Summarize NMF factors

summary method for class "nmf". Describes metadata representation in NMF factors. Returns object of class nmfSummary. Plot results using plot.

Usage

# S4 method for class 'nmf'
summary(object, group_by, stat = "sum", ...)

# S3 method for class 'nmfSummary'
plot(x, ...)

Arguments

object

an object of class "nmf", usually, a result of a call to nmf

group_by

a discrete factor giving groupings for samples or features. Must be of the same length as number of samples in object$h or number of features in object$w.

stat

either sum (sum of factor weights falling within each group), or mean (mean factor weight falling within each group).

...

Additional arguments (unused).

x

nmfSummary object, the result of calling summary on an nmf object

Value

data.frame with columns group, factor, and stat

A ggplot2 object showing factor representation by group.

See also

nmf, sparsity

summary,nmf-method, nmf

Examples

# \donttest{
library(Matrix)
A <- rsparsematrix(100, 50, 0.1)
model <- nmf(A, k = 3, seed = 42, tol = 1e-2, maxit = 10)
groups <- factor(sample(c("A", "B"), 50, replace = TRUE))
s <- summary(model, group_by = groups)
# }

# \donttest{
library(Matrix)
A <- rsparsematrix(100, 50, 0.1)
model <- nmf(A, k = 3, seed = 42, tol = 1e-2, maxit = 10)
groups <- factor(sample(c("A", "B"), 50, replace = TRUE))
s <- summary(model, group_by = groups)
if (requireNamespace("ggplot2", quietly = TRUE)) {
  plot(s)
}

# }