plotAssociation-methods: Function to draw de result of an association study

In isglobal-brge/omicRexposome: Exposome and omic data associatin and integration analysis

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.
...	Arguments given to plot from ReultSet (from MultiDataSet package)

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")

isglobal-brge/omicRexposome documentation built on Oct. 20, 2021, 10:09 a.m.