manhattan_plot: Manhattan plot

In annebozack/EWASplot: What the Package Does (One Line, Title Case)

Manhattan plot

Description

This function creates a Manhattan plot of EWAS results using ggplot2.

Usage

manhattan_plot(
  probe,
  region = NULL,
  array = c("450K", "EPIC"),
  FDR = FALSE,
  title = NULL,
  col.chr = c("gray40", "gray55"),
  col.sig = "gray18",
  col.dmr = "black",
  line.dmr = "#4393c3",
  size.line.dmr = 0.2,
  cex = 0.5,
  cex.sig = 0.75,
  alpha = 0.5,
  alpha.sig = 1,
  size.line.sig = 0.5
)

Arguments

probe	Dataframe of EWAS results, including the columns 'cpg', 'P.Value', 'chr', and 'pos'. If 'cpg' column is not included, rownames will be used as probe names. If output from limma's topTable is provided, chromosome and position will be obtained from 450K of EPIC annotations.
region	Dataframe of regional analysis results including the columns 'chr', 'start', 'end'.
array	'450K' or 'EPIC'
FDR	Should an FDR level of significance be indicated? Defaults to FALSE.
title	Title text.
col.chr	Vector of two colors that will be alternately used for probes within each chromosome. Defaults to c('gray40', 'gray55').
col.sig	Color of FDR or Bonferroni significant probes. Defaults to 'gray18'.
col.dmr	Color of probes within DMRs. Defaults to 'black'.
line.dmr	Color of line indicating DMRs. Defaults to '#4393c3'.
size.line.dmr	Size of line indicating DMRs. Defaults to 0.2.
cex	Size of non-significant probes. Defaults to 0.5.
cex.sig	Size of significant probes. Defaults to 0.5.
alpha	Alpha of non-significant probes. Defaults to 0.5.
alpha.sig	alpha Alpha of non-significant probes. Defaults to 1.
Size	of line indicating FDR and Bonferroni significance. Defaults to 0.5.

Value

Manhattan plot

annebozack/EWASplot documentation built on Aug. 5, 2023, 6:02 p.m.