PCBS (version 0.1.1)

plot_metagene: Generate a metagene plot from raw metagene data.

Description

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

Usage

plot_metagene(data, title, xaxis, yaxis, linecol)

Value

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

Arguments

data

list, score_metagene() raw data output

title

Output plot title

xaxis

Output plot x-axis title

yaxis

Output plot y-axis title

linecol

Colour for line, auto="red"

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

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

plot_metagene(hypo_metagene)