microbial (version 0.0.19)

plotalpha: 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.

Examples

# NOT RUN {
{
data("Physeq")
plotalpha(physeq,group="SampleType")
}
# }