quickPCA: Quick PCA

In genejockey33000/typGumbo: Scripts and Pipelines for RNAseq Analysis

Quick PCA

Description

Just an abbreviated wrapper for prcomp() and fviz_pca_ind because I get tired of all the lines of code. Cleans up scripts with many PCA plots.

Usage

quickPCA(
  x,
  meta = NULL,
  sample = "sample",
  scale = FALSE,
  colorBy = NULL,
  samp.labels = FALSE,
  plot.title = NULL
)

Arguments

x	Your expression matrix with samples in columns and measurements (genes/proteins/etc.) in rows.
meta	Metadata object, ideally with column labeled "sample" that matches the names of the columns in your expression matrix. all(colnames(x) == meta[,sample]) must return TRUE
sample	Name of metadata column with sample names. Default is "sample" specify if yours is different (i.e. "Sample", "samp." or some other foolish name)
scale	(Logical) Whether or not prcomp should scale the data prior to running PCA. Leave FALSE if data is already scaled/log transformed. Set to TRUE for raw data values
colorBy	(Optional) Name of the column to color dots by. (i.e. "treatment", "batch", "sex")
samp.labels	(Logical) Should individual points be
plot.title	(Optional) Title for your PCA plot.

Value

PCA plot

genejockey33000/typGumbo documentation built on July 20, 2023, 11:45 p.m.