ExposomePCA {rexposome} | R Documentation

## Class ExposomePCA

### Description

Class `ExposomePCA` contains a matrix of exposures used to compute the PCA, also a table of phenotypes and a set congtaing the multiple results of computing the PCA.

### Usage

    ## S4 method for signature 'ExposomePCA,ANY'
    plot(x, y, ...)

    ## S4 method for signature 'ExposomePCA'
    exposureNames(object)

    ## S4 method for signature 'ExposomePCA'
    extract(object, table = "exposures", ...)

    ## S4 method for signature 'ExposomePCA'
    ndim(object)

    ## S4 method for signature 'ExposomePCA'
    phenotypeNames(object)

    ## S4 method for signature 'ExposomePCA'
    plot3PCA(
      object,
      cmpX,
      cmpY,
      cmpZ,
      phenotype,
      main,
      angle = 35,
      pch = 16,
      legend = TRUE,
      plines = TRUE
    )

    ## S4 method for signature 'ExposomePCA'
    plotEXP(object, exposure)

    ## S4 method for signature 'ExposomePCA'
    plotPCA(
      object,
      set,
      cmpX = 1,
      cmpY = 2,
      show.exposures = FALSE,
      show.samples = FALSE,
      phenotype
    )

    ## S4 method for signature 'ExposomePCA'
    plotPHE(object, phenotype, exp2fac = 5)

### Arguments

`x` | Object of class `ExposomePCA`
`y` | NOT USED
`...` | NOT USED
`object` | An `ExposomePCA` object
`table` | Can takes values `"exposures"` or `"individuals"`.
`cmpX` | PC to place in X-axis
`cmpY` | PC to place in Y-axis
`cmpZ` | PC to place in Z-axis
`phenotype` | (when `set="samples"`) A phenotype can be selected so the samples are coloured by its value.
`main` | Title
`angle` | Point of view
`pch` | Size of the dots
`legend` | Boolean to show or hide the legend
`plines` | Boolean to show of hide the dotted lines that helps to place the dots in the X/Y axes
`exposure` | Vector of exposures to be shown in the plot
`set` | Can take values `"exposures"`, `"samples"` or `"all"`
`show.exposures` | When set to `TRUE`, labels for exposures are shown
`show.samples` | When set to `TRUE`, labels for samples are shown
`exp2fac` | Number of different values to considere an exposures continuous

### Value

An object of class `ExposomePCA`

### Methods (by generic)

- `plot`: Wrapper for `plotPCA` method.

- `exposureNames`: Getter to obtain the exposures's names.

- `extract`: Method to extract the raw results of the PCA.

- `ndim`: Number of principal components in an ExposomePCA.

- `phenotypeNames`: Getter to obtain the phenotype's names.

- `plot3PCA`: Methdo to draw a 3D plot for PCA

- `plotEXP`: Plot correlation between exposures and PCA

- `plotPCA`: Methdo to draw a 2D plot for PCA

- `plotPHE`: Plot association score between phentoypes and PCA

### Slots

`pca`

  list containing all elements of the PCA

`phenoData`

  Contains the phenotypes or variables experimenter-supplied (see eSet, AnnotatedDataFrame).

`featureData`

  Contains the description of the exposures including the family where they belong (see eSet, AnnotatedDataFrame).

### See Also

`correlation` to study the correlation between exposures in a `ExposomeSet`

[Package rexposome version 1.16.0 Index]