PlotValues.PCA.PSI.10x: Annotate reduced dimension space with PSI values

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

Annotate reduced dimension space with PSI values

Description

Annotates reduced dimension space, e.g., UMAP and tSNE, with PSI values.

Usage

PlotValues.PCA.PSI.10x(
  MarvelObject,
  cell.ids = NULL,
  coord.intron,
  min.gene.count = 3,
  point.size = 0.1,
  log2.transform = FALSE,
  color.gradient = c("grey90", "blue", "red"),
  type
)

Arguments

MarvelObject	Marvel object. S3 object generated from CheckAlignment.10x function.
cell.ids	Vector of character strings. Specific set of cells to plot.
coord.intron	Character string. Coordinates of splice junction whose expression will be plotted.
min.gene.count	Numeric value. Minimum raw gene count, above which, the PSI value will be calculate for the cell. Default is 3.
point.size	Numeric value. Size of data points. Default is 1.
log2.transform	Logical value. If set to TRUE, PSI values will be log2-transformed. Useful for highlighting small changes in PSI values between cell groups. Default is FALSE.
color.gradient	Vector of character strings. Colors to indicate low, moderate, and high expression. Default is c("grey90","blue","red").
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$PSI.

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 expression
marvel.demo.10x <- PlotValues.PCA.PSI.10x(
                        MarvelObject=marvel.demo.10x,
                        coord.intron="chr1:23693914:23694659",
                        min.gene.count=3,
                        log2.transform=FALSE,
                        color.gradient=c("grey","cyan","green","yellow","red"),
                        type="tsne"
                        )

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

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