ruv_svdplot function

RUV SVD Plot

A generalization of a PC (principal component) plot.

ruv_svdplot(Y.data, Y.space = NULL, info = NULL, k = c(1, 2), Z = 1, left = TRUE)

Arguments

• Y.data: The data matrix. Rows are observations and columns are features (e.g. genes).
• Y.space: Either a data matrix of the same dimension as Y.data, or the SVD of such a matrix, as returned by the svd function. The singular vectors of this matrix define the space in which Y.data will be plotted. If NULL, Y.data itself is used.
• info: Additional data to be included in the ggplot, which can be used for setting aesthetics such as color. Converted to a dataframe, which should have a number of rows equal to the number of rows of Y.data (if left=TRUE) or the number of columns of Y.data (if left=FALSE).
• k: A numeric vector of length 2. The singular vectors to be plotted. Typically integers, but fractional values can also be specified. For example, a value of 2.5 corresponds to the linear combination (singular vector 2) + (singular vector 3), rescaled to have unit length. Similarly, a value of 2.2 corresponds to the (rescaled) linear combination 8*(singular vector 2) + 2*(singular vector 3), and -2.2 corresponds to the (rescaled) linear combination 8*(singular vector 2) - 2*(singular vector 3). Note that the vectors defined by 2.2 and -2.8 are orthogonal to each other, as are those defined by 2.3 and -2.7, etc.
• Z: Any variables to regress out of Y.data 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. Similarly for Y.space, unless Y.space is already an SVD.
• left: Plot the left singular vectors (if TRUE) or the right singular vectors (if FALSE).

Details

When Y.space = NULL and Z = 1 and the values of k are integers, this is a standard PC plot.

Returns

A ggplot.

Author(s)

Johann Gagnon-Bartsch