MARVEL (version 1.4.0)

PlotValues.Exp: 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
)

Value

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

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.

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