Prepare biplot signal data

Prepare biplot stats

Get PCA components from biplot data

Biplot using ggplot2 via ordr package

BiPlot for Evidence vs Spread

Usage

biplot_signal(
  object,
  datatraits = unique(object$datatrait),
  orders = c("module", "kME", "p.value", "size")
)

biplot_stat(object, datatraits = unique(object$datatrait), orders = terms)

biplot_pca(
  bip,
  size = c("module", "kME", "p.value", "size"),
  strain = "NONE",
  threshold
)

biggplot(bip_pca, axes = 1:2, scale.factor = 2)

biplot_evidence(
  object,
  ordername,
  xlab,
  threshold,
  strain = "NONE",
  axes = 1:2,
  ...
)

Arguments

object: data frame
datatraits: `dataset: trait` names to include
orders: column names used for ordering and plot sizes
bip: object from `biplot_signal`
strain: strain name to highlight in biplot
threshold: vector of threshold values
bip_pca: object of class bip_pca
axes: axes to plot
scale.factor: scale factor for arrows vs points
ordername: name of order column
xlab: x label
...: additional paramaters ignored
transpose: transpose for `princomp` if `TRUE`

Value

data frame

data frame of PCA components

object of class ggplot2

gg plot object