plot_gene: Custom plotting gene from reference gene list

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

Description

The function is used for plotting gene from reference gene list, the standard reference gene lists was generated by 'get_refgene' function in HandyCNV.

Usage

plot_gene(
  refgene = NULL,
  chr_id,
  start,
  end,
  show_name = c(0, 160),
  cnv = NULL,
  height_1 = 2,
  width_1 = 10,
  col_gene = "gray",
  gene_font_size = 2.5
)

Arguments

refgene	reference gene list. Standard input file was generated by 'get_refgene' function.
chr_id	chromosome ID, should be the integer type only, such as 1 indicates Chromosome 1.
start	the start physical position used in the plot, the unit is Mb.
end	the end physical position used in plot, unit in Mb.
show_name	the default value of show_name = c(0, 160). accept the vectors only, unit in Mb. for example show_name = c(11.2, 12.4, 15.3, 18.4), means only plot the genes within the given interval
cnv	is support for both CNV and ROH, set cnv argument as TRUE will plot gene for CNV, otherwise will plot gene for ROH interval 11.2-12.4 Mb and 15.3-18.4 Mb, the maximum pairs of intervals are three.
height_1	set height of gene plot.
width_1	set width of gene plot.
col_gene	set the color of Gene, only work when the 'cnv' argument was set as 'TRUE'.
gene_font_size	set the size of gene font

Value

gene plot with given interval

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