In cas-bioinf/metagenboot: Diagnostics for Metagenomic Data via Model-Based Bootstrapping

From the paper "Male-specific Association Between Fat-Free Mass Index and Fecal Microbiota in 2- to 3-Year-Old Australian Children"

The data can be downloaded at https://qiita.ucsd.edu/study/description/10778# (login to qiita required)

library(tidyverse)
library(here)
library(vegan)
library(cowplot)
library(doParallel)
library(biomformat)
library(rstan)

options(mc.cores = parallel::detectCores())
rstan_options(auto_write = TRUE)
source(here("R","sample_posterior.R"))
source(here("R","plot_mds.R"))

registerDoParallel(parallel::detectCores())

otus_raw <- import_biom(here("private_data","smith-brown2018","46351_otu_table.biom"))
#otus_raw <- read_biom(here("private_data","wolfe14","47198_otu_table.biom"))
otus_raw$columns %>% purrr::map(~.x$id) %>% unlist()
otu_tab <- biom_data(otus_raw) %>% t() %>% as.matrix()

mapping <- tibble(Sample = rownames(otu_tab)) #%>% mutate(Origin = if_else(grepl("^B", Sample), "Panama", if_else(grepl("^L", Sample), "Costa Rica", "Ecuador")))

plot_mds_brown_smith <- function(base_mds, mapping, aligned_samples = NULL, ...) {
  plot_mds(base_mds, mapping, aligned_samples = aligned_samples)
}

set.seed(20190517)
base_mds <- otu_tab %>% metaMDS(trymax = 400, maxit = 500)
#base_mds$points
plot_mds_brown_smith(base_mds, mapping)

mds_samples_dm <- sample_posterior_dm(20, otu_tab, prior = "ml",N_reads = "original") %>% 
  metaMDS_per_sample(trymax = 400, maxit = 500) %>% purrr::map(vegan::procrustes, X = base_mds)

plot_mds_dunthorn(base_mds, mapping, aligned_samples = mds_samples_dm)

mds_samples_rarefy <- sample_posterior_rarefy(20, otu_tab) %>% 
  metaMDS_per_sample(try = 200, maxit = 500) %>% purrr::map(vegan::procrustes, X = base_mds)
plot_mds_dunthorn(base_mds, mapping, aligned_samples = mds_samples_rarefy)

mds_samples_rarefy_unaligned <- sample_posterior_rarefy(10, otu_tab) %>% 
  metaMDS_per_sample(try = 200, maxit = 500, autotransform = FALSE)
for(i in 1:length(mds_samples_rarefy_unaligned)) {
  plot_mds_dunthorn(mds_samples_rarefy_unaligned[[i]], mapping) %>% print()
}

cas-bioinf/metagenboot documentation built on Feb. 25, 2021, 3:58 p.m.