# R/correlationPlot.R In RUVcorr: Removal of unwanted variation for gene-gene correlations and related analysis

#### Documented in correlationPlot

```#' Correlation plot to compare estimated correlations with true correlations.
#'
#' \code{correlationPlot} produces a correlation plot to compare true and estimated
#   correlations.
#'
#' @param true A matrix of true gene-gene correlation values.
#' @param est A matrix of estimated gene expression values.
#' @param plot.genes A vector of indices of genes used in plotting;
#' the suggested length of this vector is 18.
#' @param boxes A logical scalar to indicate whether boxes
#' are drawn around sets of 6 genes; only available if \code{plot.genes} has length 18.
#' @param title A character string describing the title of the plot.
#' @return \code{correlationPlot} returns a plot.
#'
#' @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.
#' @inheritParams graphics::mtext
#' @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)))
#' @export
correlationPlot<-function(
true, ##matrix
est,
plot.genes=sample(seq_len(dim(true)[1]), 18), ## index of which genes to plot
boxes=TRUE, ## draw boxes FALSE/TRUE
title,
line=-1)
{

if(is.matrix(true)[[1]]==FALSE) stop("true needs to be a matrix object.")
if(is.matrix(est)[[1]]==FALSE) stop("est needs to be a matrix object.")

if(length(plot.genes)!=18 & boxes==TRUE){
warning("No boxes can be drawn when not exactly 18 genes are specified.")
boxes=FALSE
}

est.true<-mashUp(true, est, plot.genes)
## lower triangle estimated values, upper triangle true values

corrplot(est.true, method = c("color"), order = "original", tl.col = "black")
## draw object
mtext(paste(title), side=3, line=line, cex = 1)
if(boxes){
rect(0.5, 12.5, 6.5, 18.5, border = "black", lwd = 2)
rect(6.5, 6.5, 12.5, 12.5, border="black", lwd=2)
rect(12.5, 0.5, 18.5, 6.5, border="black", lwd=2)
}
}
```

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