plotContrasts {variancePartition} | R Documentation

## Plot representation of contrast matrix

### Description

Plot contrast matrix to clarify interpretation of hypothesis tests with linear contrasts

### Usage

    plotContrasts(L)

### Arguments

`L` | contrast matrix

### Value

ggplot2 object

### Examples

    # load library
    # library(variancePartition)

    # load simulated data:
    # geneExpr: matrix of gene expression values
    # info: information/metadata about each sample
    data(varPartData)

    # get contrast matrix testing if the coefficient for Batch2 is zero
    form <- ~ Batch + (1|Individual) + (1|Tissue)
    L1 = getContrast( geneExpr, form, info, "Batch3")

    # get contrast matrix testing if the coefficient for Batch2 is different from Batch3
    form <- ~ Batch + (1|Individual) + (1|Tissue)
    L2 = getContrast( geneExpr, form, info, c("Batch2", "Batch3"))

    # combine contrasts into single matrix
    L_combined = cbind(L1, L2)

    # plot contrasts
    plotContrasts( L_combined )

[Package variancePartition version 1.22.0 Index]