MUVR2 (version 0.1.0)

biplotPLS: 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
)

Value

A PLS biplot

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

Examples

# \donttest{
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)
# }