generateRiverplot-methods: NMF riverplot

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

NMF riverplot

Description

Generate a riverplot object that displays the similarities between signatures at different factorization ranks

Usage

generateRiverplot(nmf_exp, ...)

## S4 method for signature 'ButchR_NMF'
generateRiverplot(
  nmf_exp,
  edges.cutoff = 0,
  useH = FALSE,
  color = TRUE,
  ranks = NULL
)

Arguments

nmf_exp	an object of class ButchR_NMF.
...	additional parameters.
edges.cutoff	cutoff until which similarities are displayed
useH	whether to relate signatures (FALSE) or exposures (TRUE)
color	whether to colorize the nodes based on PCA of the signatures
ranks	numeric vector of the selected factorization ranks to generate a riverplot.

Value

ret riverplot object

Examples

## Not run: 
plt <- generateRiverplot(nmf_exp, edges.cutoff = 0.2)
plot(plt, plot_area = 1, yscale = 0.6, nodewidth = 0.5)

## End(Not run)
## Not run: 
data("leukemia")
nmf_exp <- run_NMF_tensor(leukemia$matrix, ranks = 2:10,
method = "NMF",
n_initializations = 2)
plot(generateRiverplot(nmf_exp))
plot(generateRiverplot(nmf_exp, ranks = 2:5))

## End(Not run)

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