ruv_scree {ruv}

RUV Scree Plot

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