Methylation path on chosen gene.

Function plot_methylation_path visualizes a chosen gene with marked CpG probes. Y axis describes methylation level. X axis describes a location of the probe on the chromosome. Horizontal lines show the mean methylation level for each Island in a division to groups. Groups are defined by colors. Large dots symbolize means of methylation level for CpG probes, small dots symbolize methylation levels for each observation. Also, we can exact the line corresponding to a gene. In this case, we see what are the locations of probes on a gene in HG18 coordinates. We can as well draw locations of CpG islands.

plot_methylation_path(data, condition, gene, show.gene = FALSE,
  observ = FALSE, islands = TRUE, title = TRUE, genom.data = NULL,
  mean.size = 4, observ.size = 0.5, ...)

Arguments

data	Data frame containing values from methylation: columns corespond to CpG probes, rows to samples.
condition	Vector of levels corresponding to order of samples in data.
gene	Name of chosen gene.
show.gene	Logical. If TRUE arrows corresopnding to gene will be drawn.
observ	Logical. If TRUE dots corresponding to CpG probes will be drawn.
islands	Logical. If TRUE line corresopnding to islands should be drawn.
title	Logical. If TRUE title saying what gene we visualise will be added.
genom.data	Data frame which contains information about CpG probes and corresponding genes, by default in our package we use illumina_humanmethylation_27_data. New dataset should contain 5 columns with: 1) CpG probe names, 2) CpG probe locations, 3) gene names, 4) logical value if there is a CpG island, 5) location of island.
mean.size	size of mean dots
observ.size	size of observation dots
...	Other parameters.

Value

Object of class ggplot containing visualisation of methylation on gene.

See also

plot_gene

Examples

# NOT RUN {
library(MLExpRessoData)
condition_met <- ifelse(BRCA_met$SUBTYPE == "LumA","LumA", "other")
plot_methylation_path(BRCA_met, condition_met, "BRCA2")
# }