volcanoPlot {MIMOSA} | R Documentation |
Plots effect size vs posterior probablilty of response from a MIMOSAResultList, faceting by the conditioning variables.
volcanoPlot(x, effect_expression = NA, facet_var = NA, threshold = 0.01)
x |
A |
effect_expression |
an |
facet_var |
an |
threshold |
a |
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)