plot_full_scan: Plot extended genome scan

In rscherrer/speciomer: Import Speciome Data into R

Plot extended genome scan

Description

Plots an assemblage of various genome scans at a given time point, locus- specific elements of the genetic architecture and the gene network for one of the three traits. Genome scans are shown for allele frequencies, Fst, Qst, Cst and average mutational effects.

Usage

plot_full_scan(data, grn, time, trait, trait_data = NULL)

Arguments

data	A data frame containing locus-specific data (see ?read_loci)
grn	A list of two data frames containing the genetic architecture (the output of read_architecture)
time	Which time point to plot the variables for in the genome scans.
trait	Which trait to show the network for (1, 2 or 3)
trait_data	Data frame with individual-wise trait data (see ?read_indviduals). If provided, a histogram of ecological trait values at the specified time point will be added to the patchwork.

Value

A patchwork

Note

grn is internally converted to a tbl_graph before being passed to plot_network.

See Also

read_architecture, read_loci, plot_genome_scan, plot_barcode, plot_effect_sizes, plot_degrees, plot_network, read_individuals, plot_eco_trait_histogram

Examples

## Not run: 

root <- system.file("extdata", "sim-example", package = "speciomer")
data <- read_loci(root, c("freq", "Fst", "Qst", "Cst", "alpha"))
grn <- read_architecture(root)
plot_full_scan(data, grn, time = -1000, trait = 1)


## End(Not run)

rscherrer/speciomer documentation built on March 11, 2023, 5:37 p.m.