Formatting PopGenHelpR plots

Purpose

This document contains examples of how to format PopGenHelpR plots after they are generated, but still within R.

How to format plots after they are made?

PopGenHelpR plots are created using ggplot2, which means that we can modify them after the fact. Normally, this means modifying the theme, where we can change font size, axis titles, legends, and much more (see https://ggplot2.tidyverse.org/reference/theme.html for ideas). We will go through a couple of examples to get you started. Please reach out if you have any questions or need help.

Load the data and packages

# Load PopGenHelpR
library(PopGenHelpR)
library(cowplot)
library(ggplot2)

# Load data
data("Q_dat")

# First, we separate the list elements into two separate objects. The q-matrix (Qmat) and the locality information for each individual (Loc).
Qmat <- Q_dat[[1]]
Pops <- Q_dat[[2]]

We will do this using the Ancestry_barchart output as an example, but this can be done with any of the plots that PopGenHelpR produces.

Base <- Ancestry_barchart(anc.mat = Qmat, pops = Pops, K = 5, col = c('#d73027', '#fc8d59', '#e0f3f8', '#91bfdb', '#4575b4'))
#> [1] "All information needed is present, moving onto plotting."
#> [1] "Want to change the the text size, font, or any other formatting? See https://kfarleigh.github.io/PopGenHelpR/articles/PopGenHelpR_plotformatting.html for examples and help."

No_legend <- Base$`Individual Ancestry Plot` + theme(legend.position = "none")

No_legend_lab <- Base$`Individual Ancestry Plot` + theme(legend.position = "none", axis.text.x = element_text(angle = 0, hjust = 0.5))

plot_grid(Base$`Individual Ancestry Plot`, No_legend, No_legend_lab, ncol = 1)

Note: These examples use the Ancesry_barchart function assuming that plot.type = "all". The commands to acess plots generated by PopGenHelpR may change slightly depending on the individual command that you execute. Setting plot.type = "individual", for example, means that you would need to replace Individual Ancestry Plot with Individual Ancestry Matrix. Thus, the command would look like what is below instead of what is above.

Base2 <- Ancestry_barchart(anc.mat = Qmat, pops = Pops, K = 5, col = c('#d73027', '#fc8d59', '#e0f3f8', '#91bfdb', '#4575b4'), plot.type = "individual")

No_legend <- Base$`Individual Ancestry Matrix` + theme(legend.position = "none")