DOT graph visualization for nmfae objects

nmfae.DOT generates a DOT language string for visualizing the structure of a three-layer NMF model. Two graph types are supported: "XCX" shows encoder factors, \(\Theta\), and decoder factors; "YXCXY" shows the full structure from \(Y_2\) through \(X_2\), \(\Theta\), \(X_1\) to \(Y_1\).

Edge widths are proportional to matrix element values, and edges below threshold are omitted for clarity.

Usage

nmfae.DOT(
  result,
  type = c("XCX", "YXCXY"),
  threshold = 0.01,
  sig.level = 0.1,
  rankdir = "LR",
  fill = TRUE,
  weight_scale = 5,
  weight_scale_x1 = weight_scale,
  weight_scale_theta = weight_scale,
  weight_scale_x2 = weight_scale,
  Y1.label = NULL,
  X1.label = NULL,
  X2.label = NULL,
  Y2.label = NULL,
  Y1.title = "Output (Y1)",
  X1.title = "Decoder (X1)",
  X2.title = "Encoder (X2)",
  Y2.title = "Input (Y2)",
  hide.isolated = TRUE
)

Arguments

result

An object of class "nmfae" returned by nmfae.

type

Character. Graph type: "XCX" (default) or "YXCXY".

threshold

Numeric. Edges with values below this are omitted. Default is 0.01.

sig.level

Numeric or NULL. Significance level for filtering C edges when inference results are available. Only edges with p-value below sig.level are shown, with significance stars. Set to NULL to disable. Default is 0.1.

rankdir

Character. Graph direction for DOT layout. Default is "LR" (left to right).

fill

Logical. If TRUE, nodes are filled with color. Default is TRUE.

weight_scale

Numeric. Base scale factor for edge widths. Default is 5.

weight_scale_x1

Numeric. Scale factor for \(X_1\) edges.

weight_scale_theta

Numeric. Scale factor for \(\Theta\) edges.

weight_scale_x2

Numeric. Scale factor for \(X_2\) edges.

Y1.label

Character vector of output variable labels.

X1.label

Character vector of decoder basis labels.

X2.label

Character vector of encoder basis labels.

Y2.label

Character vector of input variable labels.

Y1.title

Character. Title for output node group. Default is "Output (Y1)".

X1.title

Character. Title for decoder node group. Default is "Decoder (X1)".

X2.title

Character. Title for encoder node group. Default is "Encoder (X2)".

Y2.title

Character. Title for input node group. Default is "Input (Y2)".

hide.isolated

Logical. If TRUE (default), Y1 and Y2 nodes that have no edges at or above threshold are excluded from the graph. Only applies when type = "YXCXY".

Value

A character string containing the DOT graph specification.

See also

nmfae

Examples

# \donttest{
set.seed(1)
Y <- matrix(runif(20), nrow = 4)
res <- nmfae(Y, rank = 2)
dot <- nmfae.DOT(res)
# }