cov_density: cov_density

In SJTU-CGM/vPanG: An R package to analyze and visualize PAV results from pan-genome of "map-to-pan" strategy.

Description

cov_density

Usage

cov_density(
  cov_obj,
  genes,
  add_gene_info = NULL,
  density_color = "#F8766D",
  scale = 2,
  show_row_names = T,
  row_names_side = "left",
  row_names_size = 10,
  row_names_rot = 0,
  gene_info_color_list = NULL,
  gene_info_side = "right",
  anno_param_row_gene = list(show = T, width = 5, border = FALSE, name_size = NULL,
    name_rot = 90, name_side = "bottom"),
  legend_side = "right",
  legend_title_size = NULL,
  legend_text_size = NULL,
  legend_grid_size = grid::unit(4, "mm")
)

Arguments

cov_obj	A COV object.
genes	A vector of genes.
add_gene_info	A character vector of 'gene_info' names.
density_color	A string of color for density chart.
scale	A number indicating relative height of density distribution.
show_row_names	A logical value indicating whether show row names.
row_names_side	The position of row names ("left", "right").
row_names_size	The size of row names.
row_names_rot	The rotation of row names.
gene_info_color_list	A list contains colors for 'gene_info' annotation. e.g. list(source = c("reference" = "red", "novel" = "blue"), length = c("orange", "red"))
gene_info_side	The position of 'gene_info' annotation ("left" and "right").
anno_param_row_gene	A list contains parameters for the gene annotation. These can be any of the following: "show", "width", "border", "name_size", "name_rot" and "name_side".
legend_side	The position of legend ("top", "bottom", "right", "left").
legend_title_size	The size of legend title.
legend_text_size	The size of legend item labels.
legend_grid_size	A unit object for the size of legend grid.
legend_title	The text for the legend title.

SJTU-CGM/vPanG documentation built on Dec. 18, 2021, 11:59 a.m.