Make scatter plot with truncated axis

Load data

library(readxl)
library(tidyverse)
library(here)
library(ggh4x)
library(latex2exp)

fig1a <- read_excel(here("projects", "data", "data.xlsx"), sheet = "Figure_1A")
fig1a %>% head()
## # A tibble: 6 × 5
##   animal.number genotype Fat.mass Lean.Mass sex  
##           <dbl> <chr>       <dbl>     <dbl> <chr>
## 1           109 WT           3.87      31.4 Male 
## 2           140 WT           6.98      28.0 Male 
## 3           141 WT           5.66      29.6 Male 
## 4           144 WT           4.37      30.8 Male 
## 5           145 WT           4.32      29.1 Male 
## 6           199 WT           1.62      27.7 Male

p1 <- fig1a %>%
  filter(genotype == "WT") %>%
  ggplot(aes(x = Lean.Mass, y = Fat.mass)) +
  geom_point(shape = 21, size = 5, fill = "#929292", color = "black") +
  scale_x_continuous(
    limits = c(20, 40),
    breaks = seq(20, 40, 5),
    guide = "axis_minor",
    minor_breaks = seq(22.5, 37.5, by = 5)
  ) +
  scale_y_continuous(
    limits = c(0, 25),
    breaks = seq(0, 25, 5),
    guide = "axis_minor",
    minor_breaks = c(8, 12)
  ) +
  theme_classic() +
  theme(
    ggh4x.axis.ticks.length.minor = rel(0.5),
    axis.ticks.length.x = unit(0.5, "lines")
  ) +
  guides(
    x = guide_axis_minor(trunc_lower = 20, trunc_upper = 40),
    y = guide_axis_truncated(trunc_lower = 0, trunc_upper = 25)
  ) +
  geom_vline(xintercept = 32.5, lty = "dashed") +
  geom_hline(yintercept = 10, lty = "dashed") +
  labs(
    x = NULL,
    y = "Fat mass (g)"
  ) +
  annotate(geom = "point", x = 20, y = 23 + 1, shape = 21, size = 5, fill = "#929292") +
  annotate(geom = "text", x = 20.5, y = 23 + 1, label = "WT", size = 5, hjust = 0) +
  annotate(geom = "point", x = 20, y = 22 - 1, shape = 21, size = 5, fill = "#0533ff") +
  annotate(geom = "text", x = 20.5, y = 22 - 1, label = TeX(r"(\textit{Nnat}${^+}{^/}{^-}{^p}$)"), size = 5, hjust = 0)


p2 <- fig1a %>%
  filter(genotype == "Nnat+/-p") %>%
  ggplot(aes(x = Lean.Mass, y = Fat.mass)) +
  geom_point(shape = 21, size = 5, fill = "#0533ff", color = "black") +
  scale_x_continuous(
    limits = c(20, 40),
    breaks = seq(20, 40, 5),
    guide = "axis_minor",
    minor_breaks = seq(22.5, 37.5, by = 5)
  ) +
  scale_y_continuous(
    limits = c(0, 25),
    breaks = seq(0, 25, 5),
    guide = "axis_minor",
    minor_breaks = c(8, 12)
  ) +
  theme_classic() +
  theme(
    ggh4x.axis.ticks.length.minor = rel(0.5),
    axis.ticks.length.x = unit(0.5, "lines"),
    axis.line.y = element_blank(),
    axis.ticks.y = element_blank(),
    axis.text.y = element_blank()
  ) +
  guides(
    x = guide_axis_minor(
      trunc_lower = 20,
      trunc_upper = 40
    ),
    y = guide_axis_truncated(
      trunc_lower = 0,
      trunc_upper = 25
    )
  ) +
  geom_vline(xintercept = 32.5, lty = "dashed") +
  geom_hline(yintercept = 10, lty = "dashed") +
  labs(x = NULL, y = NULL)

library(patchwork)
p1 + p2 + labs(x = "Lean mass (g)") + theme(axis.title.x = element_text(hjust = -0.12))
## Warning: The S3 guide system was deprecated in ggplot2 3.5.0.
## ℹ It has been replaced by a ggproto system that can be extended.
## Warning in is.na(x): is.na() applied to non-(list or vector) of type
## 'expression'