plot.aphylo_prediction_score function

Visualize predictions

## S3 method for class 'aphylo_prediction_score'
plot(
  x,
  y = NULL,
  main = "Prediction Accuracy: Observed versus predicted values",
  main.colorkey = "Probability of Functional Annotation",
  which.fun = seq_len(ncol(x$expected)),
  include.labels = NULL,
  labels.col = "black",
  leafs_only = TRUE,
  ...
)

Arguments

• x: An object of class aphylo_prediction_score.
• y: Ignored.
• main: Passed to title.
• main.colorkey: Character scalar. Title of the colorkey (optional).
• which.fun: Integer vector. Which function to plot.
• include.labels: Logical scalar. When TRUE, draws nice labels at each slice which by default are specified as the rownames of x$expected. This is mostly useful when the number of predictions is small.
• labels.col: Character scalar. Color of the labels.
• leafs_only: Logical. When TRUE (default) only plots the leaf nodes.
• ...: Ignored

Returns

NULL (invisible) Generates a plot of the predictions.

Details

If include.labels = NULL and ncol(x$expected) > 40, then include.labels=FALSE by default.

Examples

set.seed(8783)
atree  <- raphylo(29)
ans    <- aphylo_mle(atree ~ mu_d + mu_s + Pi)
pred_s <- prediction_score(ans)

pred_s
plot(pred_s)