ordi: Wrapper for ade4 and vegan ordi functions

Description Usage Arguments

View source: R/ordinate.R

Description

Perform an ordination using an ade4 or vegan function, and return an mvarVis object with the annotation completed.

Usage

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ordi(X, method = "ade4_pca", rows_annot = NULL, cols_annot = NULL,
  dist_method = "euclidean", table_names = NULL, ...)

Arguments

X

Either a data frame, a distance object, a list of both a data frame and a distance, a formula and a data frame, or a list of data frames, depending on the desired method. pcm, acm, coa, fca, fpca, hillsmith, mix, and nsc require the raw data frame. pco, isomap, and metaMDS can take either a data.frame or a dist. vegan_cca and rda require a list whose first element is a formula and whose second element is a data set containing the constraining variables, as in the usual cca function in vegan. dpcoa requires a list whose first element is a data frame and whose second element is a distance between the rows on that data frame. CCorA and procuste require a list of data frames.

method

The method among those listed above that will perform the required ordination.

rows_annot

For one table methods, a data.frame whose j^th row describes the j^th sample in the coordinates matrices corresponding to row scores. For procustes and CCorA, we require a list of dataframes, one for each of the directions.

cols_annot

The analogous object for column scores.

dist_method

If a distance matrix is used by the specified method and X is not a distance object, we will call vegdist on the X using this string as the distance.#' @param rows_annot

table_names

A vector of strings specifying which tables to extract, for


krisrs1128/mvarVis documentation built on Oct. 13, 2019, 11:14 p.m.