MDScols: MDS by columns and optional plot using Minkowski metrics

In peterjuv/myHelpers: Misc helper functions for R

Description

Parametric (stats::cmdscale()) and non-parametric MDS (MASS::isoMDS() or MASS::sammon()) Data may be scales and/or centered before distance calculation. Distances are calculated between columns on a (possibly subset) of rows. Similar to limma::plotMDS in terms of subseting rows, but it allows for all rows for distance calculation, while limma uses only top=XX genes

Uses MASS::isoMDS or MASS::sammon Similar to limma::plotMDS, except that is uses all parameters for distance calculation, while limma uses only top=XX genes

Usage

MDScols(
  data,
  scale = FALSE,
  center = FALSE,
  FUN = "isoMDS",
  p = 2,
  selection = "pairwise",
  top = 500,
  k = 2,
  maxit = 50,
  trace = TRUE,
  tol = 1e-04,
  plot = FALSE,
  labels = names(data),
  col = NULL,
  cex = 1,
  main = NULL,
  cex.main = 1,
  xlab = "Coordinate 1",
  ylab = "Coordinate 2",
  ...
)

MASS_MDScols(
  data,
  scale = FALSE,
  center = FALSE,
  method = "euclidean",
  FUN = "isoMDS",
  p = 2,
  k = 2,
  maxit = 50,
  trace = TRUE,
  tol = 0.001,
  plot = FALSE,
  labels = names(data),
  col = NULL,
  cex = 1,
  main = NULL,
  cex.main = 1,
  xlab = "Coordinate 1",
  ylab = "Coordinate 2",
  ...
)

plotIsoMDS(FUN = "isoMDS", plot = TRUE, selection = NULL, ...)

Arguments

data	Matrix-like object to MDS (and plot) distances between columns
scale	Logical scale data; standardize together with center
center	Logical center data; standardize together with scale
FUN	MDS function from MASS, default "isoMDS", alternative "sammon"
p	Power of the Minkowski distance, passed to distance calculation dist(...) and isoMDS(...)
selection	Character "pairwise" or "common" for selection of rows or NULL for using all rows; default "pairwise"
top	Integer number of rows for distance calculation, default 500
k	Desired dimension for the solution, passed to cmdscale(...) through FUN
maxit	Max number of iterations, passed to isoMDS(maxit) or sammon(niter = maxit),
trace	Print trace, passed to FUN(),
tol	Tolerance, passed to FUN(),
plot	Logical, plot using R, default FALSE
labels	Character vector of alternative column names, default names(data)
col	Colors of labels
cex	Size of labels
main	String or TRUE to generate title generated automatically; default NULL
cex.main	Size of title
xlab	a label for the x axis, defaults to a description of x.
ylab	a label for the y axis, defaults to a description of y.
...	other graphical parameters (see par and section ‘Details’ below).
method	Distance metrics, passed to dist(...), must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski"

Value

A k-column vector of the fitted configuration from FUN()

A k-column vector of the fitted configuration from FUN()

TODO

add parameter dim.plot

peterjuv/myHelpers documentation built on June 12, 2021, 1:44 p.m.