tuneVis: Visualize cross validation metrics

In topherconley/spacemap: A novel conditional graphical model for integrative genomics

Description

Diagnose the quality of the tuning grid used in cvVote through plotting CV scores and network size against the tuning penalties.

Usage

tuneVis(cvOut, testSetLen, tuneParam1, tuneParam1Name = c("lam1", "lam2",
  "lam3"), tuneParam2 = NULL)

Arguments

cvOut	Output from cvVote.
testSetLen	Integer vector specifying length of each test set associated with cvOut.
tuneParam1	Numeric vector specifying the tuning penalty placed on the x-axis.
tuneParam1Name	Character vector labelling the X-axis with the specified tuning parameter.
tuneParam2	Numeric vector specifying the tuning penalty placed on the x-axis. Defaults to NULL. If non-null, the output is a heatmap where CV scores are colored intensities on a 2-D grid of tuneParam1,tuneParam2.

Value

If tuneParam2 == NULL Return a list of 4 ggplot2 objects.

1. Scatter plot of log (CV score) vs. tuneParam1.

2. Scatter plot of "Avg. Total # of Edges" vs. tuneParam1.

3. Scatter plot of "Avg. # of Edges (Y – Y)" vs. tuneParam1.

4. Scatter plot of "Avg. # of Edges (x -> Y)" vs. tuneParam1.

If tuneParam2 != NULL Returns a heatmap (see ggplot2::geom_tile) where CV scores are colored intensities on a 2-D grid of tuneParam1,tuneParam2.

See Also

cvVote

topherconley/spacemap documentation built on May 31, 2019, 6:36 p.m.