PlotValues.PCA.Gene.10x: Annotate reduced dimension space with gene expression values

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

Annotate reduced dimension space with gene expression values

Description

Annotates reduced dimension space, e.g., UMAP and tSNE, with gene expression values. Values will be automatically be log2-transformed prior to plotting.

Usage

PlotValues.PCA.Gene.10x(
  MarvelObject,
  cell.ids = NULL,
  gene_short_name,
  log2.transform = TRUE,
  point.size = 0.1,
  color.gradient = c("grey90", "blue", "red"),
  type
)

Arguments

MarvelObject	Marvel object. S3 object generated from CheckAlignment.10x function.
cell.ids	Vector of character strings. Specify specific cells to plot.
gene_short_name	Character string. Gene name whose expression will be plotting.
log2.transform	Logical value. If set to TRUE (default), normalised gene expression values will be off-set by 1 and then log2-transformed prior to analysis.
point.size	Numeric value. Size of data points. Default is 1.
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$Gene.

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.Gene.10x(
                      MarvelObject=marvel.demo.10x,
                      gene_short_name="TPM2",
                      color.gradient=c("grey","cyan","green","yellow","red"),
                      type="tsne"
                      )

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

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