In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

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

library(MiscMetabar)
data(data_fungi)

Permanova

data_fungi_woNA4height <- subset_samples(data_fungi, !is.na(data_fungi@sam_data$Height))
res_ado <- adonis_pq(data_fungi_woNA4height, "Tree_name+Height")
knitr::kable(res_ado)

Graph Test

data_fungi_woNA4height <- subset_samples(data_fungi, !is.na(data_fungi@sam_data$Height))
graph_test_pq(data_fungi_woNA4height, "Height")

Circle of ASVs

circle_pq(data_fungi_woNA4height, "Height")

Compare two (group of) samples

Biplot

data_fungi_low_high <- subset_samples(
  data_fungi,
  data_fungi@sam_data$Height %in%
    c("Low", "High")
)
data_fungi_low_high <- subset_taxa_pq(
  data_fungi_low_high,
  taxa_sums(data_fungi_low_high) > 5000
)
biplot_pq(data_fungi_low_high, fact = "Height", merge_sample_by = "Height")

Compare two (group of) samples with a table

compare_pairs_pq(data_fungi_low_high,
  bifactor = "Height",
  merge_sample_by = "Height",
  modality = "Time"
)

Venn diagram

library("grid")
venn_pq(data_fungi, fact = "Height")

ggvenn_pq(data_fungi, fact = "Height") +
  ggplot2::scale_fill_distiller(palette = "BuPu", direction = 1) +
  labs(title = "Share number of ASV among Height in tree")

ggvenn_pq(data_fungi, fact = "Height", min_nb_seq = 5000) +
  ggplot2::scale_fill_distiller(palette = "BuPu", direction = 1) +
  labs(title = "Share number of ASV with more than 5000 seqs")

ggvenn_pq(data_fungi,
  fact = "Height", taxonomic_rank = "Genus",
  min_nb_seq = 100
) +
  ggplot2::scale_fill_distiller(palette = "BuPu", direction = 1) +
  labs(title = "Share number of Genus represented by at least one ASV with more than 100 seqs")

Upset plot

Venn diagram can quickly become complex to read when the number of modalities increase. One graphical solution is upset plot. MiscMetabar propose a solution based on the package ComplexUpset.

upset_pq(data_fungi, fact = "Height")

upset_pq(data_fungi, fact = "Time")

ComplexUpset package allow powerful configuration of you plot as you can see in the following figure.

upset_pq(
  data_fungi,
  fact = "Time",
  width_ratio = 0.2,
  annotations = list(
    "Sequences per ASV \n (log10)" = (
      ggplot(mapping = aes(y = log10(Abundance)))
      +
        geom_jitter(aes(
          color =
            Abundance
        ), na.rm = TRUE)
        +
        geom_violin(alpha = 0.5, na.rm = TRUE) +
        theme(legend.key.size = unit(0.2, "cm")) +
        theme(axis.text = element_text(size = 12))
    ),
    "ASV per phylum" = (
      ggplot(mapping = aes(fill = Phylum))
      +
        geom_bar() +
        ylab("ASV per phylum") +
        theme(legend.key.size = unit(0.2, "cm")) +
        theme(axis.text = element_text(size = 12))
    )
  )
)

Change in abundance across a factor

Benchdamic

There is a lot of available methods. Please refer to R package benchdamic for a list of method and a implementation of a benchmark for your data.

Library requirement for Debian Linux OS

sudo apt-get install libgsl-dev libmpfr-dev

Using Deseq2 package

data("GlobalPatterns", package = "phyloseq")
GP <- subset_samples(
  GlobalPatterns,
  GlobalPatterns@sam_data$SampleType %in% c("Soil", "Skin")
)

plot_deseq2_pq(GP, c("SampleType", "Soil", "Skin"), pval = 0.001)

Session information

sessionInfo()

adrientaudiere/MiscMetabar documentation built on July 6, 2024, 7:02 p.m.