RunPCA.PSI.Exp: Integrated splicing and gene non-linear dimension reduction...

In wenweixiong/MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

Integrated splicing and gene non-linear dimension reduction analysis

Description

Non-linear dimension reduction analysis based on both splicing and gene expression data.

Usage

RunPCA.PSI.Exp(
  MarvelObject,
  n.dim = c(30, 30),
  seed = 42,
  sample.ids = NULL,
  cell.group.column,
  cell.group.order,
  cell.group.colors = NULL,
  point.size = 0.5,
  point.alpha = 0.75,
  point.stroke = 0.1
)

Arguments

MarvelObject	Marvel object. S3 object generated from RunPCA function.
n.dim	Numeric values. Indicate the first number of principal components for splicing and gene, respectively, to use for analysis. Default value is c(30,30), i.e., the first 30 PCs for both splicing and gene.
seed	Numeric value. To sure reproducibility of analysis. Default value is 42.
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.
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$PCA$PSI$ElbowPlot or MarvelObject$PCA$Exp$ElbowPlot when level option set to "splicing" or "gene", respectively.

wenweixiong/MARVEL documentation built on Aug. 5, 2024, 2:54 p.m.