plotMDStargets2: Plot MDS(es) of gene expression using different distance...
In peterjuv/FunGenPipe: Tools for building function genomics pipelines

Plot MDS(es) of gene expression using different distance calculation methods and alternative colors.

Depricated: Plot MDS(es) of gene expression using different distance calculation methods and alternative colors.

plotMDStargets2(
  expLog2,
  targets,
  colorsFrom = "color_",
  rename = TRUE,
  namesFrom = NULL,
  scale = FALSE,
  center = FALSE,
  FUNS = c("cmdscale", "isoMDS", "sammon"),
  p = 2,
  selection = "pairwise",
  tops = 500,
  maxit = 50,
  trace = FALSE,
  tol = 0.001,
  size = 3,
  filePath = NULL,
  width = 7,
  height = 7,
  ...
)

plotMDStargets2_MASS(
  expLog2,
  targets,
  colorsFrom = "color_",
  namesFrom = NULL,
  scale = FALSE,
  center = FALSE,
  methods = c("euclidean", "manhattan"),
  FUNS = c("isoMDS", "sammon"),
  p = 2,
  maxit = 50,
  trace = FALSE,
  tol = 0.001,
  size = 3,
  filePath = NULL,
  width = 7,
  height = 7,
  ...
)

`expLog2`	Expression matrix (preferably in log2 scale) with genes in rows and samples in columns
`targets`	Phenotype data with columns with colors, e.g., color_Sex
`colorsFrom`	String variable prefix(es) from targets, passed to `getColPats2()`; default "color_"
`rename`	Logical, default TRUE, passed to `getColPats2()`; rename colors using associated variables or a variable namesFrom (default)
`namesFrom`	Variable from targets, passed to `getColPats2()`; suggested HybName
`scale`	Logical scale data, passed to `MASS_MDScols()`
`center`	Logical center data, passed to `MASS_MDScols()`
`FUNS`	List of MDS function from pacakge MASS, passed individually to `MASS_MDScols()`
`p`	Power of the Minkowski distance, passed to `dist()` through `MASS_MDScols()`
`selection`	Character "pairwise" or "common" for selection of rows or NULL for using all rows; default "pairwise"
`tops`	Integer vector number of rows (genes), passed individually to `MDScols()`
`maxit`	Passed to `MASS_MDScols()`,
`trace`	Trace progress, passed to `MASS_MDScols()`, default FALSE
`tol`	Tolerance, passed to `MASS_MDScols()`
`size`	Size of ggplot labels, passed to `geom_text()`
`filePath`	NULL or character; if given, output a PDF; default NULL
`width`	PDF width
`height`	PDF height
`...`	Passed to ggplot2::geom_text
`methods`	List of methods for distance calulation, passed individually to `stats::dist(method)` through `MASS_MDScols()`