Plotting VEGAN multivariate ordinations with ggplot

D. Levy-Booth 04/12/2016

Suite of functions to plot four major multivariate analysis techniques.

Reference these functions in R with:

source(plot_pcoa.R)

More information on using the "capscape" and "adonis" functions for multivariate analysis by Jari Oksanen:

CAPSCALE: http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/capscale.html

ADONIS: http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/adonis.html

1. PCoA - Multidimentional Scaling of a vegan "capscale" object.

Unconstrained multivariate ordination of dissimilarity matricies

Capscale notation:

pcoa <- capscale(otu_table ~ 1, dist="bray")

pcoa.plot <- plot_pcoa(pcoa, metadata$color, metadata$shape, "Plot Title")

2. db-RDA - distance-based Redundancy Analysis (vegan).

Constrained multivariate ordination with arrows indicating regressor loadings

rda <- capscale(otu_table ~ ., continuous_metadata, dist="bray")

rda.plot <- plot_rda(rda, metadata$color, metadata$shape, "Plot Title")

3. CAP - Constrained Analysis of Principal Coordinates (vegan).

Constrained ordination of catagorical variables

cap <- capscale(otu_table ~ ., catagorical_metadata, dist="bray")

cap.plot <- plot_cap(cap, metadata$color, metadata$shape, "Plot Title")

4. PERMANOVA - plot barplot of adonis function PERMANOVA(vegan).

Permutational, non-parametric multivariate analysis of variance Statistically test influence of catagoical and continuous variables on dissimilarity matricies

adonis <- adonis(otu_table ~ ., metadata, dist="bray")

adonis.plot <- adonis_plot(adonis, "Plot Title")

Note that color and shape vectors can be "NULL"

Plot Examples:

PCOA Example

Distance-based RDA Example

PERMANOVA (adonis) Barplot Example