MARVEL (version 1.4.0)

RunPCA.Exp: 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
)

Value

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

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.

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