snm.diagnosticPlot: Produce Diagnostic Plots For SNM Algorithm

In Sage-Bionetworks/snm: Supervised Normalization of Microarrays

Description

This function produces plots useful for diagnosing problems with an assumed study-specific model.

Usage

snm.diagnostic.plot(obs.fit, obs.stat, snm.obj, basisSplineFunction, n.iter)

Arguments

obs.fit	List of estimated coefficient matrices and residuals from full and reduced models
obs.stat	List of statistic obtained from model fit.
snm.obj	An object of class snm.
basisSplineFunction	Basis spline functions for intenisty-dependent functions
n.iter	Current iteration number

Author(s)

Brig Mecham <[e-mail]>

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (obs.fit,obs.stat,snm.obj,
          basisSplineFunction)
{
  par(mfrow=c(2,2))
  bds <- ifelse(snm.obj$bin.densities > 500, 500, snm.obj$bin.densities)
  plot(rowMeans(snm.obj$M.pooled),
       bds,ylim=c(0,500),
       xlab="Estimated RNA Concentration", ylab="Probes per bin", main="Null probes per bin")

  u <- fast.svd(obs.fit$res1,tol=0);
  plot(u$d^2 / sum(u$d^2), ylim=c(0,1),
       main="Latent Structure",
       xlab="Surrogate Variable",
       ylab="Percent Variance Explained")

  if(dim(snm.obj$dat)[1] > 5000) {
    th <- sample(dim(snm.obj$dat)[1], 5000)
  }else{
    th <- 1:dim(snm.obj$dat)[1]
  }

  oo <- order(snm.obj$M[th,1])
  plot(snm.obj$M[th[oo],1], snm.obj$array.fx[th[oo],1],
       type="l",lwd=3, ylim=range(snm.obj$array.fx[th[oo],]),
       xlab="Estimated RNA Concentration", ylab="Array Effect",main="Estimated Array Effects")
  sapply(2:dim(snm.obj$r.dat)[2],function(id) {
    oo <- order(snm.obj$M[th,id])
    points(snm.obj$M[th[oo],id], snm.obj$array.fx[th[oo],id],type="l",lwd=3)
  }) -> hmm

  hist(obs.stat$pval, xlab="P values",main="P value distribution");
  abline(v=sort(obs.stat$pval)[length(obs.stat$pval)*(1-snm.obj$pi0)],col="red")

  }

Sage-Bionetworks/snm documentation built on May 9, 2019, 12:14 p.m.