Analysis in R: The “gghighlight” package is useful for highlighting parts of the plot.

#Install Package
install.packages("gghighlight")

#Loading the library
library("gghighlight")

###Creating Data#####
#Install the tidyverse package if it is not already present
if(!require("tidyverse", quietly = TRUE)){
  install.packages("tidyverse");require("tidyverse")
}

set.seed(1234)
n <- 300
PointData <- tibble(ID = rep(1:5, len = n),
                    Group = sample(c("A", "B", "C"),
                                   n, replace = TRUE),
                    Time_A = abs(rnorm(n)),
                    Time_B = log2(abs(rnorm(n))))
########

#To set data highlighting: gghighlight command
#Assigning plot labels: label_key option
ggplot(PointData, aes(x = Time_A, y = Time_B, colour = Group)) +
  geom_point() +
  gghighlight(Time_A > .8 & Time_B < -4.5) +
  scale_colour_manual(values = c("#a0b981", "#47547c", "#9f8288")) +
  theme_bw()

###Example: Creating scatter plots without using the gghighlight package#####
MendoiPointData <- PointData %>%
  #The use of the if_else and case_when commands is key
  #case_when is specified by ”conditional expression ~ result”
  mutate(col = if_else(Time_A > .8 & Time_B < -4.5,
                       case_when(Group == "A" ~ "#a0b981",
                                 Group == "B" ~ "#47547c",
                                 Group == "C" ~ "#9f8288"), "gray")) %>%
  mutate(Label = if_else(Time_A > .8 & Time_B < -4.5, as.character(Group), ""))

#The 'ggrepel' package for labelling
#https://www.karada-good.net/analyticsr/r-377
#Install the ggrepel package if it is not already present
if(!require("ggrepel", quietly = TRUE)){
  install.packages("ggrepel");require("ggrepel")
}

#scale_colour_identity command is the key
MendoiPlot <- ggplot(MendoiPointData, aes(x = Time_A, y = Time_B,
                                             label = Label, col = col))
MendoiPlot +
  geom_point() +
  geom_label_repel() +
  scale_colour_identity(guide = "none") +
  theme_bw()
########