plotbar: plot bar for relative abundance for bacteria

In guokai8/microbial: Do 16s Data Analysis and Generate Figures

plot bar for relative abundance for bacteria

Description

plot bar for relative abundance for bacteria

Usage

plotbar(
  physeq,
  level = "Phylum",
  color = NULL,
  group = NULL,
  top = 5,
  return = FALSE,
  fontsize.x = 5,
  fontsize.y = 12
)

Arguments

physeq	A phyloseq object containing merged information of abundance, taxonomic assignment, sample data including the measured variables and categorical information of the samples, and / or phylogenetic tree if available.
level	the level to plot
color	A vector of character use specifying the color
group	group (Optional). A character string specifying the name of a categorical variable containing grouping information.
top	the number of most abundance bacteria to display
return	return the data with the relative abundance
fontsize.x	the size of x axis label
fontsize.y	the size of y axis label

Value

Returns a ggplot object. This can further be manipulated as preferred by user.

Author(s)

Kai Guo

Examples

data("Physeq")
phy<-normalize(physeq)
plotbar(phy,level="Phylum")

guokai8/microbial documentation built on Oct. 15, 2024, 11:32 p.m.