In T-Heide/MLLLP: Maximum Likelihood Assignment of Low-Pass Samples to Trees

knitr::opts_chunk$set(dpi=300)

MLLPT

Maximum likelihood assignment of low-pass samples (MLLPT)

Installation

# install.packages("devtools")
devtools::install_github('dombennett/treeman') # package requires newest version of treeman (not on CRAN)
devtools::install_github("T-Heide/MLLPT")

Help and support

Getting started

library(MLLPT)
library(phangorn)

1) Input data

data("example_lp_data", package="MLLPT") # example dataset included in the package

# 1/3 a phylogenetic tree
print(example_lp_data$tree)

# 2/3 a phylo object (with id attribute)
print(example_lp_data$phydata)

head(attr(example_lp_data$phydata, "id")) # a non default attribute of mutation ids!

# 3/3 a list of sample data
str(example_lp_data$samples)

2) Add LP samples

set.seed(123)

tree_with_lp_added = 
  with(example_lp_data,  {
    MLLPT::add_lowpass_sampled(
      tree = tree, 
      phydata = phydata, 
      sample_data = samples, 
      return_details = TRUE, 
      n_bootstraps = 1000, 
      n_cores = 8
    )
  })

3) Plots

labeller_function = function(x) gsub("EPICC_C[0-9]+_", "", x)

tree_with_lp_added$tree %>% 
  MLLPT:::remove_root_tip("GL") %>%  
  MLLPT::set_lp_tiplength(0.05) %>% 
  MLLPT::plot_tree(
    labeller_function = labeller_function, 
    pointsize = 2, 
    linewidth = 0.8
  )

MLLPT::plot_lp_loglik(
    tree_with_lp_added,
    labeller_function = labeller_function
  ) + ggplot2::theme(axis.text.x = ggplot2::element_text(angle=90, vjust = 0.5))

MLLPT::plot_lp_loglik_edge(
    tree_with_lp_added,
    labeller_function = labeller_function
  ) + ggplot2::theme(strip.text = ggplot2::element_text(size=9))

MLLPT::plot_lp_position_edge(
    tree_with_lp_added,
    labeller_function = labeller_function
  ) + ggplot2::theme(strip.text = ggplot2::element_text(size=9))

MLLPT::plot_sample_data(
    tree_with_lp_added,
    external_purity_estimate = c(0.90, 0.48),
    label_external_purity = "GT",
    labeller_function = labeller_function
  )

Copyright

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.