Color Palettes for Mycobacterium Tuberculosis Data Visualization

Colour palettes and helper functions for visualising Mycobacterium tuberculosis genomic and epidemiological data with 'ggplot2' and 'ggtree'. The package provides predefined palettes, scale functions, tree/cladogram helpers, and convenient preview tools to ensure consistent branding in pathogen-omics visualisations. The palettes were developed as part of the 'mycolorsTB' project < https://github.com/PathoGenOmics-Lab/mycolorsTB>.

mycolorsTB

R Color package for Mycobacterium tuberculosis complex

Installation

You can install the released version of mycolorsTB from GitHub with:

install.packages("devtools")
devtools::install_github("PathoGenOmics-Lab/mycolorsTB")

Vector of colors

show(mycolorsTB::mycolors) #vector with lineage names
show(mycolorsTB::classicTB) #vector witout lineage names

Example - ggplot()

library(ggplot2)
library(mycolorsTB)

# Example data
data <- data.frame(
  x = 1:14,
  y = rnorm(14),
  group = rep(c(paste0("A", 1:4), paste0("L", 1:10)), each = 1)
)

# Fill: Plot with mycolors lineages names
ggplot(data, aes(x = x, y = y, fill = group)) +
  geom_bar(stat = "identity") + 
  scale_fill_mycolors() + # scale_fill_manual(values = mycolors)
  theme_minimal()

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

Newick tree

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