## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
if (!requireNamespace("ggplot2", quietly = TRUE) ||
      !requireNamespace("phylotypr", quietly = TRUE) ||
      !requireNamespace("phyloseq", quietly = TRUE)) {
  message(paste(
    "Suggested packages 'ggplot2', 'phyloseq' or 'phylotypr'",
    "are not installed."
  ))
  knitr::opts_chunk$set(eval = FALSE)
} else {
  library(strollur)
  library(phylotypr)
  library(phyloseq)
  library(ggplot2)
}

## -----------------------------------------------------------------------------
strollur_data <- read_mothur(
  fasta = strollur_example("final.fasta.gz"),
  count = strollur_example("final.count_table.gz"),
  design = strollur_example("mouse.time.design"),
  otu_list = strollur_example("final.opti_mcc.list.gz"),
  asv_list = strollur_example("final.asv.list.gz"),
  phylo_list = strollur_example("final.tx.list.gz"),
  sample_tree = strollur_example("final.opti_mcc.jclass.ave.tre"),
  sequence_tree = strollur_example("final.phylip.tre.gz"),
  dataset_name = "miseq_sop"
)

metadata <- readRDS(strollur_example("miseq_metadata.rds"))
add(strollur_data, table = metadata, type = "metadata")

## ----eval = FALSE-------------------------------------------------------------
# database_reference <- build_kmer_database(trainset9_pds)
# classify_sequences(strollur_data, database_reference)

## -----------------------------------------------------------------------------
phyloseq_data <- write_phyloseq(strollur_data)
phyloseq_data

alpha_div <- phyloseq::estimate_richness(phyloseq_data,
  measures = "Shannon"
)

metadata <- data.frame(sample_data(phyloseq_data))
shannon_plot_data <- cbind(metadata, Shannon = alpha_div$Shannon)

ps_rel <- transform_sample_counts(
  phyloseq_data,
  function(x) x / sum(x)
)
pcoa_ord <- ordinate(ps_rel, method = "PCoA", distance = "bray")

## -----------------------------------------------------------------------------
ggplot2::ggplot(shannon_plot_data, aes(
  x = treatment,
  y = Shannon,
  fill = treatment
)) +
  geom_boxplot(alpha = 0.7, outlier.shape = NA) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.5) +
  scale_fill_brewer(palette = "Set2") +
  labs(
    title = "Alpha Diversity",
    x = "Experimental Group",
    y = "Shannon Diversity Score"
  ) +
  theme_bw() +
  theme(
    legend.position = "none",
    plot.title = element_text(face = "bold", hjust = 0.5),
    axis.text = element_text(size = 11),
    axis.title = element_text(size = 12, face = "bold")
  )

## -----------------------------------------------------------------------------
pcoa_df <- plot_ordination(ps_rel, pcoa_ord, justDF = TRUE)

ggplot2::ggplot(pcoa_df, aes(x = Axis.1, y = Axis.2, color = treatment)) +
  geom_point(size = 4, alpha = 0.8) +
  stat_ellipse(aes(group = treatment), linetype = 2, level = 0.95) +
  scale_color_brewer(palette = "Set1") +
  labs(
    title = "PCoA Ordination",
    x = paste0(
      "Axis 1 [",
      round(pcoa_ord$values$Relative_eig[1] * 100, 1), "%]"
    ),
    y = paste0(
      "Axis 2 [",
      round(pcoa_ord$values$Relative_eig[2] * 100, 1), "%]"
    ),
    color = "Experimental Group"
  ) +
  theme_bw() +
  theme(
    plot.title = element_text(face = "bold", hjust = 0.5, size = 14),
    axis.title = element_text(face = "bold", size = 11),
    legend.title = element_text(face = "bold"),
    panel.grid.minor = element_blank()
  )