HTSSIP (version 1.4.1)

phyloseq_ord_plot: Plotting beta diversity ordination

Description

For each data.frame object in a list (coverted from ordination objects), creates a ggplot figure.

Usage

phyloseq_ord_plot(physeq_ord_df, title = NULL,
  point_size = "Buoyant_density", point_fill = "Substrate",
  point_alpha = 0.5, point_shape = NULL)

Arguments

physeq_ord_df

A list of data.frame objects (see phyloseq_list_ord_dfs)

title

Plot title

point_size

The data.frame column determining point size

point_fill

The data.frame column determining point fill color

point_alpha

The data.frame column (or just a single value) determining point alpha

point_shape

The data.frame column (or just a single value) determining point shape

Value

ggplot2 object

Examples

# NOT RUN {
data(physeq_S2D2_l)
# }
# NOT RUN {
# make a list of beta diversity distance matrix objects
physeq_S2D2_l_d = physeq_list_betaDiv(physeq_S2D2_l)
# make a list of ordinations
physeq_S2D2_l_d_ord = physeq_list_ord(physeq_S2D2_l, physeq_S2D2_l_d)
# convert ordination information to data.frame objects
physeq_S2D2_l_d_ord_df = phyloseq_list_ord_dfs(physeq_S2D2_l, physeq_S2D2_l_d_ord)
# make ordination plots with ggplot2
phyloseq_ord_plot(physeq_S2D2_l_d_ord_df)
# }
# NOT RUN {
# }