## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) library(mycolorsTB) ## ----fig.width=7, fig.height=5, out.width="100%"------------------------------ # View the main palette with lineage names view_palette(palette_name = "mycolors") # View the pathogenomics palette view_palette(palette_name = "pathogenomics") ## ----fig.width=7, fig.height=4, out.width="100%"------------------------------ library(ggplot2) # To ensure the vignette builds correctly, we define the lineage names locally. # The functions from the package will use the actual package data. local_mycolors <- c("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 data using the local color vector data <- data.frame( x = factor(names(local_mycolors), levels = names(local_mycolors)), y = abs(rnorm(14, mean = 10, sd = 3)), group = names(local_mycolors) ) # Create a bar plot using the fill scale ggplot(data, aes(x = x, y = y, fill = group)) + geom_bar(stat = "identity") + scale_fill_mycolors() + theme_minimal() + labs(title = "Bar Plot with scale_fill_mycolors()", x = "Lineage", y = "Value") + theme(axis.text.x = element_text(angle = 45, hjust = 1)) ## ----fig.width=7, fig.height=4, message=FALSE, warning=FALSE, out.width="100%"---- tree_text <- "(L8,((L1,(L7,(L4,(L2,L3)))),(L5,((A2,(A3,A4)),(A1,(L10,(L6,L9)))))));" plot_tb_tree(tree_text) ## ----fig.width=7, fig.height=4, message=FALSE, warning=FALSE, out.width="100%"---- plot_tb_cladogram(tree_text) ## ----fig.width=7, fig.height=5, out.width="100%"------------------------------ # Generate 25 colors from the 'classicTB' palette my_custom_colors <- tb_palette(25, "classicTB") # Create a plot to display the interpolated colors plot(1:25, rep(1, 25), col = my_custom_colors, pch = 19, cex = 5, xlab = "", ylab = "", axes = FALSE, main = "25 Interpolated Colors from 'classicTB' Palette")