amp_ordinate: Generates a ggplot2 style ordinate plot of amplicon data.
In MadsAlbertsen/ampvis: Tools for visualising amplicon data

Description Usage Arguments Value Author(s)

A nice long description

1	amp_ordinate(data)

`data`	(required) A phyloseq object including sample data.
`scale`	A variable from the associated sample data to scale the abundance by.
`trans`	Transform the raw counts, currently supports "none" or "sqrt" (default: "sqrt").
`ordinate.type`	Either "PCA" or "NMDS" (default: "PCA").
`ncomp`	The number of principal components to extract if using PCA (default: 5)
`plot.x`	Variable to plot on the x-axis if using PCA (default: "PC1")
`plot.y`	Variable to plot on the y-axis if using PCA (default: "PC2")
`plot.color`	Color the points by a sample variable, e.g "treatment".
`plot.color.order`	Order the groups used for coloring by a vector.
`plot.point.size`	Size of the plotted sample points (default: 3)
`plot.shape`	Shape points by a sample variable, e.g "treatment".
`plot.species`	Plot loadings as points (default: F)
`plot.nspecies`	Plot the n most extreme species with their taxonomic classification (default: 0).
`plot.nspecies.tax`	Taxonomic level used in plot.nspecies (default: "Genus").
`plot.label`	Label points using a sample variable.
`plot.group`	Uses plot.color and groups samples by either "chull" or "centroid".
`plot.group.label`	Add label based on the centroid of the specified group.
`envfit.factor`	A vector of factor variables from the sample data used for envfit to the model.
`envfit.numeric`	A vector of numerical variables from the sample data used for envfit to the model.
`envfit.significant`	The significance treshold for displaying envfit parameters (default: 0.01).
`envfit.resize`	Scale the size of the numeric arrows (default: 1).
`envfit.color`	Color of the envfit text on the plot (default: "darkred").
`envfit.textsize`	Size of the envfit text on the plot (default: 3).
`envfit.show`	Show the results on the plot (default: T).
`tax.empty`	Option to add "best" classification or just the "OTU" name to each "OTU" (default: best).
`output`	Either "plot" or "complete" (default: "plot").
`constrain`	Constrain the PCA by a sample variable.
`scale.species`	Rescale the plotted loadings to maximise visability (default: F).
`trajectory`	Connects points based on a sample variable e.g. "date".
`trajectory.group`	Split the trajectory by a sample variable, e.g "treatment".
`plot.group.label.size`	Text size of the labels.
`plot.theme`	Choose different standard layouts choose from "normal" or "clean" (default: "normal").
`plot.group.manual`	Manual definition of the plot.group, overrides plot.color.
`plot.label.size`	Text size of the labels (default: 3).
`plot.label.repel`	Repels labels to avoid cluttering (default: F).
`plot.label.seqment.color`	Color segments in when using repel (default = "black).
`plot.nspecies.repel`	Repels labels to avoid cluttering (default: F).
`plot.species.size`	Size of the points (default: 2)
`plot.nspecies.size`	Text size of the labels (default: 4).