mycolorsTB

August 1, 2025 ยท View on GitHub

R Color Package for Mycobacterium tuberculosis complex

mycolorsTB is an R package that provides color palettes and helper functions to visualize genomic and epidemiological data from the Mycobacterium tuberculosis complex, integrating with ggplot2 and ggtree.

Installation

You can install the stable version of mycolorsTB from CRAN or the development version from GitHub.

This is the easiest way to install the package for most users.

install.packages("mycolorsTB")

Note on Dependencies: mycolorsTB requires the ggtree package from Bioconductor. If you don't have it installed, you can add it by running:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install("ggtree")

Development Version from GitHub

Install this version if you want the latest features or fixes that have not yet been released to CRAN.

1. Install BiocManager and Dependencies

First, ensure you have BiocManager and the core dependencies ggtree, ggplot2, and ape.

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install("ggtree")
install.packages(c("ggplot2", "ape", "remotes"))

2. Install mycolorsTB

Finally, install the package from GitHub using remotes.

remotes::install_github("PathoGenOmics-Lab/mycolorsTB")

Usage and Examples

Available Color Palettes

You can access the color vectors directly:

library(mycolorsTB)

# Vector with lineage names (A1, L1, etc.)
show(mycolorsTB::mycolors)

# Vector of pure colors, without names
show(mycolorsTB::classicTB)

Example with ggplot2

Use scale_fill_mycolors() or scale_color_mycolors() to easily apply the palettes to your plots.

library(ggplot2)

# Example data
data <- data.frame(
  x = 1:14,
  y = rnorm(14),
  group = names(mycolorsTB::mycolors)
)

# Bar plot using the default palette
ggplot(data, aes(x = x, y = y, fill = group)) +
  geom_bar(stat = "identity") +
  scale_fill_mycolors() +
  theme_minimal()

Color Reference

HEX Codes

  • A1: #d1ae00
  • A2: #8ef5c8
  • A3: #73c2ff
  • A4: #ff9cdb
  • L1: #ff3091
  • L2: #001aff
  • L3: #8a0bd2
  • L4: #ff0000
  • L5: #995200
  • L6: #1eb040
  • L7: #fbff00
  • L8: #ff9d00
  • L9: #37ff30
  • L10: #8fbda1

Example Newick Tree

(L8,((L1,(L7,(L4,(L2,L3)))),(L5,((A2,(A3,A4)),(A1,(L10,(L6,L9)))))));