PlotValues.Exp: Plot gene expression values

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

Plot gene expression values

Description

Boxplot of gene expression values across different groups of cells.

Usage

PlotValues.Exp(
  MarvelObject,
  cell.group.list,
  feature,
  maintitle = "gene_short_name",
  xlabels.size = 8,
  cell.group.colors = NULL,
  point.alpha = 0.2
)

Arguments

MarvelObject	Marvel object. S3 object generated from TransformExpValues function.
cell.group.list	List of character strings. Each element of the list is a vector of cell IDs corresponding to a cell group. The name of the element will be the cell group label.
feature	Character string. gene_id for plotting. Should match gene_id column of MarvelObject$GeneFeature slot.
maintitle	Character string. Column to use as plot main title as per MarvelObject$GeneFeature. Default is "gene_short_name" column.
xlabels.size	Numeric value. Size of x-axis labels as per ggplot2 function. Default is 8.
cell.group.colors	Character string. Vector of colors for the cell groups specified for PCA analysis using cell.type.columns, cell.type.variable, and cell.type.labels. If not specified, default ggplot2 colors will be used.
point.alpha	Numeric value. Transparency of the data points. Takes any values between 0-1. Default value is 0.2.

Value

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

Examples

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

df.pheno <- marvel.demo$SplicePheno
cell.group.g1 <- df.pheno[which(df.pheno$cell.type=="iPSC"), "sample.id"]
cell.group.g2 <- df.pheno[which(df.pheno$cell.type=="Endoderm"), "sample.id"]
cell.group.list <- list(cell.group.g1, cell.group.g2)
names(cell.group.list) <- c("iPSC", "Endoderm")

# Plot
marvel.demo <- PlotValues.Exp(MarvelObject=marvel.demo,
                              cell.group.list=cell.group.list,
                              feature="ENSG00000161970.15",
                              xlabels.size=8
                              )

# Check output
marvel.demo$adhocPlot$Exp

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