EpiMix_PlotModel: The EpiMix_PlotModel function.

In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation

The EpiMix_PlotModel function.

Description

Produce the mixture model and the gene expression plots representing the EpiMix results.

Usage

EpiMix_PlotModel(
  EpiMixResults,
  Probe,
  methylation.data,
  gene.expression.data = NULL,
  GeneName = NULL,
  axis.title.font = 20,
  axis.text.font = 16,
  legend.title.font = 18,
  legend.text.font = 18,
  plot.title.font = 20
)

Arguments

EpiMixResults	resulting list object from the EpiMix function.
Probe	character string indicating the name of the CpG probe for which to create a mixture model plot.
methylation.data	Matrix with the methylation data with genes in rows and samples in columns.
gene.expression.data	Gene expression data with genes in rows and samples in columns (optional). Default: NULL.
GeneName	character string indicating the name of the gene whose expression will be ploted with the EpiMix plot (optional). Default: NULL.
axis.title.font	font size for the axis legend.
axis.text.font	font size for the axis label.
legend.title.font	font size for the legend title.
legend.text.font	font size for the legend label.
plot.title.font	font size for the plot title.

Details

The violin plot and the scatter plot will be NULL if the gene expression data or the GeneName is not provided

Value

A list of EpiMix plots:

MixtureModelPlot	a histogram of the distribution of DNA methylation data
ViolinPlot	a violin plot of gene expression levels in different mixutures in the MixtureModelPlot
CorrelationPlot	a scatter plot between DNA methylation and gene expression

Examples

{
data(MET.data)
data(mRNA.data)
data(Sample_EpiMixResults_Regular)

probe = "cg14029001"
gene.name = "CCND3"
plots <- EpiMix_PlotModel(
                          EpiMixResults = Sample_EpiMixResults_Regular,
                          Probe = probe,
                          methylation.data = MET.data,
                          gene.expression.data = mRNA.data,
                          GeneName = gene.name
                           )
plots$MixtureModelPlot
plots$ViolinPlot
plots$CorreilationPlot
}

gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.