Custom Visualizing ROH

This function is designed to custom visualizing ROH. It support to plot ROH by Chromosome, Interested region, Single sample, Target gene, and combine ROH plot with Gene annotation plot. It also support users to customize the color and size of final graph.

roh_visual(
  clean_roh,
  max_chr = NULL,
  chr_id = NULL,
  chr_length = NULL,
  start_position = NULL,
  end_position = NULL,
  individual_id = NULL,
  refgene = NULL,
  target_region = c(0, 160),
  plot_title = NULL,
  report_id = NULL,
  pedigree = NULL,
  show_name = c(0, 160),
  width_1 = 13,
  height_1 = 10,
  col_short = "deepskyblue",
  col_mid = "black",
  col_long = "deeppink2",
  folder = "roh_visual",
  gene_font_size = 2.2
)

Arguments

clean_roh

support roh results from Plink or generated by cnv_clean form CNVPartition results
max_chr

the maximum number of chromosomes to plot, it used for plot all chromosomes at once
chr_id

the number of chromosome want to plot, integer type, such as '1' indicate the Chromosome 1.
chr_length

set the length for the chromosome, unnecessary at the moment.
start_position

decimal digit, default unit in 'Mb'. such as 23.2112
end_position

decimal digit, default unit in 'Mb'. such as 23.2112
individual_id

sample ID, which used to plot ROH by interested Samples.
refgene

if true, will plot gene above roh plot
target_region

plot target region by setting given interval in 'c(value1, value2)'.
plot_title

add title in the plot
report_id

report the sample ID while plotting
pedigree

pedigree list, require at least three columns, Sample_Id, Sire and Dam
show_name

default value is show_name = c(0, 160). accept the vectors only, unit is Mb. for example show_name = c(11.2, 12.4, 15.3, 18.4), means only plot the genes within the given interval
width_1

number to set the width of final plot size, unit is 'cm'
height_1

number to set the height of final plot size, unit is 'cm'
col_short

set color to shorter length of roh in distribution plot
col_mid

set color to middle length of roh in distribution plot
col_long

set color to longer length of roh in distribution plot
folder

set new folder to save results
gene_font_size

set the font size of gene in ROH annotation plot

Value

ROH distribution plot