pcascree {pcaExplorer} | R Documentation

## Scree plot of the PCA on the samples

### Description

Produces a scree plot for investigating the proportion of explained variance, or alternatively the cumulative value

### Usage

    pcascree(obj, type = c("pev", "cev"), pc_nr = NULL, title = NULL)

### Arguments

`obj` | A `prcomp` object
`type` | Display absolute proportions or cumulative proportion. Possible values: "pev" or "cev"
`pc_nr` | How many principal components to display max
`title` | Title of the plot

### Value

An object created by `ggplot`, which can be assigned and further customized.

### Examples

    dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3, betaSD_tissue = 1)
    rlt <- DESeq2::rlogTransformation(dds)
    pcaobj <- prcomp(t(SummarizedExperiment::assay(rlt)))
    pcascree(pcaobj, type = "pev")
    pcascree(pcaobj, type = "cev", title = "Cumulative explained proportion of variance - Test dataset")

[Package pcaExplorer version 2.20.2 Index]