multiple_metagenes: Plot multiple metagene data objects on a single plot.

In PCBS: Principal Component BiSulfite

Plot multiple metagene data objects on a single plot.

Description

Plots multiple metagene object using the raw data generated by score_metagene().

Usage

multiple_metagenes(data_list, set_names, title, xaxis, yaxis, legend.title, col, se_alpha)

Arguments

data_list	List of score_metagene() raw data output
set_names	Character vector of names for score_metagene() object
title	Output plot title
xaxis	Output plot x-axis title
yaxis	Output plot y-axis title
legend.title	T/F, whether to show legend title
col	Vector of colours to use for lines
se_alpha	0-1, alpha value for standard error shading

Value

Returns a grob containing a plot of the input metagene data.

Examples

ranks <- getPCRanks(eigen, IDs = c("trt", "ctl"), PC = 1)
DMRs <- Get_Novel_DMRs(ranks, 2940, minCpGs=10)

# Select all significantly hypomethylated DMRs:
hypo_DMRs <- DMRs[DMRs$FDR <= 0.05 & DMRs$DMR_Zscore < 0,] 
# Select all significantly hypermethylated DMRs:
hyper_DMRs <- DMRs[DMRs$FDR <= 0.05 & DMRs$DMR_Zscore > 0,]

# select chrom, start, and end of all hyper DMRs
regions_hypo <- hypo_DMRs[c(1:3)] 
regions_hyper <- hyper_DMRs[c(1:3)] 

# return.data = T returns raw data instead of a plot:
hyper_metagene <- score_metagene(ranks, regions_hyper, return.data = TRUE)
hypo_metagene <- score_metagene(ranks, regions_hypo, return.data = TRUE)

# The multiple_metagenes function plots multiple metagenes 
# using a list of raw data objects from score_metagene().
multiple_metagenes(data_list = list(hyper_metagene, hypo_metagene),
set_names = c("Hyper DMRs", "Hypo DMRs"),
title="Metagenes of DMR Regions", legend.title = FALSE)

PCBS documentation built on Sept. 11, 2024, 6:11 p.m.