volcanoPlot: Volcano plot for a MIMOSA model

In RGLab/MIMOSA: Mixture Models for Single-Cell Assays

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)

RGLab/MIMOSA documentation built on Nov. 13, 2020, 5:04 a.m.