phyloseq_ord_plot: Plotting beta diversity ordination

In nick-youngblut/HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

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

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)

## End(Not run)

nick-youngblut/HTSSIP documentation built on May 23, 2019, 4:46 p.m.