PlotValues.PCA.CellGroup.10x: Annotate reduced dimension space with cell feature

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

Annotate reduced dimension space with cell feature

Description

Annotates reduced dimension space, e.g., UMAP and tSNE, with cell features such as cell group, donor ID, sample ID, etc.

Usage

PlotValues.PCA.CellGroup.10x(
  MarvelObject,
  cell.group.list,
  legendtitle = "Cell group",
  alpha = 0.75,
  point.size = 1,
  point.stroke = 0.1,
  point.colors = NULL,
  point.size.legend = 2,
  type
)

Arguments

MarvelObject	Marvel object. S3 object generated from CheckAlignment.10x function.
cell.group.list	List of character strings. Each element of the list is a vector of cell IDs corresponding to a feature, e.g. cell group. The names of the element will be the cell feature label.
legendtitle	Character string. Legend title. Default is "Cell group".
alpha	Numeric value. Transparency of the data points. Takes any values between 0-1 whereby 0 is totally transparent and 1 is opaque. Default is 0.75.
point.size	Numeric value. Size of data points. Default is 1.
point.stroke	Numeric value. Outline thickness of data points. Default is 0.1.
point.colors	Vector of character strings. Colors of cell groups and should be same length as cell.group.list. Default ggplot2 colors are used.
point.size.legend	Numeric value. Size of legend keys. Default is 2.
type	Character string. Type of reduced dimension space. Options are "umap" and "tsne".

Value

An object of class S3 with new slot MarvelObject$adhocPlot$PCA$CellGroup.

Examples

marvel.demo.10x <- readRDS(system.file("extdata/data",
                               "marvel.demo.10x.rds",
                               package="MARVEL")
                               )

# Define cell groups
    # Retrieve sample metadata
    sample.metadata <- marvel.demo.10x$sample.metadata

    # iPSC
    index <- which(sample.metadata$cell.type=="iPSC")
    cell.ids.1 <- sample.metadata[index, "cell.id"]
    length(cell.ids.1)

    # Cardio day 10
    index <- which(sample.metadata$cell.type=="Cardio day 10")
    cell.ids.2 <- sample.metadata[index, "cell.id"]
    length(cell.ids.2)

    # Save into list
    cell.group.list <- list("iPSC"=cell.ids.1,
                            "Cardio d10"=cell.ids.2
                            )

# Plot cell groups
marvel.demo.10x <- PlotValues.PCA.CellGroup.10x(
                            MarvelObject=marvel.demo.10x,
                            cell.group.list=cell.group.list,
                            legendtitle="Cell group",
                            type="tsne"
                            )

# Check output
marvel.demo.10x$adhocPlot$PCA$CellGroup

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