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Bubble plot of phyloseq object with observablehq lifecycle-experimental

Source: R/bubbles_pq.R
bubbles_pq.Rd

Creates an interactive bubble plot visualization of taxa abundances from a phyloseq object using an Observable notebook.

Usage

bubbles_pq(
  physeq,
  rank_label = "Taxa",
  rank_color = "Family",
  categorical_scheme = "d3.schemeCategory10",
  label_color = "grey10",
  value_color = "grey20",
  label_size = 8,
  log1ptransform = FALSE,
  min_nb_seq = 0,
  randomize = FALSE,
  seed = 32,
  width = 600,
  include = c("TitleCell", "key", "chart"),
  notebook = "https://observablehq.com/d/d755af3197af2320",
  return_dataframe = FALSE,
  title = "",
  title_size = "22px"
)

Arguments

physeq

(required) A phyloseq-class object obtained using the phyloseq package.

rank_label

(character, default "Taxa") The name of the column in the @tax_table slot to label the points. If set to "Taxa", the taxa name is used.

rank_color

(character, default "Family") The name of the column in the @tax_table slot to color the points.

categorical_scheme

(character, default "d3.schemeCategory10") A color scheme from d3js.

label_color

(character, default "grey10") Color for the label text.

value_color

(character, default "grey20") Color for the value text.

label_size

(integer, default 8) Font size for the label.

log1ptransform

(logical, default FALSE) If TRUE, the number of sequences is log1p transformed.

min_nb_seq

(integer, default 0) Minimum number of sequences to filter out taxa with low abundance.

randomize

(logical, default FALSE) If TRUE, shuffles the order of the taxa.

seed

(integer, default 32) Seed for the randomization.

width

(integer, default 600) The notebook width for visualization in pixels.

include

(character vector, default c("TitleCell", "key", "chart")) You can modify include to remove the title and/or the legend, for example using include = c("chart").

notebook

(character, default "https://observablehq.com/d/d755af3197af2320") You can change the notebook url if you know what you are doing.

return_dataframe

(logical, default FALSE) If TRUE, the plot is not returned, but the resulting dataframe to plot is returned.

title

(character, default "") Title of the plot.

title_size

(character, default "22px") Font size for the title.

Value

A htmlwidget

Author

Adrien Taudière

Examples

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, min_nb_seq = 1000, categorical_scheme = "d3.schemeTableau10", label_color = "purple", value_color = "white")


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)


bubbles_pq(physeq = as_binary_otu_table(data_fungi), min_nb_seq = 20, title = "Nb of samples per OTU. <br> Only OTU present in more than 20 samples are shown", title_size = "12px")