ruv_scree: RUV Scree Plot

In ruv: Detect and Remove Unwanted Variation using Negative Controls

Description

A scree plot (on the log scale)

Usage

ruv_scree(Y = NULL, Z = 1, Y.svd = NULL)

Arguments

Y	The data matrix. Rows are observations and columns are features (e.g. genes). If not specified, Y.svd must be specified instead (which is faster).
Z	Any variables to regress out of Y as a preprocessing step. May simply be 1 (the default) for an intercept term, i.e. the columns of Y are mean centered. May also be NULL.
Y.svd	The SVD of Y, as returned by the svd function.

Details

Because 0 cannot be plotted on a log scale, if any singular values are equal to 0, they will be changed to the minimum non-zero singular value and plotted in red. Exception: singular values that are 0 as a result of regressing out Z are simply not plotted.

Value

A ggplot.

Author(s)

Johann Gagnon-Bartsch

ruv documentation built on Aug. 31, 2019, 1:04 a.m.