essai

Adrien Taudière

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library(MiscMetabar)

Loading required package: phyloseq

Loading required package: ggplot2

Loading required package: dada2

Loading required package: Rcpp

Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: purrr

data("Glom_otu")

Warning in data("Glom_otu"): data set 'Glom_otu' not found

bubbles_pq <- function(physeq,
                       rank_label = "Taxa",
                       rank_color = "Family",
                       categorical_scheme = "d3.schemeCategory10",
                       label_color = "grey20",
                       label_size = 8,
                       log1ptransform = FALSE,
                       min_nb_seq = 0,
                       randomize = FALSE,
                       seed = 32,
                       width = 600,
                       include = c("key", "chart"),
                       notebook = "https://observablehq.com/d/d755af3197af2320",
                       return_dataframe = FALSE) {
  if (rank_label == "Taxa") {
    label <- taxa_names(physeq)
  } else {
    label <- as.vector(physeq@tax_table[, rank_label])
  }

  df <- data.frame(
    "value" = taxa_sums(physeq),
    "label" = label,
    "color" = fac2col(physeq@tax_table[, rank_color]),
    "rank_value_color" = as.vector(physeq@tax_table[, rank_color]),
    "textColor" = label_color
  )

  df$id <- paste0(df$label, ".", df$rank_value_color, ".", df$label)

  if (min_nb_seq > 0) {
    df <- df |>
      dplyr::filter(value > min_nb_seq)
  }

  if (log1ptransform) {
    df$value <- log1p(df$value)
  }

  if (randomize) {
    set.seed(seed)
    df <- df[sample(nrow(df)), ]
  }

  if (return_dataframe) {
    return(df)
  }
  robservable::robservable(
    notebook = notebook,
    include = include,
    input = list(data = df, categorical_scheme = categorical_scheme),
    width = width
  )
}

bubbles_pq(physeq = data_fungi, rank_color = "Class", randomize = TRUE)

bubbles_pq(physeq = data_fungi, min_nb_seq = 10000, categorical_scheme = "d3.schemePastel1")

bubbles_pq(physeq = data_fungi, rank_color = "Order", include = c("chart"), log1ptransform = TRUE)

bubbles_pq(physeq = data_fungi, rank_label = "Genus", rank_color = "Class", include = c("chart"), randomize = TRUE, seed = 3)