volcanoPlot: Volcano plot for a MIMOSA model

In 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)

Example output

Loading required package: MASS
Loading required package: plyr
Loading required package: reshape

Attaching package: 'reshape'

The following objects are masked from 'package:plyr':

    rename, round_any

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2

This is package 'modeest' written by P. PONCET.
For a complete list of functions, use 'library(help = "modeest")' or 'help.start()'.

Warning message:
In .local(formula, data, ...) :
  Formula does not contain the RefTreat variable. It will be added automatically. Set RT=FALSE to disable this.

MIMOSA documentation built on Nov. 12, 2020, 2:02 a.m.