Heatmap_plot: Heat map plot for chromosomes and features.

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

Heat map plot for chromosomes and features.

Description

This function outputs the heat map plot for methylation level in different chromosomes of differentially methylated genes with features based on R package pheatmap.

Usage

Heatmap_plot(
  regiongeneall_significant,
  featurename = NULL,
  title = "Methylation level",
  display_numbers = FALSE,
  number_format = "%.0f",
  cluster_rows = FALSE,
  cluster_cols = TRUE,
  gaps_row = c(1, 2),
  gaps_col = NULL
)

Arguments

regiongeneall_significant	refers to the input file of methylation levels with differentially methylated genes or the genes in different gene body features.
featurename	refers to the feature name of the output file from Significant_filter() for genefeatureall_cpgfeature file, that is "CpGisland" or "Shore", with default NULL.
title	refers to the figure title, with the default "Methylation level".
display_numbers	refers to whether to display the methylation value in the figure, with default FALSE.
number_format	refers to the displayed number of the methylation value in round format.
cluster_rows	refers to whether to cluster the row, with the default FALSE.
cluster_cols	refers to whether to cluster the column, with the default TRUE.
gaps_row	refers to whether to divide the row, with the default c(1,2) that divide the rows into three parts by row 1 and row 2.
gaps_col	refers to whether to divide the column, with the NULL.

Value

Outputs a heat map figure with methylation levels.

Examples

Heatmap_plot(regiongeneall_significant)
Heatmap_plot(genefeatureall_cpgfeature_significantcpgisland, featurename = "CpGisland", display_numbers = FALSE, title = "Methylation level (%) for genes with CpG island")
Heatmap_plot(genefeatureall_cpgfeature_significantshore, featurename = "Shore", title = "Methylation level (%) for genes with shores")
Heatmap_plot(genefeatureall_cpgfeature_significantshore, featurename = "Shore", title = "Methylation level (%) for genes with shores", cluster_cols = FALSE)
Heatmap_plot(regiongeneall_significant, title = "Methylation level (%) for genes", display_numbers = FALSE)
Heatmap_plot(regiongeneall_significant, title = "Methylation level (%) for genes", display_numbers = FALSE, cluster_rows = TRUE, gaps_row = NULL)

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