biplotPLS: PLS biplot

In MUVR2: Multivariate Methods with Unbiased Variable Selection

PLS biplot

Description

Makes a biplot of a fitted object (e.g. from a MUVR with PLS core).

Usage

biplotPLS(
  fit,
  comps = 1:2,
  xCol,
  labPlSc = TRUE,
  labs,
  vars,
  labPlLo = TRUE,
  pchSc = 16,
  colSc,
  colLo = 2,
  supLeg = FALSE
)

Arguments

fit	A PLS fit (e.g. from MUVRclassObject$Fit[[2]])
comps	Which components to plot
xCol	(Optional) Continuous vector for grey scale gradient of observation (sample) color (e.g. Y vector in regression analysis)
labPlSc	Boolean to plot observation (sample) names (defaults to TRUE)
labs	(Optional) Label names
vars	Which variables to plot (names in rownames(loadings))
labPlLo	Boolean to plot variable names (defaults to TRUE)
pchSc	Plotting character for observation scores
colSc	Colors for observation scores (only if xCol omitted)
colLo	Colors for variable loadings (defaults to red)
supLeg	Boolean for whether to suppress legends

Value

A PLS biplot

Examples

data("freelive2")
nRep <- 2 # Number of MUVR2 repetitions
nOuter <- 3 # Number of outer cross-validation segments
varRatio <- 0.75 # Proportion of variables kept per iteration
method <- 'PLS' # Selected core modeling algorithm
regrModel <- MUVR2(X = XRVIP2,
                  Y = YR2,
                  nRep = nRep,
                  nOuter = nOuter,
                  method = method,
                  modReturn = TRUE)
biplotPLS(regrModel$Fit[[2]],
          comps = 1:2,
          xCol = YR2,
          labPlSc = FALSE,
          labPlLo = FALSE)

MUVR2 documentation built on Sept. 16, 2024, 9:06 a.m.