recovery_plot-methods: Recovery plot

In hdsu-bioquant/ButchR: Non-Negative Matrix Factorization Suite

Recovery plot

Description

Generate a recovery plot to visualize the association between the NMF signatures and a biological or clinical annotation factor.

Usage

recovery_plot(x, annot, ...)

## S4 method for signature 'matrix'
recovery_plot(x, annot)

Arguments

x	an object of class matrix, ButchR_NMF, ButchR_joinNMF, or ButchR_integrativeNMF.
annot	input named factor/character with biological/clinical annotation for the columns of the input data.
...	additional parameters.

Value

recovery plot or a data frame with the association analysis results.

Examples

## Not run: 
recovery_plot(x, annot_factor)

## End(Not run)
## Not run: 
data(leukemia)
leukemia_nmf_exp <- run_NMF_tensor(X = leukemia$matrix,
                                   ranks = 2:4,
                                   method = "NMF",
                                   n_initializations = 10,
                                   extract_features = TRUE)
recovery_plot(HMatrix(leukemia_nmf_exp, k = 4),
              leukemia$annotation$ALL_AML)

## End(Not run)

hdsu-bioquant/ButchR documentation built on Jan. 28, 2023, 6:06 p.m.