Inserting plot objects into the axis

[Diegocastano]

Dear,

I'm using ggplot2 to make a plot like this:

According to the graph, I would like to know to how can I realize the object which is like a bar, which is close to the X-axis?

If anyone has the knowledge or I should use an additional package, please let me know. I would be very grateful

[arthur.t]

Easiest way is just to make a geom_line which has a large value of size.

library(tidyverse)
iris %>% 
    arrange(Species) %>% 
    mutate(id = 1:n()) %>% 
    ggplot() + 
    geom_point(aes(id, Sepal.Width)) + 
    geom_line(aes(id, 0, color = Species), size = 10)

^{Created on 2021-06-22 by the reprex package (v1.0.0)}

[Diegocastano]

Thanks! Is possible this bar could be out of the main graph? A bit more below

[arthur.t]

library(tidyverse)
iris %>% 
  arrange(Species) %>% 
  mutate(id = 1:n()) %>% 
  ggplot() + 
  geom_point(aes(id, Sepal.Width)) + 
  geom_line(aes(id, -0.25, color = Species), size = 10)

^{Created on 2021-06-22 by the reprex package (v1.0.0)}

[Diegocastano]

Sorry, your script didn't work to me. I'm looking for another solution

[arthur.t]

What issue are you having?

It's easier to help with a reproducible example.

FAQ: What's a reproducible example (`reprex`) and how do I create one?

Why reprex? Getting unstuck is hard. Your first step here is usually to create a reprex, or reproducible example. The goal of a reprex is to package your code, and information about your problem so that others can run it and feel your pain. Then, hopefully, folks can more easily provide a solution. What's in a Reproducible Example? Parts of a reproducible example: background information - Describe what you are trying to do. What have you already done? complete set up - include any library() calls and data to reproduce your issue. data for a reprex: Here's a discussion on setting up data for a reprex make it run - include the minimal code required to reproduce your error on the data…

[Diegocastano]

I'm analyzing SARS variants, which I manipulated the data with tidyverse and acquired the following dataset

> glimpse(data)
Rows: 2,861
Columns: 5
$ Position <int> 67, 67, 70, 70, 72, 72, 1782, 2557, 2601, 3165, 3852, 3852, 3852, 4952, 5681, 7919, 7919, 7919, 7919, 7930…
$ ORF      <chr> "5UTR", "5UTR", "5UTR", "5UTR", "5UTR", "5UTR", "ORF1a", "ORF1a", "ORF1a", "ORF1a", "ORF1a", "ORF1a", "ORF…
$ Mutation <chr> "intergenic", "intergenic", "intergenic", "intergenic", "intergenic", "intergenic", "synonymous", "missens…
$ Seq_ID   <chr> "H3-USA", "H4-USA", "H3-USA", "H4-USA", "H3-USA", "H4-USA", "H6-TWN", "H11-CHA", "H12-CHA", "H10-TWN", "H6…
$ Host     <chr> "Human", "Human", "Human", "Human", "Human", "Human", "Human", "Human", "Human", "Human", "Human", "Human"...

From this data I made the follow figure using the ggplot2 and the script employed is the one shown below:

data$Seq_ID <- factor(data$Seq_ID, levels = rev(unique(data$Seq_ID)))
ggplot(data) + geom_point(aes(Position, Seq_ID, color = Mutation), size = 1) + theme_minimal() + theme(legend.position = "bottom") + scale_color_brewer(palette = "Dark2")

Rplot01.pdf (122.3 KB)

Visually it looks like what I want. However, several aspects are still to be annotated according to the figure I show below

These are the tasks I need help:

1. To each type of host assign a different color as background (bat, intermediate, human) that is seen in the Y-axis.
2. Build the bar chart near the X-axis, where it shows the different ORFs.

I appreciate very much any help you can contribute.

[arthur.t]

Perhaps something like this?

library(tidyverse)
lev <- c("_grp", as.character(1:9))
expand_grid(x = 1:100, y = as.character(1:9) %>% factor(lev)) %>%
  mutate(z = ntile(runif(nrow(.)), 3) %>% as.factor(),
         id = 1:n(),
         grp = ntile(id, 5) %>% as.factor()) %>%
  ggplot() +
  geom_point(aes(x, y, fill = z), pch = 21, color = "grey") + 
  geom_line(aes(x, factor("_grp", lev), color = grp), size = 10)

^{Created on 2021-06-24 by the reprex package (v1.0.0)}

[martin.R]

You are probably better off using patchwork or a similar package to stitch different plots together rather than forcing different objects together.

[Diegocastano]

Hi Arthur.
It's very interesting your contribution, although I noticed that the figure generated with the script you shared differs drastically the visualization of the data that I have.

Check that in the Y axis must be the Seq_ID and in the X axis the position that will be represented according to the size of each gene (ORF).

[Diegocastano]

Hi Martin. It's great idea, could you please share an example to understand how to do it?

[arthur.t]

Here's an example with patchwork. It's a nice package - I need to start using it more!

The examples I share will not look exactly like your plot because I don't have access to your data, and so I just made up some data in an similar format with simple column names x, y, z. It will be your responsibility to adapt this to your own problem

library(tidyverse)
library(patchwork)
#> Warning: package 'patchwork' was built under R version 4.0.5
df <- expand_grid(x = 1:100, y = as.character(1:9)) %>%
  mutate(z = ntile(runif(nrow(.)), 5) %>% as.factor(),
         id = 1:n(),
         grp = ntile(id, 5) %>% as.factor()) 

p1 <- df %>%
  na.omit() %>%
  ggplot() +
  geom_point(aes(x, y, color = z))

p2 <- df %>%
  ggplot() + 
  geom_line(aes(x, 0, color = grp), size = 10) + 
  theme(axis.text.y = element_blank(),
        legend.position = "bottom")

p1 + p2 + plot_layout(heights = c(5, 1))

^{Created on 2021-06-24 by the reprex package (v1.0.0)}