plotAssociation {omicRexposome} | R Documentation

## Function to draw de result of an association study

### Description

This function draws two type of plots for the ResultSet from association functions

### Usage

    plotAssociation(object, rid = 1, coef = 2, contrast = 1,
      type = c("manhattan", "qq", "volcano"), tPV = NULL, tFC = NULL,
      show.effect = FALSE)

    ## S4 method for signature 'ResultSet'
    plotAssociation(object, rid = 1, coef = 2,
      contrast = NULL, type = c("manhattan", "qq", "volcano"), tPV = NULL,
      tFC = NULL, show.effect = FALSE)

### Arguments

`object` | An object of class ResultSet obtained from assoc_* functions.
`rid` | (default `1`) Index or name of the test to be plotted.
`coef` | (default `2`) Index of the coefficient to be extracted.
`contrast` | (default `1`) When `code` corresponds to a multicategorical variable, contasr selects the comparison.
`type` | Can take `"volcano"`, `"qq"`, `"manhattan"` and `"protein"`. `"protein"` lot is a type of Manhattan plot designed for protein association analysis.
`tPV` | (optional) Threshold for P.Value when `type="volcano"`.
`tFC` | (optional) Threshold for Fold Change or Effect when `type="volcano"`.
`show.effect` | (default `FALSE`) If set to `TRUE`, when `type="volcano"` the X-axis will show `2^logFC` instead of `logFC`.

### Value

A ggplot2 object

### See Also

`plotIntegration` for plotting integration results. `association` to create a `ResultSet` to be passed to this function.

### Examples

    data("asr", package = "omicRexposome")
    plotAssociation(asr, type = "qq")
    plotAssociation(asr, type = "volcano")

[Package omicRexposome version 1.9.0 Index]