CVPlot {MCbiclust} | R Documentation

## Make correlation vector plot

### Description

A function to visualise the differences between different found biclusters. Output is a matrix of plots. Each correlation vector is plotted against each other across the entire measured gene set in the lower diagonal plots, and a chosen gene set (e.g. mitochondrial) in the upper diagonal plots. The diagnal plots themselves show the density plots of the entire measured and chosen gene set. There are addition options to set the transparancy of the data points and names of the correlation vectors.

### Usage

    CVPlot(cv.df, geneset.loc, geneset.name, alpha1 = 0.005, alpha2 = 0.1,
      cnames = NULL)

### Arguments

`cv.df` | A dataframe containing the correlation vectors of one or more patterns.
`geneset.loc` | A gene set of interest (e.g. mitochondrial) to be plotted separately from rest of genes.
`geneset.name` | Name of geneset (e.g. mitochondrial genes)
`alpha1` | Transparency level of non-gene set genes
`alpha2` | Transparency level of gene set genes
`cnames` | Character vector containing names for the correlation vector

### Value

A plot of the correlation vectors

### Examples

    data(CCLE_small)
    data(Mitochondrial_genes)

    mito.loc <- which(row.names(CCLE_small) %in% Mitochondrial_genes)
    CCLE.mito <- CCLE_small[mito.loc,]

    CCLE.seed <- list()
    CCLE.cor.vec <- list()

    for(i in 1:3){
        set.seed(i)
        CCLE.seed[[i]] <- FindSeed(gem = CCLE.mito,
                                   seed.size = 10,
                                   iterations = 100,
                                   messages = 100)}

    for(i in 1:3){
        CCLE.cor.vec[[i]] <-  CVEval(gem.part = CCLE.mito,
                                     gem.all = CCLE_small,
                                     seed = CCLE.seed[[i]],
                                    splits = 10)}

    CCLE.cor.df <- (as.data.frame(CCLE.cor.vec))

    CVPlot(cv.df = CCLE.cor.df, geneset.loc = mito.loc,
           geneset.name = "Mitochondrial",alpha1 = 0.5)

[Package MCbiclust version 1.4.0 Index]