| Type: | Package |
| Title: | Color Palettes for Mycobacterium Tuberculosis Data Visualization |
| Version: | 0.1.1 |
| Description: | 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. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| Imports: | ggplot2, ape, ggtree |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| RoxygenNote: | 7.3.1 |
| NeedsCompilation: | no |
| Packaged: | 2025-07-13 15:59:23 UTC; pauru |
| Author: | Paula Ruiz-Rodriguez [aut, cre] |
| Maintainer: | Paula Ruiz-Rodriguez <paula.ruiz.rodriguez@csic.es> |
| Repository: | CRAN |
| Date/Publication: | 2025-07-16 17:10:02 UTC |
ClassicTB Color Palette
Description
An unnamed vector of 14 colors derived from the classicTB theme.
Usage
classicTB
Format
A character vector of 14 hex color codes.
Source
Color palette designed by the PathoGenOmics Lab.
Mycolors Color Palette
Description
A named vector of 14 colors designed for visualizing Mycobacterium tuberculosis lineages.
Usage
mycolors
Format
A character vector of 14 hex color codes, named with lineage identifiers.
Source
Color palette designed by the PathoGenOmics Lab.
PathoGenOmics Color Palette
Description
A palette of 8 colors from the PathoGenOmics Lab theme.
Usage
pathogenomics
Format
A character vector of 8 hex color codes.
Source
Color palette designed by the PathoGenOmics Lab.
Plot a Phylogenetic Cladogram with TB Lineage Colors
Description
Visualizes a phylogenetic tree as a cladogram, coloring tips with the mycolors palette.
Usage
plot_tb_cladogram(newick_text)
Arguments
newick_text |
A character string with the tree in Newick format. |
Value
A ggplot object representing the phylogenetic cladogram.
Examples
tree_text <- "(L8,((L1,(L7,(L4,(L2,L3)))),(L5,((A2,(A3,A4)),(A1,(L10,(L6,L9)))))));"
plot_tb_cladogram(tree_text)
Plot a Phylogenetic Tree with TB Lineage Colors
Description
Reads a tree in Newick format and plots it using ggtree, coloring tips with the mycolors palette.
Usage
plot_tb_tree(newick_text)
Arguments
newick_text |
A character string with the tree in Newick format. |
Value
A ggplot object representing the phylogenetic tree.
Examples
tree_text <- "(L8,((L1,(L7,(L4,(L2,L3)))),(L5,((A2,(A3,A4)),(A1,(L10,(L6,L9)))))));"
plot_tb_tree(tree_text)
Scale Color for ggplot2 Using classicTB Palette
Description
Applies the classicTB palette to the color aesthetic in a ggplot.
Usage
scale_color_classicTB()
Value
A ggplot2 scale object.
Scale Color for ggplot2 Using mycolors Palette
Description
Applies the mycolors palette to the color aesthetic in a ggplot.
Usage
scale_color_mycolors()
Value
A ggplot2 scale object.
Scale Fill for ggplot2 Using classicTB Palette
Description
Applies the classicTB palette to the fill aesthetic in a ggplot.
Usage
scale_fill_classicTB()
Value
A ggplot2 scale object.
Scale Fill for ggplot2 Using mycolors Palette
Description
Applies the mycolors palette to the fill aesthetic in a ggplot.
Usage
scale_fill_mycolors()
Value
A ggplot2 scale object.
Generate n colors from a mycolorsTB palette
Description
Uses color interpolation to create a custom number of colors from a given palette.
Usage
tb_palette(n, palette_name = "classicTB")
Arguments
n |
The number of colors to generate. |
palette_name |
The name of the palette to use ("mycolors", "classicTB", or "pathogenomics"). |
Value
A character vector of n hex color codes.
Examples
# Generate 20 colors from the 'classicTB' palette
my_custom_colors <- tb_palette(20, "classicTB")
plot(1:20, 1:20, col = my_custom_colors, pch = 19, cex = 3)
Display a color palette
Description
Generates a ggplot visualization of a specified package palette.
Usage
view_palette(palette_name = "mycolors")
Arguments
palette_name |
The name of the palette to display ("mycolors", "classicTB", or "pathogenomics"). |
Value
A ggplot object showing the colors of the chosen palette.
Examples
view_palette("mycolors")
view_palette("classicTB")