In mailund/adrift: Models of Drift on Admixture Graphs

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

adrift -- Modelling drift on admixture graphs

The goal of adrift is to have an improved admixturegraph package with better visualisation of graphs and graph statistics.

Installation

You can install the released version of adrift from CRAN with:

install.packages("adrift")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("mailund/adrift")

Example

library(magrittr)
library(adrift)

graph <- parse_dot(readr::read_file("data-raw/Basic_OngeEA_wArch.dot"))
graph %>% 
    make_graph_plot() %>%
    show_leaf_labels(nudge_y = -0.5) %>%
    show_inner_node_labels()

library(magrittr)
library(adrift)

graph <- parse_qpgraph(readr::read_file("data-raw/Basic_OngeEA_wArch.graph"))
graph %>% 
    make_graph_plot(edge_colour = "darkblue") %>%
    show_leaf_labels(nudge_y = -0.5, angle = 15) %>%
    show_inner_node_labels()

graph <- parse_dot(readr::read_file("data-raw/BosGraph.dot"))
graph %>% 
    make_graph_plot(edge_colour = "red") %>%
    show_leaf_labels(angle = -90, size = 2.8, nudge_y = -1, hjust = 0)

graph <- parse_qpgraph(readr::read_file("data-raw/Basic_OngeEA_wArch.graph"))
plt <- graph %>%
    make_graph_plot(
        ggplot2::aes(filter = !admixed),
        edge_colour = "darkblue"
    ) %>%
    show_leaf_labels(nudge_y = -0.5, angle = 15)

admixture_vars <- c(
    "P_P2" = "alpha",
    "K_K2" = "beta",
    "AfrAnc_AdmixedNonAfr" = "gamma",
    "SuperArch_DenisovaAncAnc" = "delta"
)
plt %>% add_admixture_labels(
    admixture_vars,
    linetype = "dotted",
    colour = "darkred"
)

plt %>% add_admixture_labels(
    attr(graph, "admixture_proportions"),
    label_size = 3,
    linetype = "dashed",
    colour = "darkgray"
)