degPCA {DEGreport} | R Documentation

## smart PCA from count matrix data

### Description

nice plot using ggplot2 from prcomp function

### Usage

    degPCA(
      counts,
      metadata = NULL,
      condition = NULL,
      pc1 = "PC1",
      pc2 = "PC2",
      name = NULL,
      shape = NULL,
      data = FALSE
    )

### Arguments

`counts` | matrix with count data
`metadata` | dara.frame with sample information
`condition` | character column in metadata to use to color samples
`pc1` | character PC to plot on x-axis
`pc2` | character PC to plot on y-axis
`name` | character if given, column in metadata to print label
`shape` | character if given, column in metadata to shape points
`data` | Whether return PCA data or just plot the PCA.

### Value

if `results <-` used, the function return the output of `prcomp()`.

### Author(s)

Lorena Pantano, Rory Kirchner, Michael Steinbaugh

### Examples

    data(humanGender)
    library(DESeq2)
    idx <- c(1:10, 75:85)
    dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],
    colData(humanGender)[idx,], design=~group)
    degPCA(log2(counts(dse)+0.5), colData(dse),
      condition="group", name="group", shape="group")

[Package DEGreport version 1.28.0 Index]