plot.eigenR2: Graphical display of eigenR2 objects

Description Usage Arguments Details Value Author(s) References See Also Examples

Description

Graphical display of the information captured the eigenvectors.

Usage

1
2
  eigenR2plot(eigenR2obj)
  plot.eigenR2(x,...)

Arguments

eigenR2obj, x

An eigenR2 object.

...

Plotting arguments.

Details

The function graphically displays the information captured by the eigenvectors, including:

  1. A plot that shows the proportion of total variation each eigen-vector captures.

  2. A plot of the R-square value for each significant eigenvectors.

  3. A plot of the p-values for each eigenvector, if eigen.sig is specified.

Value

None.

Author(s)

Lin S. Chen lschen@princeton.edu and John D. Storey jstorey@princeton.edu

References

Chen LS and Storey JD (2008) Eigen-R2 for dissecting the variation in high-dimensional studies.

See Also

eigenR2

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
  ## Not run: 
  ## Load the simulated data.
  ## The data set contains age, genotype and IDs for 50 arrays.
  ## The expression matrix is a 200 genes by 50 array matrix
  data(eigSdat)
  exp <- eigSdat$exp
  exp <- t(apply(exp, 1, function(x) x-mean(x)))
  varList <- eigSdat$varList
  age <- varList$age
  geno <- varList$geno
  ID <- varList$ID

  ## the eigen R-square for variable "age"
  mod2 <- model.matrix(~1+age+as.factor(geno))
  eigenR2.g <- eigenR2(dat=exp, model=mod2)
  
  plot.eigenR2(eigenR2.g)
 
## End(Not run)

StoreyLab/eigenR2 documentation built on May 9, 2019, 3:10 p.m.