ordin_annotatedplot: Create an annotated ordination graph

In CMET-UGent/CMETNGS: Convenience functions for CMET NGS automated pipeline

Description

This function is a wrapper around CMETNGS::ordin_annotate and CMETNGS::ordin_legend: it uses a vegan ordination object (e.g. from metaMDS) and a valid metadata table with Factor1 and Factor2 to create an annotated plot.

Usage

ordin_annotatedplot(
  ordinobj,
  metadata,
  location = "bottomleft",
  addLabels = TRUE,
  addLegend = TRUE
)

Arguments

ordinobj	a vegan-created ordination object (i.e. ordinobj$points must exist)
metadata	a valid CMET metadata object, containing minimally the sample names, Factor1 and Factor2.
location	where to put the legend on the plot, defaults to "bottomleft"
addLabels	wether or not to add sample labels to the ordination ( defaults to TRUE)
addLegend	a logical, indicating wether or not to add a legend to the plot. Defaults to TRUE.

Value

A list with the colvector and pchvector

Examples

## Short example

# Load precomputed example data
library(vegan)
data(dune)
dune.dis <- vegdist(wisconsin(dune))
dune.mds <- cmdscale(dune.dis, eig = TRUE)
#create completely made-up metadata for dune
dune.md <- data.frame(Factor1=c(rep("Dune1",nrow(dune)/2),
rep("Dune2",nrow(dune)/2)),Factor2=c(rep("Grass",7),rep("Shrub",7),
rep("Tree",6)))
ordin_annotatedplot(dune.mds,dune.md)

CMET-UGent/CMETNGS documentation built on Dec. 12, 2020, 8:22 a.m.