HTSSIP (version 1.4.1)

SIP_betaDiv_ord: Calculating & plotting beta diversity for a list of phyloseq objects

Description

For each phyloseq object in a list, calculates beta-diversity between all samples using the phyloseq::distance function.

Usage

SIP_betaDiv_ord(physeq_l, method = "unifrac", weighted = TRUE,
  fast = TRUE, normalized = TRUE, parallel = FALSE, plot = FALSE)

Arguments

physeq_l

A list of phyloseq objects

method

See phyloseq::distance

weighted

Weighted Unifrac (if calculating Unifrac)

fast

Fast calculation method

normalized

Normalized abundances

parallel

Calculate in parallel

plot

Return a plot (instead of a data.frame of ordination data)

Value

If plot==FALSE, a data.frame object of beta-diversity values. If plot==TRUE, a glob object for plotting.

Examples

# NOT RUN {
data(physeq_S2D2_l)
# }
# NOT RUN {
physeq_S2D2_l_df = SIP_betaDiv_ord(physeq_S2D2_l)
head(physeq_S2D2_l_df, n=3)
# }
# NOT RUN {
# }