GFA (version 1.0.5)

visualizeComponents: Visualize GFA components

Description

visualizeComponents illustrates the factorization inferred by GFA, averaging over the posteriors of the parameters, if they have been stored.

Usage

visualizeComponents(
  model,
  Y = NULL,
  norm = NULL,
  mode = 1,
  showAll = TRUE,
  hclust = FALSE,
  topK = 3,
  topFeatures = NA,
  topSamples = NA
)

Value

A list containing the matrices that have been visualized.

Arguments

model

The learned GFA model.

Y

The used input data to be plotted, if supplied. Default NULL.

norm

The normalization acquired from normalizeData, if applied. If provided, the reconstruction is shown in the original data space. Default NULL.

mode

Determines which mode to visualize in case of pairing in two modes (default: 1).

showAll

Show the full predictions and factorizations? May be cumbersome for large data. Default TRUE.

hclust

Order features and samples based on hierarchical clustering? Default FALSE.

topK

Number of strongest components visualized in the data space. Default 3.

topFeatures

How many most relevant features to show for the data space visualizations? Default NA, showing all the features.

topSamples

How many most relevant samples to show for the data space visualizations? Default NA, showing all the samples.