tidyplots for R plotting – Jie Hua’s Bioinformatics Notes

Basic Information

I noticed a new R package called “tidyplots” produced by Jan Broder Engler. This package could generate publication ready plots with simple commands, which largely simplified the R plotting process.

The manual: https://jbengler.github.io/tidyplots/

I had a try and it works very well. I hope there will be more useful functions.

It is based on ggplot2 system, it is also very easy to add more features as we want.

Installation

pak::pkg_install("tidyplots")

The development version could be installed with

pak::pkg_install("jbengler/tidyplots")

Plotting

library(tidyplots)

Barplot

First 6 rows of the demo dataframe ‘study’
treatment	group	dose	participant	age	sex	score
A	placebo	high	p01	23	female	2
A	placebo	high	p02	45	male	4
A	placebo	high	p03	32	female	5
A	placebo	high	p04	37	male	4
A	placebo	high	p05	24	female	6
B	placebo	low	p06	23	female	9

study |> 
  tidyplot(x = treatment, y = score, color = treatment) |> 
  add_data_points() |> 
  add_mean_bar(alpha = 0.4) |> 
  add_sem_errorbar() |> 
  adjust_colors(new_colors = colors_discrete_seaside)

Barstack plot

energy |> 
  tidyplot(x = year, y = energy, color = energy_source) |> 
  add_barstack_absolute()

It provided many useful types of plotting function, it is better to go to its official website to learn how to use this package.

Other example

energy |> 
  dplyr::filter(year %in% c(2005, 2010, 2015, 2020)) |> 
  tidyplot(y = energy, color = energy_source) |> 
  add_donut() |> 
  adjust_size(width = 25, height = 25) |>
  split_plot(by = year)

✔ split_plot: split into 4 plots across 1 page

library(tidyverse)

Warning: package 'tibble' was built under R version 4.4.2

Warning: package 'tidyr' was built under R version 4.4.2

Warning: package 'readr' was built under R version 4.4.2

Warning: package 'dplyr' was built under R version 4.4.2

Warning: package 'stringr' was built under R version 4.4.2

Warning: package 'forcats' was built under R version 4.4.2

── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.4     ✔ readr     2.1.5
✔ forcats   1.0.0     ✔ stringr   1.5.1
✔ ggplot2   3.5.2     ✔ tibble    3.2.1
✔ lubridate 1.9.4     ✔ tidyr     1.3.1
✔ purrr     1.0.4     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

#library(tidyplots)

df <- 
  read_csv("https://tidyplots.org/data/correlation-matrix.csv")

Rows: 202500 Columns: 5
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (2): x, y
dbl (3): correlation, order_x, order_y

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

df |> 
  tidyplot(x = x, y = y, color = correlation) |> 
  add_heatmap() |> 
  sort_x_axis_labels(order_x) |> 
  sort_y_axis_labels(order_y) |> 
  remove_x_axis() |> 
  remove_y_axis() |> 
  remove_legend_title() |> 
  adjust_legend_position("right") |> 
  adjust_colors(colors_continuous_inferno) |> 
  adjust_theme_details(legend.key.height = unit(1, "null")) |> 
  add_caption("Data source: Spellman PT, et al. 1998. Mol Biol Cell 9(12): 3273-97.")

If tidyplots could directly read .mcool or .hic files, it will be very helpful.

I guess it is what he plans to do, we can use other R packages to read the contact matrix files into a dataframe to have a try, but it will take more efforts.