Setting Individual Axis Limits With Facet_Wrap and Scales = "Free" in Ggplot2

Setting individual axis limits with facet_wrap and scales = free in ggplot2

Here's some code with a dummy geom_blank layer,

range_act <- range(range(results$act), range(results$pred))

d <- reshape2::melt(results, id.vars = "pred")

dummy <- data.frame(pred = range_act, value = range_act,
variable = "act", stringsAsFactors=FALSE)

ggplot(d, aes(x = pred, y = value)) +
facet_wrap(~variable, scales = "free") +
geom_point(size = 2.5) +
geom_blank(data=dummy) +
theme_bw()

Sample Image

Adjusting y axis limits in ggplot2 with facet and free scales

First, reproducibility with random data needs a seed. I started using set.seed(42), but that generated negative values which caused completely unrelated warnings. Being a little lazy, I changed the seed to set.seed(2021), finding all positives.

For #1, we can add limits=, where the help for ?scale_y_continuous says that

  limits: One of:

• 'NULL' to use the default scale range

• A numeric vector of length two providing limits of the
scale. Use 'NA' to refer to the existing minimum or
maximum

• A function that accepts the existing (automatic) limits
and returns new limits Note that setting limits on
positional scales will *remove* data outside of the
limits. If the purpose is to zoom, use the limit argument
in the coordinate system (see 'coord_cartesian()').

so we'll use c(0, NA).

For Q2, we'll add expand=, documented in the same place.

data %>%
gather(Gene, Levels, -Patient, -Treatment) %>%
mutate(Treatment = factor(Treatment, levels = c("Pre", "Post"))) %>%
mutate(Patient = as.factor(Patient)) %>%
ggplot(aes(x = Treatment, y = Levels, color = Patient, group = Patient)) +
geom_point() +
geom_line() +
facet_wrap(. ~ Gene, scales = "free") +
theme_bw() +
theme(panel.grid = element_blank()) +
scale_y_continuous(limits = c(0, NA), expand = expansion(mult = c(0, 0.1)))

Sample Image

ggplot2 change axis limits for each individual facet panel

preliminaries

Define original plot and desired parameters for the y-axes of each facet:

library(ggplot2)
g0 <- ggplot(mpg, aes(displ, cty)) +
geom_point() +
facet_grid(rows = vars(drv), scales = "free")

facet_bounds <- read.table(header=TRUE,
text=
"drv ymin ymax breaks
4 5 25 5
f 0 40 10
r 10 20 2",
stringsAsFactors=FALSE)

version 1: put in fake data points

This doesn't respect the breaks specification, but it gets the bounds right:

Define a new data frame that includes the min/max values for each drv:

ff <- with(facet_bounds,
data.frame(cty=c(ymin,ymax),
drv=c(drv,drv)))

Add these to the plots (they won't be plotted since x is NA, but they're still used in defining the scales)

g0 + geom_point(data=ff,x=NA)

This is similar to what expand_limits() does, except that that function applies "for all panels or all plots".

version 2: detect which panel you're in

This is ugly and depends on each group having a unique range.

library(dplyr)
## compute limits for each group
lims <- (mpg
%>% group_by(drv)
%>% summarise(ymin=min(cty),ymax=max(cty))
)

Breaks function: figures out which group corresponds to the set of limits it's been given ...

bfun <- function(limits) {
grp <- which(lims$ymin==limits[1] & lims$ymax==limits[2])
bb <- facet_bounds[grp,]
pp <- pretty(c(bb$ymin,bb$ymax),n=bb$breaks)
return(pp)
}
g0 + scale_y_continuous(breaks=bfun, expand=expand_scale(0,0))

The other ugliness here is that we have to set expand_scale(0,0) to make the limits exactly equal to the group limits, which might not be the way you want the plot ...

It would be nice if the breaks() function could somehow also be passed some information about which panel is currently being computed ...

ggplot: limit axis limits/breaks of individual facet

Try this.

  1. I expanded the y axis.
  2. I adjusted the breaks. I borrowed the general idea from here. Function my_breaks returns pretty_breaks but removes the last value.

(Note: I also switched the aesthetics, y = nobs and x = cyl and used coord_flip, because running your code on my machine has not reproduced your plot (ggplot 3.3.0)):

library(tidyverse)
#> Warning: package 'forcats' was built under R version 3.6.3

my_breaks <- function(x, n = 5, drop = 2) {
breaks <- seq(x[[1]], x[[2]], length.out = n)
breaks <- scales::pretty_breaks()(breaks)
breaks <- breaks[1:(length(breaks) - drop)]
breaks
}

mtcars %>%
group_by(cyl, gear) %>%
summarise(n_obs = n()) %>%
mutate(n_obs = case_when(
gear == 4 ~ n_obs * 100,
TRUE ~ as.numeric(n_obs))) %>%
group_by(gear) %>%
mutate(n_obs_max = max(n_obs, na.rm=T)) %>%
ggplot(aes(x = cyl))+
geom_bar(aes(y = n_obs), stat="identity")+
geom_text(aes(y = n_obs_max * 1.2, label = n_obs))+
facet_wrap(vars(gear), scales = "free_x") +
scale_y_continuous(breaks = function(x) my_breaks(x, 5, 2),
expand = expand_scale(mult = c(0.05, .2))) +
coord_flip()
#> Warning: 'expand_scale()' is deprecated; use 'expansion()' instead.

Sample Image

Created on 2020-03-09 by the reprex package (v0.3.0)

How to increase the default y-axis limit in ggplot when scales in facet_wrap() are set to free

An option is to expand the axis limits.

ggplot(d, aes(id, mean)) +
geom_point() +
geom_errorbar(aes(ymin = mean - sd,
ymax = mean + sd)) +
geom_text(aes(
x = id,
y = mean + sd,
vjust = -2,
label = diff
)) +
facet_wrap( ~ var, scales = "free_y") +
scale_y_continuous(expand = expansion(mult = c(0.1, 0.2)))

Sample Image

This increases the top range by 20% and the bottom by 10%. AFAIK, the defaults are mult = c(0.05, 0).

How to set dynamic data limits across facets in ggplot2?

I agree with the comments, although I think this accomplishes the original goal. Based on this.

library(tidyverse)

location <- rep(c("1001", "1002", "1003", "1004"), c(3, 3, 3, 3))
period <- rep(c(2019, 2020, 2021), 4)
change <- c(-3.1, 5.4, -2.2, 190.8, 2.3, 150, 0.34, -0.44, -0.67, 1.2, 3, 4)

tot <- data.frame(location, period, change)

ggplot(data = tot, aes(x = period, y = change)) +
geom_blank(aes(y=-change)) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
facet_wrap(~location, ncol = 1, scales = "free")

Changing multiple y scales when using facet_wrap

The limits are automatically set based on the x,y values... but ignore the ymax and ymin values used for the error bar geoms, which is why the errorbars are outside the viewable area on the plot. One option could be to reset your own limits manually, but much better would be to use the expand= argument with scale_y_continuous() to expand the viewable area a bit past the automatically-set limits.

To use the argument, you assign expand=expansion(mult=c(lower,upper)) or expand=expansion(add=c(lower,upper)). The numbers for upper and lower set the expansion on the high or low end of the axis, respectively. Using add expands the axis by adding a discrete amount, whereas mult expands the axis by adding a multiplier. mult is more useful in this case, since the facets have different limits by default. Here's the some numbers that worked okay for me and the code:

ggplot(df, aes(x =time,y=mean)) + 
geom_point(size = 3)+
geom_errorbar(ymax=df$mean+df$sd,ymin=df$mea-df$sd,width=0.1)+
scale_y_continuous(expand=expansion(mult=c(0.8,0.8))) +
facet_wrap(~df$var, scales="free_y", ncol = 1, strip.position = "left")+
theme_bw()+
theme(
axis.line=element_line(colour="black"),
axis.text.y= element_text(size=18),
axis.text.x=element_text(size=18,angle = 90,vjust=0.1),
axis.title=element_blank())

Sample Image



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