create_bar: Create a per-sample barplot of the top _n_ OTUs/ASVs

In wsteenhu/microbiomer: Package Containing Utility-functions to Work with Microbiota-data

Description

Takes either a phyloq-object or an (edited) result of prep_bar as an input. And creates a per-sample barplot.

Usage

create_bar(
  ps = NULL,
  df_topn = NULL,
  id = "sample_id",
  n = 15,
  ncol_legend = 3,
  name_legend = "OTU",
  RA = TRUE
)

Arguments

ps	phyloseq-object (optional)
df_topn	topn-data.frame (result of prep_bar)
id	name of the 'id'-column (default: 'sample_id')
n	number of OTUs/ASVs to plot
ncol_legend	number of columns in the legend
name_legend	name of the legend
RA	specify whether or not the phyloseq is based on relative abundances (logical). Default: TRUE

Value

returns a per-sample barplot showing the n most abundant OTUs.

Examples

data(ps_NP)
ps_NP %>%
  phyloseq::subset_samples(visit_name == "w1" & birth_mode == "vag") %>%
  create_bar() +
  ggplot2::coord_flip()

wsteenhu/microbiomer documentation built on March 11, 2021, 6:05 p.m.