subMDS: MDS plot with class labels

In peterawe/CMScaller: CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

Description

Multi-dimensional scaling (MDS) plot with class labels. Wrapper for plotMDS.

Usage

subMDS(
  emat,
  class = NULL,
  keepN = TRUE,
  nGenes = 1000,
  normMethod = NULL,
  dim = c(1, 2),
  labelSamp = FALSE,
  labelCenters = TRUE,
  classConfusion = NULL,
  legend = "bottomleft",
  classCol = getOption("subClassCol"),
  ...
)

Arguments

emat	a numeric matrix with row features and sample columns.
class	a factor vector specifying subtypes compared length(class)==ncol(emat).
keepN	a logical or numeric vector specifying which samples to keep (defaults to all).
nGenes	an integer specifying number of features to used for MDS
normMethod	a character, passed to calcNormFactors if element in c("TMM","RLE", "upperquartile","none") or voom ("scale", "quantile", "cyclicloess").
dim	a numeric vector of length 2, specifying which principal components to plot.
labelSamp	a logical indicating whether points (FALSE) or colnames(emat) are plotted.
labelCenters	a logical indicating whether class centers should be labeled.
classConfusion	a factor vector with same length and levels as class specifying alternative classifications.
legend	a character specifying legend placement (e.g. "topleft", "bottomright").
classCol	a character vector of hexcolors with length(classCol)>=levels(class). If NULL, a pre-defined RColorBrewer based palette is used.
...	arguments to be passed to plotMDS.

Details

plotMDS provides a MDS plot of emat with points colored according to class labels. If classConfusion is specified, samples where class != classConfusion are highlighted.

Value

A labeled MDS plot

Examples

# sample subset for reduced run-time
subset <- 25:50
subMDS(emat=crcTCGAsubset, class=crcTCGAsubset$CMS,
        keepN=subset, normMethod="quantile")

peterawe/CMScaller documentation built on June 13, 2020, 4:49 a.m.