Score plots of effect matrices — lmpScorePlot • limpca

Draws the score plots of each (augmented) effect matrix provided in lmpPcaEffects. As a wrapper of the plotScatter function, it allows to visualize the scores of the effect matrices for two components at a time with all the available options in plotScatter.

Usage

lmpScorePlot(resLmpPcaEffects, effectNames = NULL, axes = c(1, 2), ...)

Arguments

resLmpPcaEffects: A list corresponding to the output value of lmpPcaEffects.
effectNames: Names of the effects to be plotted. If NULL, all the effects are plotted.
axes: A numerical vector with the 2 Principal Components axes to be drawn.
...: Additional arguments to be passed to plotScatter.

Value

A list of score plots (ggplot).

Details

lmpScorePlot is a wrapper of plotScatter.

Examples


data("UCH")
resLmpModelMatrix <- lmpModelMatrix(UCH)
resLmpEffectMatrices <- lmpEffectMatrices(resLmpModelMatrix)

# PCA decomposition of effect matrices (ASCA)
resASCA <- lmpPcaEffects(resLmpEffectMatrices)
# Score plot of Hippurate effect matrix
lmpScorePlot(resASCA,
  effectNames = "Hippurate",
  color = "Hippurate", shape = "Hippurate"
)


# PCA decomposition of augmented effect matrices (APCA)
resASCA <- lmpPcaEffects(resLmpEffectMatrices, method = "APCA")
# Score plot of Hippurate augmented effect matrix
lmpScorePlot(resASCA,
  effectNames = "Hippurate",
  color = "Hippurate", shape = "Hippurate", drawShapes = "ellipse"
)