volcanoPlot {MIMOSA} | R Documentation

## Volcano plot for a MIMOSA model

### Description

Plots effect size vs posterior probablilty of response from a MIMOSAResultList, faceting by the conditioning variables.

### Usage

    volcanoPlot(x, effect_expression = NA, facet_var = NA, threshold = 0.01)

### Arguments

`x` | A `MIMOSAResultList`
`effect_expression` | an `expression` that defines the effect size. Usually a function of the stimulated and unstimulated proportions from `countsTable(x,proportion=TRUE)`
`facet_var` | an `expression` defining the faceting in ggplot parlance. i.e. `~ faceting + variables`
`threshold` | a `numeric` value between [0,1] for coloring significant observations (based on the q-value)

### See Also

`countsTable`

### Examples

    data(ICS)
    E<-ConstructMIMOSAExpressionSet(ICS,
      reference=ANTIGEN%in%'negctrl',measure.columns=c('CYTNUM','NSUB'),
      other.annotations=c('CYTOKINE','TCELLSUBSET','ANTIGEN','UID'),
      default.cast.formula=component~UID+ANTIGEN+CYTOKINE+TCELLSUBSET,
      .variables=.(TCELLSUBSET,CYTOKINE,UID),
      featureCols=1,ref.append.replace='_REF')

    result<-MIMOSA(NSUB+CYTNUM~UID+TCELLSUBSET+CYTOKINE|ANTIGEN,
        data=E, method='EM',
        subset=RefTreat%in%'Treatment'&ANTIGEN%in%'ENV',
        ref=ANTIGEN%in%'ENV'&RefTreat%in%'Reference')
    volcanoPlot(result,CYTNUM-CYTNUM_REF)

[Package MIMOSA version 1.30.0 Index]