Chromosome_pieplot: Pie plot based on different chromosomes.

In xiaowangCN/GeneDMRs: GeneDMRs: an R package for Gene-based differentially methylated regions analysis

Pie plot based on different chromosomes.

Description

This function outputs the pie plot for the percentages of sites or regions in different chromosomes.

Usage

Chromosome_pieplot(
  genefeatureall_cpgfeature_significantcpgisland,
  genefeatureall_cpgfeature_significantshore = NULL,
  methdirection = "both",
  title = "Pie plot for chromosome"
)

Arguments

genefeatureall_cpgfeature_significantcpgisland	refers to the input file with chromosomes, which can be files with/without significant filter().
genefeatureall_cpgfeature_significantshore	refers to another input file with chromosomes, e.g., genefeatureall_cpgfeature_significantshore file for comparison, with default NULL.
methdirection	refers to the methylation direction when the input file contains the methylation difference column i.e., Methdiff1 after Logic_regression(), which can be "hypo", "hyper" and "both", with the default "both" for both directions.
title	refers to figure titles, with the default "Pie plot for chromosome".

Value

Outputs pie figure in different chromosomes.

Examples

Chromosome_pieplot(genefeatureall_cpgfeature_significantcpgisland, title = "")
Chromosome_pieplot(genefeatureall_cpgfeature_significantcpgisland, title = "CpGisland")
Chromosome_pieplot(genefeatureall_cpgfeature_significantcpgisland, genefeatureall_cpgfeature_significantshore = genefeatureall_cpgfeature_significantshore, title = c("CpGisland","Shore"))
Chromosome_pieplot(siteall, title = "All cytosine sites") # Only consider the annotated chromosomes and the unannotated chromosomes will be discarded #
Chromosome_pieplot(siteall_Qvalue, title = "All cytosine sites")
Chromosome_pieplot(siteall_significant, title = "Significant cytosine sites")
Chromosome_pieplot(siteall_Qvalue, methdirection = "hyper", title = "Hyper-methylated distribution")
Chromosome_pieplot(siteall_significant, methdirection = "hypo", title = "Hypo-methylated pie plot")
Chromosome_pieplot(regiongeneall_Qvalue, methdirection = "hyper", title = "Hyper-methylated genes")

xiaowangCN/GeneDMRs documentation built on Nov. 22, 2023, 11:19 p.m.