CODEWITHSUNDEEP
rggplot2bioinformatics
Criss D
Criss D

Reputation: 35

how to graph coordinates below a plot - ggplot2?

I'm trying to make a single gene coverage plot like the one shown here.

image_1.png

I have already plotted the coverage but I still need to insert the exons and introns in the corresponding coordinates. Thank you! My code:

ggplot(z, aes(x=inicio, y=promedio, fill=Technology, group=Technology, color=Technology))+ 
stat_smooth(
    geom = 'area', method = 'loess', span = 1/3,
    alpha = 1/2) + 
scale_x_continuous(limits=c(30689060,30748122))+ 
theme_set(theme_bw())+ 
theme(legend.text = element_text (size = 12))+ 
xlab("Coordinates")+
ylab("Depth")+
ggtitle("TEX15")

image_2.png

Upvotes: 1

Views: 657

Answers (1)

jared_mamrot
jared_mamrot

Reputation: 26690

Without a minimal reproducible example (MRE) containing some input data and expected output it's difficult to know how to help you. For instance, here is an MRE with some 'fake' data:

library(tidyverse)

df <- data.frame(Coverage = runif(1000, 0, 7900))

p1 <- df %>%
  ggplot(aes(x = Coverage)) +
  geom_density(outline.type = "full", fill = "#D6B7C9") +
  theme_minimal(base_size = 14) +
  theme(axis.title.x = element_blank())

features1 <- tribble(~"feature", ~"start", ~"end",
                     "E1", 1, 1950,
                     "E5", 2986, 3237,
                     "L1", 4775, 6292)

features2 <- tribble(~"feature", ~"start", ~"end",
                     "E2", 1892, 2989,
                     "L2", 3373, 4794,
                     "E6", 7125, 7601,
                     "E7", 7604, 7900)

p2 <- features1 %>%
  ggplot() +
  geom_rect(aes(xmin = start, xmax = end, 
                   ymin = 0, ymax = 1,
                   fill = feature),
            color = "black") +
  geom_text(aes(x = (start + end) / 2, y = 0.5, label = feature)) +
  theme_void() +
  theme(legend.position = "none")

p3 <- features2 %>%
  ggplot() +
  geom_rect(aes(xmin = start, xmax = end, 
                ymin = 0, ymax = 1,
                fill = feature),
            color = "black") +
  geom_text(aes(x = (start + end) / 2, y = 0.5, label = feature)) +
  theme_void() +
  theme(legend.position = "none")

library(patchwork)
p1 / p2 / p3 + plot_layout(nrow = 3, heights = c(1, 0.1, 0.1))

Created on 2022-06-16 by the reprex package (v2.0.1)

Would this approach be suitable for your single gene coverage plot? If not, what would you want to change?

Upvotes: 1

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