correlationPlot: Correlation plot to compare estimated correlations with true...

In RUVcorr: Removal of unwanted variation for gene-gene correlations and related analysis

Description

correlationPlot produces a correlation plot to compare true and estimated

Usage

correlationPlot(
  true,
  est,
  plot.genes = sample(seq_len(dim(true)[1]), 18),
  boxes = TRUE,
  title,
  line = -1
)

Arguments

true	A matrix of true gene-gene correlation values.
est	A matrix of estimated gene expression values.
plot.genes	A vector of indices of genes used in plotting; the suggested length of this vector is 18.
boxes	A logical scalar to indicate whether boxes are drawn around sets of 6 genes; only available if plot.genes has length 18.
title	A character string describing the title of the plot.
line	on which MARgin line, starting at 0 counting outwards.

Details

The upper triangle of the correlation plot shows the true gene-gene correlation values, while the lower triangle of the correlation plot shows the gene-gene correlation values calculated from the estimated gene expression values. This is possible because correlation matrices are symmetric.

Value

correlationPlot returns a plot.

Author(s)

Saskia Freytag

See Also

corrplot

Examples

Y<-simulateGEdata(500, 500, 10, 2, 5, g=NULL, Sigma.eps=0.1, 
250, 100, intercept=FALSE, check.input=FALSE)
correlationPlot(Y$Sigma, Y$Y, title="Raw", 
plot.genes=c(sample(1:100, 6), sample(101:250, 6), sample(251:500, 6)))

Example output

RUVcorr documentation built on Nov. 8, 2020, 5:10 p.m.