Editing legend in ggplot2 - R

Question

I'm learning to use ggplot to make graphs for my research and I'm having some trouble setting legends for them.

Initially I thought about just using the aes() function inside geom_point and geom_line to get the aesthetics I'm looking for. However, I realized the legends weren't being generated by doing it this way. Code and exemple below.

#Stablish the variables as vectors

MexxJan_hydrogen <- c(0, 1.38, 3.19, 8.30)
MexyJan_hydrogen <- c(0, 1.25, 2.78, 6.23)
MexzJan_hydrogen <- c(0, 2.46, 5.68, 12.18)
MexwJan_hydrogen <- c(0, 7.56, 9.20, 10.19)
time_hydrogen <- c(0, 60, 120, 180)

#Create the data frame
hydrogen_data <- data.frame(time_hydrogen, MexxJan_hydrogen, MexyJan_hydrogen, MexzJan_hydrogen, MexwJan_hydrogen)
view(hydrogen_data)

#Code the plot
hydrogen_plot <- ggplot(data = hydrogen_data) +
  geom_line(aes(x = time_hydrogen, y = MexxJan_hydrogen), color = "palegreen3", lwd = 1) +
  geom_line(aes(x = time_hydrogen, y = MexyJan_hydrogen), color = "tan1", lwd = 1) +
  geom_line(aes(x = time_hydrogen, y = MexzJan_hydrogen), color = "tomato2", lwd = 1) +
  geom_line(aes(x = time_hydrogen, y = MexwJan_hydrogen), color = "cadetblue", lwd = 1) +
  geom_point(aes(x = time_hydrogen, y = MexxJan_hydrogen), color = "palegreen3", shape = 15, size = 5) +
  geom_point(aes(x = time_hydrogen, y = MexyJan_hydrogen), color = "tan1", shape = 16, size = 5) +
  geom_point(aes(x = time_hydrogen, y = MexzJan_hydrogen), color = "tomato2", shape = 17, size = 5) +
  geom_point(aes(x = time_hydrogen, y = MexwJan_hydrogen), color = "cadetblue", shape = 18, size = 5) +
  theme_bw() +
  theme(axis.text = element_text(family = "Arial", size = 15, color = "black"),
        axis.title.x = element_text(family = "Arial", size = 16, margin = margin(t = 15)),
        axis.title.y = element_text(family = "Arial", size = 16, margin = margin(r = 15)),axis.line = element_line(color = "black"),
        plot.background = element_rect(fill = "transparent", color = NA),
        panel.border = element_rect(color = "black"),
        panel.background = element_rect(fill = "transparent"),
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        panel.grid.major.y = element_blank(),
        panel.grid.minor.y = element_blank(),
        axis.ticks.length = unit(0.20, units = "cm"),
        legend.background = element_rect(fill = "transparent"),
        legend.key = element_rect(fill = "transparent", colour = NA),
        legend.position = "top",
        legend.key.width = unit(0, unit = "cm"),
        legend.key.height = unit(0, unit = "cm"),
        legend.title = element_blank(),
        legend.text = element_text(size = 13.5),
        legend.spacing.x = unit(0.1, "cm"),
        legend.text.align = unit(0.05, unit = "cm")) +
  labs(x = "Time (min)", y = "Gas Evolution (µmol.g"^-1~")") +
  coord_cartesian(ylim = c(0,15), xlim = c(0,180)) +
  scale_y_continuous(expand = expansion(mult = c(0.02, 0.02)),
                     n.breaks = 5) +
  scale_x_continuous(expand = expansion(mult = c(0.02, 0.02)),
                     breaks = c(0, 60, 120, 180))

I then found that I could use the function scale_colors_manual to get the desired colors and show the legend. Also, using scale_colors_manual I managed to change the legend text to a shorter option. Code and exemple below.

#Stablish the variables as vectors

MexxJan_hydrogen <- c(0, 1.38, 3.19, 8.30)
MexyJan_hydrogen <- c(0, 1.25, 2.78, 6.23)
MexzJan_hydrogen <- c(0, 2.46, 5.68, 12.18)
MexwJan_hydrogen <- c(0, 7.56, 9.20, 10.19)
time_hydrogen <- c(0, 60, 120, 180)

#Create the data frame
hydrogen_data <- data.frame(time_hydrogen, MexxJan_hydrogen, MexyJan_hydrogen, MexzJan_hydrogen, MexwJan_hydrogen)
view(hydrogen_data)

hydrogen_plot <- ggplot(data = hydrogen_data) +
  geom_line(aes(x = time_hydrogen, y = MexxJan_hydrogen, color = "MexxJan_hydrogen"), lwd = 1) +
  geom_line(aes(x = time_hydrogen, y = MexyJan_hydrogen, color = "MexyJan_hydrogen"), lwd = 1) +
  geom_line(aes(x = time_hydrogen, y = MexzJan_hydrogen, color = "MexzJan_hydrogen"), lwd = 1) +
  geom_line(aes(x = time_hydrogen, y = MexwJan_hydrogen, color = "MexwJan_hydrogen"), lwd = 1) +
  geom_point(aes(x = time_hydrogen, y = MexxJan_hydrogen, color = "MexxJan_hydrogen"), shape = 15, size = 5) +
  geom_point(aes(x = time_hydrogen, y = MexyJan_hydrogen, color = "MexyJan_hydrogen"), shape = 16, size = 5) +
  geom_point(aes(x = time_hydrogen, y = MexzJan_hydrogen, color = "MexzJan_hydrogen"), shape = 17, size = 5) +
  geom_point(aes(x = time_hydrogen, y = MexwJan_hydrogen, color = "MexwJan_hydrogen"), shape = 18, size = 5) +
  theme_bw() +
  theme(axis.text = element_text(family = "Arial", size = 15, color = "black"),
        axis.title.x = element_text(family = "Arial", size = 16, margin = margin(t = 15)),
        axis.title.y = element_text(family = "Arial", size = 16, margin = margin(r = 15)),axis.line = element_line(color = "black"),
        plot.background = element_rect(fill = "transparent", color = NA),
        panel.border = element_rect(color = "black"),
        panel.background = element_rect(fill = "transparent"),
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        panel.grid.major.y = element_blank(),
        panel.grid.minor.y = element_blank(),
        axis.ticks.length = unit(0.20, units = "cm"),
        legend.background = element_rect(fill = "transparent"),
        legend.key = element_rect(fill = "transparent", colour = NA),
        legend.position = "top",
        legend.key.width = unit(0, unit = "cm"),
        legend.key.height = unit(0, unit = "cm"),
        legend.title = element_blank(),
        legend.text = element_text(size = 13.5),
        legend.spacing.x = unit(0.1, "cm"),
        legend.text.align = unit(0.05, unit = "cm")) +
  labs(x = "Time (min)", y = "Gas Evolution (µmol.g"^-1~")") +
  coord_cartesian(ylim = c(0,15), xlim = c(0,180)) + #Limit the size of the plot
  scale_y_continuous(expand = expansion(mult = c(0.02, 0.02)),
                     n.breaks = 5) +
  scale_x_continuous(expand = expansion(mult = c(0.02, 0.02)),
                     breaks = c(0, 60, 120, 180)) +
  scale_color_manual(labels = c("15Me-NT", "15Me-nNT", "15Me-NNT", "15Me-nnt"),
                     values = c("MexxJan_hydrogen" = "palegreen3", "MexyJan_hydrogen" = "tan1", "MexzJan_hydrogen" = "cadetblue", "MexwJan_hydrogen" = "tomato2"))

In this case, I got the colors and the legend. However, as you can see in the image, the legend keys look like a bunch of geometric forms stacked. I couldn't find a way to solve this. Tried using scale_shape_manual but I couldn't get the code right.

May you help me getting this plot some beautiful aesthetics? hehehe

Thank you. Stay safe.

Answer 1

To fix your issue you have to move shape inside aes similar to what you have done for color and afterwards set your shapes via scale_shape_manual . However, you could simplify your approach considerably by first reshaping your data to long or tidy data format. Doing so allows to add your lines and points which just one geom_point and geom_line :

library(tidyr)
library(ggplot2)

hydrogen_data_long <- hydrogen_data %>%
  tidyr::pivot_longer(-time_hydrogen, names_to = "hydrogren")

ggplot(hydrogen_data_long, aes(x = time_hydrogen, y = value, color = hydrogren)) +
  geom_line(lwd = 1) +
  geom_point(aes(shape = hydrogren), size = 5) +
  scale_shape_manual(
    labels = c("15Me-NT", "15Me-nNT", "15Me-NNT", "15Me-nnt"),
    values = c(
      "MexxJan_hydrogen" = 15, "MexyJan_hydrogen" = 16,
      "MexzJan_hydrogen" = 17, "MexwJan_hydrogen" = 18
    )
  ) +
  scale_color_manual(
    labels = c("15Me-NT", "15Me-nNT", "15Me-NNT", "15Me-nnt"),
    values = c(
      "MexxJan_hydrogen" = "palegreen3", "MexyJan_hydrogen" = "tan1",
      "MexzJan_hydrogen" = "cadetblue", "MexwJan_hydrogen" = "tomato2"
    )
  ) +
  theme_bw() +
  theme(
    axis.text = element_text(family = "Arial", size = 15, color = "black"),
    axis.title.x = element_text(family = "Arial", size = 16, margin = margin(t = 15)),
    axis.title.y = element_text(family = "Arial", size = 16, margin = margin(r = 15)), 
    axis.line = element_line(color = "black"),
    plot.background = element_rect(fill = "transparent", color = NA),
    panel.border = element_rect(color = "black"),
    panel.background = element_rect(fill = "transparent"),
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    axis.ticks.length = unit(0.20, units = "cm"),
    legend.background = element_rect(fill = "transparent"),
    legend.key = element_rect(fill = "transparent", colour = NA),
    legend.position = "top",
    legend.key.width = unit(0, unit = "cm"),
    legend.key.height = unit(0, unit = "cm"),
    legend.title = element_blank(),
    legend.text = element_text(size = 13.5),
    legend.spacing.x = unit(0.1, "cm"),
    legend.text.align = unit(0.05, unit = "cm")
  ) +
  labs(x = "Time (min)", y = "Gas Evolution (µmol.g"^-1 ~ ")") +
  coord_cartesian(ylim = c(0, 15), xlim = c(0, 180)) + # Limit the size of the plot
  scale_y_continuous(
    expand = expansion(mult = c(0.02, 0.02)),
    n.breaks = 5
  ) +
  scale_x_continuous(
    expand = expansion(mult = c(0.02, 0.02)),
    breaks = c(0, 60, 120, 180)
  )

Answer 2

You are making life harder for yourself by passing your data frame in the wrong format. If you pivot to long format, you only need a single geom_line and geom_point . It's also far easier to map your colors and shapes, which will automatically appear in the legend.

Also, try to choose a default theme that's closer to the look you want to achieve to cut down on the number of tweaks you have to make via theme . One of the key things you'll learn in R, as in other languages, is that cutting down code to a minimum makes it easier to change or debug your code later on.

library(tidyverse)

hydrogen_data %>%
  pivot_longer(-time_hydrogen) %>%
  ggplot(aes(time_hydrogen, value, color = name, shape = name)) +
  geom_line(lwd = 1) +
  geom_point(size = 5) +
  scale_color_manual(values = c("tomato2",  "palegreen", "tan1", "cadetblue"),
                     labels = paste0("15Me-", c("NT", "nNT", "NNT", "nnt"))) +
  scale_shape_manual(values = c(18, 15, 16, 17),
                     labels = paste0("15Me-", c("NT", "nNT", "NNT", "nnt"))) +
  scale_y_continuous(expression(Gas~Evolution~(µmol.g^-1)),
                     expand = expansion(mult = c(0.02, 0.02)), n.breaks = 5) +
  scale_x_continuous("Time (min)", expand = expansion(mult = c(0.02, 0.02)),
                     breaks = c(0, 60, 120, 180)) +
  theme_classic(base_size = 16) +
  theme(axis.text = element_text(family = "Arial", size = 15, color = "black"),
        plot.background = element_blank(),
        panel.border = element_rect(color = "black", fill = NA),
        panel.background = element_blank(),
        axis.ticks.length = unit(0.20, units = "cm"),
        legend.background = element_blank(), 
        legend.position = "top",
        legend.title = element_blank()) +
  coord_cartesian(ylim = c(0, 15), xlim = c(0, 180))