RunPCA.Exp: Principle component analysis for gene Data

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

Principle component analysis for gene Data

Description

Performs principle component analysis using gene expression values.

Usage

RunPCA.Exp(
  MarvelObject,
  sample.ids = NULL,
  cell.group.column,
  cell.group.order = NULL,
  cell.group.colors = NULL,
  features,
  min.cells = 25,
  point.size = 0.5,
  point.alpha = 0.75,
  point.stroke = 0.1
)

Arguments

MarvelObject	Marvel object. S3 object generated from TransformExpValues function.
sample.ids	Character strings. Specific cells to plot.
cell.group.column	Character string. The name of the sample metadata column in which the variables will be used to label the cell groups on the PCA.
cell.group.order	Character string. The order of the variables under the sample metadata column specified in cell.group.column to appear in the PCA cell group legend.
cell.group.colors	Character string. Vector of colors for the cell groups specified for PCA analysis using cell.type.columns and cell.group.order. If not specified, default ggplot2 colors will be used.
features	Character string. Vector of gene_id for analysis. Should match gene_id column of MarvelObject$GeneFeature.
min.cells	Numeric value. The minimum no. of cells expressing the gene to be included for analysis.
point.size	Numeric value. Size of data points on reduced dimension space.
point.alpha	Numeric value. Transparency of the data points on reduced dimension space. Take any values between 0 to 1. The smaller the value, the more transparent the data points will be.
point.stroke	Numeric value. The thickness of the outline of the data points. The larger the value, the thicker the outline of the data points.

Value

An object of class S3 containing with new slots MarvelObject$PCA$Exp$Results, MarvelObject$PCA$Exp$Plot, and MarvelObject$PCA$Exp$Plot.Elbow.

Examples

marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))

# Define genes for analysis
gene_ids <- marvel.demo$Exp$gene_id

# PCA
marvel.demo <- RunPCA.Exp(MarvelObject=marvel.demo,
                          sample.ids=marvel.demo$SplicePheno$sample.id,
                          cell.group.column="cell.type",
                          cell.group.order=c("iPSC", "Endoderm"),
                          min.cells=5,
                          features=gene_ids,
                          point.size=2
                          )

# Check outputs
head(marvel.demo$PCA$Exp$Results$ind$coord)
marvel.demo$PCA$Exp$Plot

MARVEL documentation built on Oct. 31, 2022, 5:07 p.m.