Plot DMR region

Visualizing DMR region by plotting methylation rate within two probes

draw_methylation(data, chromosom, start, end, bind.probes = T,
  smooth.methylation = T, size.x.dot = 15, size.y.dot = 9,
  plot.title = 26, axis.title.x = 23, axis.title.y = 23,
  legend.position = "right", axis.text.x = 20, axis.text.y = 20,
  legend.text = 16, legend.title = 18)

Arguments

data	There are two options: 1. dataframe with specific columns: chr, poz, prob, no, meth, unmeth, meth.rate. This dataframe is result of function preprocessing. 2. dataframe with specific columns: chr, poz, prob, no, meth, unmeth, meth.rate, tiles and possible tiles.common columns. This dataframe is result of function create.tiles.min.gap or create.tiles.fixed.length.
start	minimum position of region that are being plotted
end	maximum position of region that are being plotted
bind.probes	if TRUE methylation rates on the same position will be binded by vertical lines
smooth.methylation	if TRUE methylation rates in two probes will be smoothed
chr	chromosome name of region that are being plotted

Value

ggplot object with visualization of regions

Examples

data('schizophrenia')
control <- schizophrenia %>% filter(category == 'control') %>%
dplyr::select(-category)

disease <- schizophrenia %>% filter(category == 'disease') %>%
 dplyr::select(-category)

data <- preprocessing(control, disease)
draw_methylation(data, chr = 'chr1', start = 80000, end = 95000)

#without binding lines and smoothing
draw_methylation(data, chr = 'chr1', start = 80000, end = 95000,
bind.probes = F, smooth.methylation = F)

# with changing some ggplot2 arguments:
draw_methylation(data, chr = 'chr1', start = 80000, end = 95000, legend.title = 20,
legend.position = 'bottom', plot.title = 28, size.x.dot = 10, size.y.dot = 4)