2 + ylab2
plot2
plot3 <- plot_grid(plot1, plot2, labels = c("A", "B"), align = "hv",nrow = 1, ncol = 2)
plot3 # Quite large margin between the two plots
I am aware that I could avoid this problem by using facets, however my real plot is rather more complicated than this graph.
Increasing the space between plots in plot_grid was also addressed in this issue.
An extra interesting solution is the one suggested in this comment - try to add an extra empty plot between the two plots and adjust the relative columns widths:
plot4 <- plot_grid(plot1, NULL, plot2, rel_widths = c(1, 0, 1), align = "hv",
labels = c("A", "B"), nrow = 1)
plot4
Can even try negative values in rel_widths, which gives better results:
plot5 <- plot_grid(plot1, NULL, plot2, rel_widths = c(1, -0.1, 1), align = "hv",
labels = c("A", "B"), nrow = 1)
plot5
So, try a combination of adjusting the plot.margin (as answered by #J.Con) and adding an extra empty plot with tweaking rel_widths.
EDIT 2019-12-11
Also check out this comment of the author of cowplot (Claus Wilke):
For those kinds of problems I would now recommend the patchwork library. It's inherently difficult with plot_grid(), due to its underlying design
So, a fast example with patchwork based on their vignette Adding Annotation and Style goes like this:
library(patchwork)
plot3 <- plot1 + plot2 +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 8))
plot3
Created on 2019-12-11 by the reprex package (v0.3.0)
Your plot.margins were actually working against you. Set them to zero to fill up that white space.
plot1 <- ggplot(data1, aes(x=x, y = y1)) +
geom_bar(stat ="identity", position=position_dodge(), fill = "grey")+
theme(plot.margin = unit(c(0,0,0,0), "cm")) + xlab1 + ylab1
plot1
ylab2 <- ylab("")
xlab2 <- xlab("Very nice factors")
plot2 <- ggplot(data2, aes(x=x, y = y2)) +
geom_bar(stat = "identity",position=position_dodge(), fill = "grey")+
theme(plot.margin = unit(c(0,0,0,0), "cm")) + xlab2 + ylab2
plot2
plot3 <- plot_grid(plot1, plot2, labels = c("A", "B"), align = "hv",nrow = 1, ncol = 2)
plot3
Related
A similar question was asked here, however I cant adapt the answer to my issue.
I am trying to correctly align two legends when using cowplot. For example, if I create some data and a cowplot with two legends like so:
library(cowplot)
library(ggplot2)
# create some data
dat <- NULL
for(i in 1:20){
x <- LETTERS[1:5]
y <- paste0("var", seq(1,5))
dat[[i]] <- expand.grid(X=x, Y=y)
dat[[i]]$Z <- runif(25, 0, 1)
}
# plotting function
plotFun <- function(data){
ggplot(data, aes(X, Y, fill= Z)) +
geom_tile() +
theme(aspect.ratio = 1,
legend.justification = c(0,1),
axis.text.x=element_blank(),
axis.ticks.x=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank()) +
xlab("") + ylab("")
}
# set up to plot on a grid
allPlots <- lapply(dat, plotFun)
allPlotsAlter <- lapply(allPlots, function(x) x + theme(legend.position = "none"))
n <- length(allPlotsAlter)
nRow <- floor(sqrt(n))
plotGrid <- gridExtra::arrangeGrob(grobs=allPlotsAlter, nrow=nRow)
# create a different type of legend
newPlot <- ggplot(iris, aes(x = Sepal.Length, y = Petal.Length, fill = Species)) +
geom_bar(stat = 'identity') + theme(legend.justification = c(0,1))
# get both legends and combine
legend <- cowplot::get_legend(allPlots[[1]])
legend1 <- cowplot::get_legend(newPlot)
combineLegend <- cowplot::plot_grid(
legend,
legend1,
nrow = 2)
# now make plot
cowplot::plot_grid(plotGrid,
combineLegend,
rel_widths = c(0.9, 0.11),
ncol = 2)
That creates this type of plot:
As you can see, the two legends have quite a bit of vertical space between them and they are not centred with the plot.
Is there a way to align the two legends so they look something like this:
I'm not sure if it is possible using cowplot... or is there a way to maybe use ggplot's annotate to place the legends?
I would probably go for patchwork, as Stefan suggests, but within cowplot you probably need to adjust the legend margins:
theme_margin <- theme(legend.box.margin = margin(100, 10, 100, 10))
legend <- cowplot::get_legend(allPlots[[1]] + theme_margin)
legend1 <- cowplot::get_legend(newPlot + theme_margin)
combineLegend <- cowplot::plot_grid(
legend,
legend1,
nrow = 2)
# now make plot
cowplot::plot_grid(plotGrid,
combineLegend,
rel_widths = c(0.9, 0.11),
ncol = 2)
If switching to another package is an option for you I would suggest to use patchwork to glue your plots together. One feature offered by patchwork is that using plot_spacer you could easily add some empty panels above and below your legends to "move" them to the center and thereby getting rid of the empty space. Depending on your final result or the height of your final plot you probably have to play a bit around with the heights and/or widths arguments:
library(cowplot)
library(ggplot2)
library(patchwork)
set.seed(123)
# create some data
dat <- NULL
for (i in 1:20) {
x <- LETTERS[1:5]
y <- paste0("var", seq(1, 5))
dat[[i]] <- expand.grid(X = x, Y = y)
dat[[i]]$Z <- runif(25, 0, 1)
}
# plotting function
plotFun <- function(data) {
ggplot(data, aes(X, Y, fill = Z)) +
geom_tile() +
theme(
aspect.ratio = 1,
legend.justification = c(0, 1),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank()
) +
labs(x = NULL, y = NULL)
}
# set up to plot on a grid
allPlots <- lapply(dat, plotFun)
allPlotsAlter <- lapply(allPlots, function(x) x + theme(legend.position = "none"))
n <- length(allPlotsAlter)
nRow <- floor(sqrt(n))
plotGrid <- wrap_plots(grobs = allPlotsAlter, nrow = nRow)
# create a different type of legend
newPlot <- ggplot(iris, aes(x = Sepal.Length, y = Petal.Length, fill = Species)) +
geom_bar(stat = "identity") +
theme(legend.justification = c(0, 1))
# get both legends and combine
legend <- cowplot::get_legend(allPlots[[1]])
legend1 <- cowplot::get_legend(newPlot)
combineLegend <- plot_spacer() + legend + legend1 + plot_spacer() + plot_layout(ncol = 1, heights = c(.5, 1, 1, .5))
wrap_elements(plotGrid) + combineLegend + plot_layout(widths = c(4, 1))
I have two plots, one with legend and another one without.
The legend should be on the right.
Now I want to have two jpg files and the 'inner' plot (everything except the legend) should have the same size in both plots.
I thought of specifying the legend width with legend.key.width and add that width to the argument width in ggsave. Here it's 2 inches.
That's my code:
library(tidyverse)
tb <- tibble(a = 1:10, b = 10:1, c = rep(letters[1:2], 5))
plot1 <-
ggplot(tb, aes(a, b)) +
geom_point()
plot1
plot2 <-
ggplot(tb, aes(a, b, colour = c)) +
geom_point() +
theme(legend.key.width = unit(2, "in"))
plot3
ggsave("plot1.jpg", plot1, width = 5, height = 5, units = "in")
ggsave("plot2.jpg", plot2, width = 7, height = 5, units = "in")
Unfortunately the inner plot in plot2 is still not that wide than the inner plot in plot1.
What I really want are two plots that look exactly the same (except of the colors) that I can 'put the one on top of the other and it seems that there is one plot' but plot2 should have this legend additionally.
Is there any chance? I've tried quite much and looked at every argument of theme. I'm sorry for my strange explanation ...
As far as I get it, similar to the option proposed by #MrGumble you could glue plots together on top of one another using e.g. patchwork. If you prefer separate plots then one option would be to make the first plot with a color legend but make all text, colors etc. invisible using scale_color_manual, guide_legend and theme.
1. Separate plots
library(tidyverse)
tb <- tibble(a = 1:10, b = 10:1, c = rep(letters[1:2], 5))
plot1 <-
ggplot(tb, aes(a, b, colour = c)) +
geom_point() +
labs(color = "") +
scale_color_manual(values = rep("black", length(unique(tb$c)))) +
guides(color = guide_legend(override.aes = list(color = NA))) +
theme(legend.key = element_rect(fill = NA), legend.text = element_text(color = NA))
plot1
plot2 <-
ggplot(tb, aes(a, b, colour = c)) +
geom_point()
plot2
2. Using patchwork:
library(patchwork)
plot1 <- ggplot(tb, aes(a, b)) +
geom_point()
plot1 / plot2
I have three different subplotts, each with their own legend. I want to combine each of these 3 legends into one common legend at the bottom of the plot. I have found many similar questions combining the legends of different sub plots into one common legend when all the subplots had the same legend. Yet, not when the legends are different. Attempts to change the code were not succesful.
grid_arrange_shared_legend <- function(...) {
plots <- list(...)
g <- ggplotGrob(plots[[1]] + theme(legend.position = "bottom"))$grobs
legend <- g[[which(sapply(g, function(x) x$name) == "guide-box")]]
lheight <- sum(legend$height)
grid.arrange(
do.call(arrangeGrob, lapply(plots, function(x)
x + theme(legend.position="none"))),
legend,
ncol = 1,
heights = unit.c(unit(1, "npc") - lheight, lheight))
}
data = read.table("fermentation_run.csv", header=TRUE, sep=",", fileEncoding="UTF-8-BOM")
p1 <- ggplot(data, aes(x = time)) +
geom_line(aes(y = cdw*5, colour = "CDW"), size=1) +
geom_line(aes(y = glucose, colour = "glucose"), size=1) +
geom_step(aes(y = substrate, colour = "substrate"), size=1) +
theme_classic() + ylab("Concentration (g/l)") +
xlab("Time (h)") +
scale_colour_manual(values = c("grey", "red", "black"))
theme(legend.position="bottom", legend.title=element_blank())
p2 <- ggplot(data, aes(x=time)) +
geom_line(aes(y = alkyl, colour = "alkyl SS"), size=1) +
geom_line(aes(y = oleyl, colour = "oleyl alcohol"), size=1) +
theme_classic() +
xlab("Time (h)") +
ylab("Concentration (g/l)") +
scale_colour_manual(values = c("green", "blue"))
theme(legend.position="bottom", legend.title=element_blank())
p3 <- ggplot(data, aes(x=time)) +
geom_step(aes(y = aeration, colour="aeration"), size=1) +
geom_line(aes(y = do/2, colour="dissolved oxygen"), size=1) +
theme_classic() +
xlab("Time (h)") +
ylab("Aeration (lpm)") +
scale_y_continuous(sec.axis = sec_axis(~.*2, name = "Dissolved oxygen (%)")) +
theme(legend.position="bottom", legend.title=element_blank())
grid_arrange_shared_legend(p1, p2,p3)
This returns only the legend of the first plot and not of the three plots combined.
I think the key is to add all the legends in your first plot. To achieve this, you could add some fake rows in your data and label them according to your legends for all plots. Let's assume those legends are "a", "b", "c", "d", "e", and "f" in the following:
library(tidyverse)
# insert several rows with values outside your plot range
data <- add_row(mtcars,am=c(2, 3, 4, 5), mpg = 35, disp = 900)
data1<-data %>%
mutate (
by1 = factor(am, levels = c(0, 1, 2, 3, 4, 5),
labels = c("a", "b","c","d", "e","f")))
p1 <- ggplot(data1, aes(x = mpg, y=disp, col=by1)) +
geom_point() +
ylim(50,500)
You will get all the legends you need, and grid_arrange_shared_legend(p1, p2,p3) will pick up this. As you can see only "a" and "b" are for the first plot, and the rest are for other plots.
I don't have your data so I'll illustrate it with some basic datasets. The method isn't perfect with respect to some whitespace around the legends, but maybe someone in the comments knows a solution.
The answer I'm proposing is getting dirty with gtables and patchwork and internal functions thereof.
library(ggplot2)
library(grid)
library(patchwork) #https://github.com/thomasp85/patchwork
# Make plots as usual
g1 <- ggplot(iris, aes(Sepal.Width, Sepal.Length)) +
geom_point(aes(colour = Species))
g2 <- ggplot(mtcars, aes(mpg, disp)) +
geom_point(aes(colour = as.factor(cyl)))
# specify a legend position and a orientation for plots
position <- "bottom"
orientation <- "vertical"
# Add as many plots as you want to this list
plots <- list(g1, g2)
# Grab legends from plots in list
legends <- lapply(plots, function(p) {
p <- ggplotGrob(p + theme(legend.position = position))$grobs
p[[which(sapply(p, function(x) x$name) == "guide-box")]]
})
# Combine the legends
legend <- switch(position,
"bottom" = do.call(gtable:::cbind.gtable, legends),
"right" = do.call(gtable:::rbind.gtable, legends))
# Now make versions of the plots without the legend
stripped <- lapply(plots, function(p) p + theme(legend.position = "none"))
# Combine all the plots
stripped <- switch(orientation,
"horizontal" = do.call(patchwork:::ggplot_add.ggplot, stripped),
"vertical" = do.call(patchwork:::`/.ggplot`, stripped))
# Combine plots with legend
out <- switch(position,
"bottom" = stripped / legend,
"right" = stripped + legend)
out
Created on 2019-08-17 by the reprex package (v0.3.0)
If the whitespace really is a problem, you could supply a plot layout, but this would have to be a manual judgement to make:
out + plot_layout(heights = c(1,1,0.2))
I have been using the plot_grid command from cowplot to arrange my plots. I use the labeling feature, and my plots all look the same in that regard. However, when I 'hv' align some plots that have very different y-axis limits, such as the one below, it appears the height of the plot with shortest range of y is used.
If I just 'v' align the plot it looks better in some respects, but it is hard to resize the plot and have the labels looking good. I'd prefer the plot height not consider the x-axis labels, etc, like above.
Using gtables, I can get the desired width/height (below), but these leaves me without the consistent labels across all the figures in a document. Can I use the 'hv' alignment with cowplot and specify which plot height to use?
library(ggplot2)
library(dplyr)
library(scales)
library(grid)
library(cowplot)
data(iris)
iris <- iris %>% mutate(Petal.Width2 = ifelse(Species == "setosa", Petal.Width * 75, Petal.Width))
p1 <- ggplot(data=iris, aes(x = factor(Species), y=Sepal.Width)) +
geom_bar(stat="identity") +
labs(x = NULL, y = "Plot One") +
scale_y_continuous(labels = percent) +
theme(axis.text.x = element_blank(),
axis.title.y = element_text(vjust=1), plot.margin=unit(c(2,2,0,2),"mm"))
p2 <- ggplot(data=iris, aes(x = factor(Species), y=Petal.Width2)) + geom_bar(stat="identity") +
labs(x = NULL, y = "Plot Two") +
scale_y_continuous(labels = percent) +
theme(axis.text.x = element_blank(),
axis.title.y = element_text(vjust=1), plot.margin=unit(c(0,2,0,2),"mm"))
p3 <- ggplot(data=iris, aes(x = factor(Species), y=Petal.Length*0+.01)) + geom_bar(stat="identity") +
labs(x = "SPECIES", y = "The Third plot") +
scale_y_continuous(labels = percent) +
theme( axis.title.y = element_text(vjust=1, color="blue"), plot.margin=unit(c(0,2,0,2),"mm"),
axis.text.x = element_text(angle = 90, hjust=1, vjust=1,face ="italic", size=10))
plot_grid(p1,p2,p3,ncol=1, align="v", labels=c("A", "B", "C"))
# https://stackoverflow.com/a/27408589/1670053
plots <- list(p1, p2, p3)
grobs = lapply(plots, ggplotGrob)
g = do.call(rbind, c(grobs, size="first"))
g$widths = do.call(unit.pmax, lapply(grobs, "[[", "widths"))
grid.newpage()
grid.draw(g)
it's easy as to add labels,
plots <- list(p1, p2, p3)
grobs = lapply(plots, ggplotGrob)
library(gridExtra)
g = do.call(rbind, grobs) # uses gridExtra::rbind.gtable
panels <- g$layout[g$layout$name=="panel",]
g <- gtable::gtable_add_grob(g, lapply(LETTERS[1:nrow(panels)],
textGrob, vjust=1, y=1,
gp=gpar(fontface=2)),
t=panels$t, l=2)
grid.newpage()
grid.draw(g)
I realize that the align.plots function from the ggExtra package has been deprecated and removed. However, I am using my own version as it seems to provide the specific functionality I need. I have looked into faceting to solve my problem but I don't think it will work for my particular issue. What seems to be the problem is that the top-to-bottom images don't align when I use coord_equal on one of them. This doesn't seem to affect left-to-right though. Here is a simplified (or at least as simple as I can make it) version of what I am trying to achieve.
Create some dummy data frames:
source('https://raw.github.com/jbryer/multilevelPSA/master/r/align.R')
require(psych)
df = data.frame(x=rnorm(100, mean=50, sd=10),
y=rnorm(100, mean=48, sd=10),
group=rep(letters[1:10], 10))
dfx = describe.by(df$x, df$group, mat=TRUE)[,c('group1', 'mean', 'n', 'min', 'max')]
names(dfx) = c('group', 'x', 'x.n', 'x.min', 'x.max')
dfy = describe.by(df$y, df$group, mat=TRUE)[,c('group1', 'mean', 'n', 'min', 'max')]
names(dfy) = c('group', 'y', 'y.n', 'y.min', 'y.max')
df2 = cbind(dfx, dfy[,2:ncol(dfy)])
range = c(0,100)
This will setup the three plots:
p1a = ggplot(df2, aes(x=x, y=y, colour=group)) + geom_point() +
opts(legend.position='none') +
scale_x_continuous(limits=range) + scale_y_continuous(limits=range)
p1 = p1a + coord_equal(ratio=1)
p2 = ggplot(df, aes(x=x, y=group, colour=group)) + geom_point() +
scale_x_continuous(limits=range) + opts(legend.position='none')
p3 = ggplot(df, aes(x=group, y=y, colour=group)) + geom_point() +
scale_y_continuous(limits=range) + opts(legend.position='none')
The alignment top to bottom does not work with coord_equal
grid_layout <- grid.layout(nrow=2, ncol=2, widths=c(1,2), heights=c(2,1))
grid.newpage()
pushViewport( viewport( layout=grid_layout, width=1, height=1 ) )
align.plots(grid_layout, list(p1, 1, 2), list(p3, 1, 1), list(p2, 2, 2))
Broken Plot http://bryer.org/alignplots1.png
The fix is to add respect=TRUE to the grid.layout call:
grid_layout <- grid.layout(nrow=2, ncol=2, widths=c(1,2), heights=c(2,1), respect=TRUE)
But if I don't use coord_equal the alignment works fine:
grid_layout <- grid.layout(nrow=2, ncol=2, widths=c(1,2), heights=c(2,1))
grid.newpage()
pushViewport( viewport( layout=grid_layout, width=1, height=1 ) )
align.plots(grid_layout, list(p1a, 1, 2), list(p3, 1, 1), list(p2, 2, 2))
Working Plot http://bryer.org/alignplots2.png
ggplot2 now has ggplotGrob(), which may help with this.
First, we need to update the code used to generate the plots:
p1a = ggplot(df2, aes(x=x, y=y, colour=group)) + geom_point() +
scale_x_continuous(limits=range) + scale_y_continuous(limits=range)
p1 = p1a + coord_equal(ratio=1) + theme_minimal() + theme(legend.position='none')
p2 = ggplot(df, aes(x=x, y=group, colour=group)) + geom_point() +
scale_x_continuous(limits=range) + theme_minimal() + theme(legend.position='none')
p3 = ggplot(df, aes(x=group, y=y, colour=group)) + geom_point() +
scale_y_continuous(limits=range) + theme_minimal() + theme(legend.position='none')
p4 <- ggplot(df, aes(x = group, y = y)) +
geom_blank() +
theme(line = element_blank(),
rect = element_blank(),
text = element_blank(),
title = element_blank())
p4 will be blank; we just need the grob to draw.
Then we load the grid package and draw the grobs in a list arranged in rows and columns using cbind() and rbind().
library(grid)
grid.newpage()
grid.draw(
cbind(
rbind(ggplotGrob(p3), ggplotGrob(p4), size = "first"),
rbind(ggplotGrob(p1), ggplotGrob(p2), size = "first"),
size = "first"))
I'm not sure if this method will let you plot p3 in a different width and p2 in a different height, as you have them in the original example; I normally need a grid of similarly-sized graphs, and haven't needed to figure out different sizes.
This answer is partially based on partially based on https://stackoverflow.com/a/17463184/393354
Here is an example:
m <- matrix(c(3, 1, 0, 2), 2, byrow = T)
lay <- gglayout(m, widths = c(1, 3), heights = c(3, 1))
ggtable(p1, p2, p3, layout = lay)
you can use this by
install.packages('devtools')
library(devtools)
dev_mode()
install_github("ggplot2", "kohske", "cutting-edge")
library(ggplot2)
note that this branch is experimental, so maybe there are bugs.
To solve the problem using the align.plots method, specify respect=TRUE on the layout call:
grid_layout <- grid.layout(nrow=2, ncol=2, widths=c(1,2), heights=c(2,1), respect=TRUE)