cnv_visual: Custom visualizing CNV

In JH-Zhou/HandyCNV: HandyCNV: An R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH

Description

This function is designed to custom plot CNVs, it now support to visualize CNVs by Chromosome, Interested Individual, Interested Region, Target Gene, et al.

Usage

cnv_visual(
  clean_cnv,
  max_chr = NULL,
  chr_id = NULL,
  species = NULL,
  start_position = NULL,
  end_position = NULL,
  individual_id = NULL,
  target_gene = NULL,
  max_chr_length = 160,
  refgene = NULL,
  plot_title = NULL,
  report_id = NULL,
  pedigree = NULL,
  show_name = c(0, 160),
  width_1 = 13,
  height_1 = 10,
  folder = "cnv_visual",
  col_0 = "hotpink",
  col_1 = "turquoise",
  col_2 = "gray",
  col_3 = "tomato",
  col_4 = "deepskyblue",
  col_gene = "gray",
  gene_font_size = 2.2
)

Arguments

clean_cnv	cnv list file, standard file was generated by 'cnv_clean' function
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
species	which species in the input data, unused at the moment
start_position	decimal digit, default unit is 'Mb'. such as 23.2112
end_position	decimal digit, default unit is 'Mb'. such as 23.2112
individual_id	the ID of individual in cnv list, used to plot all chromosome for specific Individual
target_gene	the
max_chr_length	the maximum length of chromosome, default unit is 'Mb'
refgene	if true, will plot gene above the CNV plot, need to combine with the clean_cnv, and the stardard clean_cnv file need the annotated cnv list which was generated from call_gene function, internal reference gene-list are "ARS_ens", "ARS_UCSC" and "UMD_UCSC". Or provide the reference genes list corresponding to your data
plot_title	set the title of final 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'
folder	set the name of folder to save results
col_0	set color for 0 copy of CNV
col_1	set color for 1 copy of CNV
col_2	set color for 2 copy of CNV (which might be ROH)
col_3	set color for 3 copy of CNV
col_4	set color for 4 copy of CNV
col_gene	set the color of Gene, only work in Gene annotated at CNV plot
gene_font_size	set the size of Gene in CNV Annotation plot

Value

CNV distribution plot

JH-Zhou/HandyCNV documentation built on Dec. 18, 2021, 12:25 a.m.