bars_fun: Barplots plotly

In erifa1/ExploreMetabar: ExploreMetabar

Barplots plotly

Description

Barplots plotly

Usage

bars_fun(
  data = data,
  rank = "Genus",
  top = 10,
  Ord1 = NULL,
  sample_labels = FALSE,
  split = FALSE,
  split_sid_order = FALSE,
  relative = TRUE,
  autoorder = TRUE,
  ylab = "Abundance",
  outfile = "plot_compo.html",
  verbose = TRUE
)

Arguments

data	a phyloseq object (output from decontam or generate_phyloseq)
rank	Taxonomy rank to merge features that have same taxonomy at a certain taxonomic rank (among rank_names(data), or 'ASV' for no glom)
top	Number of top taxa to plot
Ord1	Variable used to order sample (X axis) or split the barplot if split = TRUE
sample_labels	If true, x axis labels are sample IDS, if false labels displayed are levels from Ord1 argument. Ignored if split = TRUE (FALSE)
split	if TRUE make a facet_wrap like grouped by Ord1 (default FALSE)
relative	Plot relative (TRUE, default) or raw abundance plot (FALSE)
autoorder	Automatic ordering xaxis labels based on Ord1 factor levels with gtools::mixedorder function (TRUE).
ylab	Y axis title ("Abundance")
outfile	Output html file.

Value

Returns barplots in an interactive plotly community plot

erifa1/ExploreMetabar documentation built on Jan. 12, 2023, 1:51 a.m.