How can I display two plots in one row with R function ggarrange() so that they have the same dimensions, in particular the same height?
In this example, the second plot is a bit higher than the first plot. I would like to increase the size of a1_plot, so that it matches the size of a2_plot.
# required packages
library(ggplot2)
library(ggbreak)
library(directlabels)
library(ggpubr)
# make dataframe
df1 <- data.frame(first_column=c("value_1","value_2","value_3","value_4","value_4","value_5"),
second_column=c("123","123","325","325","656","656"),
third_column=c(12,13,1,19,200,360),
fourth_column=c(1,124,155,3533,5533,6666))
# plot 1
a1_plot <-
ggplot(df1, aes(x=third_column, y=fourth_column, colour=second_column)) +
scale_x_continuous(breaks = c(0,50,100,150,200,250,300)) +
ylab("Fourth column")+ xlab("Third column") +
scale_x_break(breaks = c(210,400)) +
geom_dl(mapping=aes(x=third_column, y=fourth_column, label=second_column),
method = list(dl.trans(x = x + 0.1), dl.combine("last.points"))) +
theme(legend.position = "none")
# plot 2
a2_plot <-
ggplot(data=df1)+
geom_point(aes(x=second_column, y=fourth_column) +
xlab("X axis")+ ylab("Y axis") +
theme(legend.position = "none")
# merge plot1 and plot2
ggarrange(print(a1_plot), print(a2_plot), labels = c('a1', 'a2'))
I was unable to change the height of plot 1. By adjusting the margins of plot 2, the problem has been solved.
theme(legend.position = "none", plot.margin = unit(x=c(3.6,5,3.9,0), units = "mm"))
Related
I've created a plot (below) and basically want the left and right ends of each facet to state "Ov" and "Cx." I've tried using scale_x_continuous but the issue is that the x-axis for each facet is different.
What I have right now (image):
What I'd like to get ideally:
all_prm %>% ggplot(aes(y_coord, prominence)) +
geom_point() +
facet_wrap(~interaction(ms, sample), scales="free_x") +
scale_x_continuous(breaks=c(10000), labels=c("Ov")) +
theme(
axis.title.y=element_text(margin=margin(r=7)),
axis.title.x=element_text(margin=margin(t=7)),
panel.background = element_rect(fill='white', color='grey10')) +
xlab("Oviduct-Cervical Axis") +
ylab("Prominence")
You can use a custom function to set the break points, in this case using the range of the x limit values with an adjustment argument to move the labels away from the axis limits relative to their scale.
Using the iris dataset:
break_range <- function(x, adjust = .025) {
rng <- range(x)
rng + diff(rng) * c(adjust, -adjust)
}
ggplot(iris, aes(Petal.Length, Sepal.Length )) +
geom_point() +
facet_wrap(. ~ Species, nrow = 3, scales="free_x") +
scale_x_continuous(breaks = break_range, labels = c("Ov", "Cx")) +
theme(
axis.title.y=element_text(margin=margin(r=7)),
axis.title.x=element_text(margin=margin(t=7)),
panel.background = element_rect(fill='white', color='grey10'))
This is a follow up problem to this question. The OP asked for a way to arrange parts of a plot in specific distances. I think teunbrand gave a very good answer.
My own suggestion (extract the legend with cowplot, and stitch them to a plot in desired proportions) is not fully satisfactory, because it worked only "by chance" in the given example - the legend labels were long enough to center the legend grob into the viewport for the third plot.
Having shorter labels reveals the problem - when adding a grob, patchwork centres this grob, basically padding equally to all sides.
My question is, do you know of a way to control this padding behaviour?
Cowplot (or any other ggplot combining package for that sake) also very welcome.
library(tidyverse)
library(patchwork)
data <- midwest %>%
head(5) %>%
select(2,23:25) %>%
pivot_longer(cols=2:4,names_to="Variable", values_to="Percent") %>%
mutate(Variable=factor(Variable,
levels=c("percbelowpoverty","percchildbelowpovert","percadultpoverty"),
labels = paste0("perc", 1:3)))
p1 <-
ggplot(data=data, mapping=aes(x=county, y=Percent, fill=Variable)) +
geom_col() +
scale_fill_manual(values = c("#CF232B","#942192","#000000")) +
theme(legend.background = element_rect(fill = "grey50"))
p_legend <- cowplot::get_legend(p1)
p_main <- p1 <-
ggplot(data=data, mapping=aes(x=county, y=Percent, fill=Variable)) +
geom_col(show.legend = FALSE) +
scale_fill_manual(values = c("#CF232B","#942192","#000000"))
p_main + plot_spacer() + p_legend +
plot_layout(widths = c(12.5, 1.5, 4)) &
theme(plot.margin = margin(),
plot.background = element_rect(colour = "black"))
Not so desired result - the legend grob (with grey background) should be aligned to the left plot border (black line)
Created on 2021-04-09 by the reprex package (v1.0.0)
As far as I get it the issue is not on patchworks side. Having a look at the layout of the legend's gtable we see that it is made up of 5 rows and 5 columns and that the legend is to be placed in the cell in the center:
p_legend <- cowplot::get_legend(p1)
p_legend
#> TableGrob (5 x 5) "guide-box": 2 grobs
#> z cells name
#> 99_a788e923bf245af3853cee162f5f8bc9 1 (3-3,3-3) guides
#> 0 (2-4,2-4) legend.box.background
#> grob
#> 99_a788e923bf245af3853cee162f5f8bc9 gtable[layout]
#> zeroGrob[NULL]
gtable::gtable_show_layout(p_legend)
Hence, when adding the legend patchwork centers is as demanded by the gtable layout.
One option to control the positioning or the padding of the legend would be to squash the first column via cowplot::gtable_squash_cols and if desired add some padding by adding a new column with the desired amount of padding via gtable::gtable_add_cols:
# Squash first column
p_legend <- cowplot::gtable_squash_cols(p_legend, 1)
# Add some padding by adding a new col
p_legend <- gtable::gtable_add_cols(p_legend, unit(.1, "cm"), pos = 1)
p_main <- p1 <-
ggplot(data=data, mapping=aes(x=county, y=Percent, fill=Variable)) +
geom_col(show.legend = FALSE) +
scale_fill_manual(values = c("#CF232B","#942192","#000000"))
p_main + plot_spacer() + p_legend +
plot_layout(widths = c(12.5, 1.5, 4)) &
theme(plot.margin = margin(),
plot.background = element_rect(colour = "black"))
I have a problem with combining ggplots using cowplot and ggpubr which is driving me crazy.
The problem is with the legend. When it's displayed with its original graph on its own, the spacing between the elements of the legend (guide title, key, key-label) are absolutely fine.
However, if I extract the legend from the original plot, and then display it in a combined plot (using either plot_grid from cowplot or ggarrange from ggpubr) then the spacing goes haywire. The longer the text, the more the spacing expands.
What is wrong here, and how do I fix it so that the legend in the combined plot looks exactly like the one in the original individual plot?
Example
This example uses ggarrange from ggpubr; my results with get_legend and plot_grid using cowplot are similar. Treatment names are entirely made up.
library(survival)
library(broom)
library(dplyr)
library(foreach)
library(ggpubr)
fit <- survfit(Surv(time,status == 2) ~ trt + sex, data=pbc)
time.xticks <- seq(0, 4000, 1000)
delta <- 0.00001
# Survival plot
kmdata <- tidy(fit) %>%
mutate(trt=factor(gsub('trt=(.*),.*','\\1',strata)),
sex=factor(gsub('.*sex=(.*)','\\1',strata), levels=levels(pbc$sex)))
p1 <- ggplot(data=filter(kmdata, time<=max(time.xticks)), aes(x=time, y=estimate, colour=sex, linetype=trt)) + geom_step() +
scale_x_continuous(breaks = time.xticks,
limits = c(min(time.xticks), max(time.xticks))) +
scale_colour_discrete(name="Sex", labels=c("Male","Female")) +
scale_linetype_discrete(name="Treatment group", labels=c("Zyxatrxilbroh 35 mg", "Placebo 35 mg")) +
theme(legend.position = "bottom", legend.box = "horizontal",
legend.background = element_rect(fill="grey90", colour="black", size=0),
legend.key.height=unit(0.2, "cm"),
text=element_text(size=18))
tardata <- foreach(s=unique(kmdata$strata), .combine="rbind") %do% {
filter(kmdata, strata==s)[findInterval(pmax(0, time.xticks-delta), filter(kmdata, strata==s)$time)+1,] %>%
bind_cols(tibble(time.xticks))
} %>%
mutate(ypos = -((as.integer(sex)-1)*(length(unique(pbc$trt))+2) + as.integer(trt) + 1))
tarheads <- tibble(xpos=0,
ypos=-(((1:length(unique(pbc$sex))) - 1)*(length(unique(pbc$trt)) + 2) + 1),
lab=levels(pbc$sex))
risk.yticks <- sort(unique(tardata$ypos))
risk.ylabels <- rep(rev(paste("trt =",levels(kmdata$trt))), length(unique(kmdata$sex)))
# Number-at-risk table
p2 <- ggplot(data=tardata, aes(x=time.xticks, y=ypos, label=n.risk, colour=sex)) + geom_text() +
geom_text(data=tarheads, aes(x=xpos, y=ypos, label=lab), colour="black", hjust="left") +
scale_x_continuous(breaks = time.xticks,
limits = c(min(time.xticks), max(time.xticks))) +
scale_y_continuous(breaks = risk.yticks,
labels = risk.ylabels) +
theme(text=element_text(size=18))
# put the two together
p.comb <- ggarrange(p1, p2, heights = c(2, 0.8), ncol=1,
align="v", common.legend = TRUE, legend="bottom")
# alternate version with guide headings at the top left instead of at the side
p1.a <- p1 + guides(colour = guide_legend(order=1,
title.position = "top",
title.hjust = 0),
linetype = guide_legend(order=1,
title.position = "top",
title.hjust = 0))
p.comb.a <- ggarrange(p1.a, p2, heights = c(2, 0.8), ncol=1,
align="v", common.legend = TRUE, legend="bottom")
# send to png
png("test-p1.png", width=8, height=4.5, units="in", res=200, type="cairo")
plot(p1)
dev.off()
png("test-pcomb.png", width=8, height=4.5, units="in", res=200, type="cairo")
plot(p.comb)
dev.off()
Results
Individual plot with correct legend spacing:
[
Combined plot with legend spacing expanded so much that the legend no longer fits in the image:
I want to display related ggplots together, with axes all the same size, but with some plots displaying the axis title and other plots blanking the axis title. However, using element_blank() to remove the axis also changes the size of the plot. Here's an example:
library(tidyverse)
library(cowplot)
tb <- tibble(a = 1:5, b = 1:5)
with_x_title <- ggplot(tb, aes(a,b)) +
geom_point()
without_x_title <- ggplot(tb, aes(a,b)) +
geom_point() +
theme(axis.title.x = element_blank())
ggdraw() +
draw_plot(with_x_title, x = 0, y = 0, width = 0.5, height = 1) +
draw_plot(without_x_title, x = 0.5, y = 0, width = 0.5, height = 1)
Here, the y-axis of the plot without an x-axis title is expanded. Is there a way to prevent this happening?
I'm aware I can fudge a fix by changing the height and position in the call to ggdraw, but I'd like a fix that works on the ggplots. I also imagine this is a common problem, but haven't been able to find a solution out there.
Specify the name of the x-axis as empty string, i.e. "" instead of element_blank()
...
without_x_title <- ggplot(tb, aes(a,b)) +
geom_point() +
# theme(axis.title.x = element_blank()) +
labs(x = "")
...
I am trying to plot the parameter estimates and levels of hierarchy from a stan model output. For the legend, I am hoping to remove all labels except for the "Overall Effects" label but I can't figure out how to remove all of the species successfully.
Here is the code:
ggplot(dfwide, aes(x=Estimate, y=var, color=factor(sp), size=factor(rndm),
alpha=factor(rndm))) +
geom_point(position =pd) +
geom_errorbarh(aes(xmin=(`2.5%`), xmax=(`95%`)), position=pd,
size=.5, height = 0, width=0) +
geom_vline(xintercept=0) +
scale_colour_manual(values=c("blue", "red", "orangered1","orangered3", "sienna4",
"sienna2", "green4", "green3", "purple2", "magenta2"),
labels=c("Overall Effects", expression(italic("A. pensylvanicum"),
italic("A. rubrum"), italic("A. saccharum"),
italic("B. alleghaniensis"), italic("B. papyrifera"),
italic("F. grandifolia"), italic("I. mucronata"),
italic("P. grandidentata"), italic("Q. rubra")))) +
scale_size_manual(values=c(3, 1, 1, 1, 1, 1, 1, 1, 1, 1)) +
scale_shape_manual(labels="", values=c("1"=16,"2"=16)) +
scale_alpha_manual(values=c(1, 0.4)) + guides(size=FALSE, alpha=FALSE) +
ggtitle(label = "A.") +
scale_y_discrete(limits = rev(unique(sort(dfwide$var))), labels=estimates) +
ylab("") +
labs(col="Effects") + theme(legend.title=element_blank())
The key points you need to notice is that remove part of the labels in legend can't be achieved by the function in ggplot2, what you need to do is interact with grid, which more underlying since both lattice and ggplot2 are based grid，to do some more underlying work, we need some functions in the grid.
To remove part of the labels in legend, there are three functions need to be used, they are grid.force(), grid.ls() and grid.remove() . After draw the picture by ggplot2, then using grid.force() and grid.ls(), we can find all the elements in the picture, they all are point, line, text, etc. Then we may need to find the elements we are interested, this process is interactive, since names of the element in ggplot2 are made by some numbers and text, they are not always meanful, after we identify the names of the element we are interested, we can use the grid.remove() function to remove the elements, blew is the sample code I made.
library(grid)
library(ggplot2)
set.seed(1)
data <- data.frame(x = rep(1:10, 2), y = sample(1:100, 20),
type = sample(c("A", "B"), 20, replace = TRUE))
ggplot(data, aes(x = x, y =y,color = type))+
geom_point()+
geom_line()+
scale_color_manual(values = c("blue", "darkred"))+
theme_bw()
until now, we have finished draw the whole picture, then we need to do some works remove some elements in the picture.
grid.force()
grid.ls()
grid.ls() list all the element names
grid.remove("key-4-1-1.5-2-5-2")
grid.remove("key-4-1-2.5-2-5-2")
grid.remove("label-4-3.5-4-5-4")
It's not perfect, but my solution would be to actually make two plots and combine them together. See this post where I lifted the extraction code from.
I don't have your data, but I think you will get the idea below:
library(ggplot2)
library(gridExtra)
library(grid)
#g_table credit goes to https://stackoverflow.com/a/11886071/2060081
g_legend<-function(a.gplot){
tmp <- ggplot_gtable(ggplot_build(a.gplot))
leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
legend <- tmp$grobs[[leg]]
return(legend)}
p_legend = ggplot(dfwide[sp=='Overall Effects'], aes(x=Estimate, y=var, color=factor(sp),
size=factor(rndm),
alpha=factor(rndm))) +
geom_point(position =pd) +
geom_errorbarh(aes(xmin=(`2.5%`), xmax=(`95%`)), position=pd,
size=.5, height = 0, width=0) +
geom_vline(xintercept=0) +
scale_colour_manual(values=c("blue"),
labels=c("Overall Effects"))) +
scale_size_manual(values=c(3)) +
scale_shape_manual(labels="", values=c("1"=16,"2"=16)) +
scale_alpha_manual(values=c(1, 0.4)) + guides(size=FALSE, alpha=FALSE) +
ggtitle(label = "A.") +
scale_y_discrete(limits = rev(unique(sort(dfwide$var))), labels=estimates) +
ylab("") +
labs(col="Effects") + theme(legend.title=element_blank())
p_legend = g_legend(p_legend)
One of your plots will just be the legend. Subset your data based on the Overall Effects and then plot the two plots together as a grid.