plotalpha: plot alpha diversity

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

plot alpha diversity

Description

plot alpha diversity

Usage

plotalpha(
  physeq,
  group,
  method = c("Observed", "Simpson", "Shannon"),
  color = NULL,
  geom = "boxplot",
  pvalue = 0.05,
  padj = NULL,
  sig.only = TRUE,
  wilcox = FALSE,
  show.number = FALSE
)

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.
group	group (Required). A character string specifying the name of a categorical variable containing grouping information.
method	A list of character strings specifying method to be used to calculate for alpha diversity in the data. Available methods are: "Observed","Chao1","ACE","Richness", "Fisher", "Simpson", "Shannon", "Evenness","InvSimpson".
color	A vector of character use specifying the color
geom	different geom to display("boxplot","violin","dotplot")
pvalue	pvalue threshold for significant dispersion results
padj	adjust p value threshold for significant dispersion results
sig.only	display the significant comparsion only(TRUE/ FALSE)
wilcox	use wilcoxon test or not
show.number	to show the pvalue instead of significant symbol(TRUE/FALSE)

Value

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

Author(s)

Kai Guo

Examples

{
data("Physeq")
plotalpha(physeq,group="SampleType")
}

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