PlotValues.PCA.PSI.10x {MARVEL}

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