Diary of an Autodidact: R: Line graph with a color gradient using ggplot2

Yedomon Ange Bovys Zoclanclounon

Brainstorming

The purpose here is to plot a line graph that shows the nucleotide diversity (Pi) alongside a chloroplast genome. More specifically, we want to emphasis using a gradient color a certain value up to a threshold (here 0.015).

Let’s get into it!

Solution

Package loading

library(ggplot2)

Data importaion

data_pi = read.table("C:/Users/ange_/Downloads/My website/data.csv", sep = ";" , h = T)

Our data looks like this…

library(rmarkdown)
paged_table(data_pi)

Let’s write the code

ggplot(data_pi, aes(x=Position, y=Pi, colour = Pi)) +
  
  geom_line() +
  
  scale_colour_gradient2(low = "#0000b3", mid = "#3333ff" , high = "#ff0000", midpoint=0.015) +
  
  geom_hline(yintercept=0.015, color="#00b300", size=.4, linetype = "dotted") +
  
  labs(y = expression(Nucleotide~diversity~(pi)), x = "Nucleotide position") +
  
  theme_minimal()+
  theme(panel.grid.major = element_line(colour = "grey", size = 0.2, linetype = "dotted")) +
  theme(panel.grid.minor = element_line(colour = "grey", size = 0.2, linetype = "dotted")) +
  theme(plot.background = element_rect(colour = "white", size = 1))+
  theme(axis.text = element_text(colour = "black")) +
  
  scale_x_continuous(limits=c(0,155000),
  breaks = seq(0, 155000, by = 25000)) +
  scale_y_continuous(limits=c(0,0.035),
                     breaks = seq(0, 0.035, by = 0.005))

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Citation

For attribution, please cite this work as

Zoclanclounon (2021, Jan. 10). Diary of an Autodidact: R: Line graph with a color gradient using ggplot2. Retrieved from https://yedomon.netlify.app/posts/2021-01-10-r-line-graph-with-a-color-gradient-using-ggplot2/

BibTeX citation

@misc{zoclanclounon2021r:,
  author = {Zoclanclounon, Yedomon Ange Bovys},
  title = {Diary of an Autodidact: R: Line graph with a color gradient using ggplot2},
  url = {https://yedomon.netlify.app/posts/2021-01-10-r-line-graph-with-a-color-gradient-using-ggplot2/},
  year = {2021}
}