aphylo (version 0.3-3)

plot.aphylo_prediction_score: Visualize predictions

Description

Visualize predictions

Usage

# S3 method for 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,
  ...
)

Value

NULL (invisible) Generates a plot of the predictions.

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

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)