pav_stackbar: pav_stackbar

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

Description

The composition of genes in all samples can be viewed in 'pav_stackbar()'. The chart consists of a hierarchical cluster tree and a bar plot.

Usage

pav_stackbar(
  pav_obj,
  show_relative = F,
  add_phen_info = NULL,
  type_colors = NULL,
  phen_info_color_list = NULL,
  cluster_distance = "euclidean",
  cluster_method = "complete",
  bar_width = 1,
  sample_name_size = 4,
  legend_side = "right",
  legend_title = "Gene",
  legend_title_size = NULL,
  legend_text_size = NULL,
  dend_width = 0.05,
  name_width = 0.1
)

Arguments

pav_obj	A PAV object.
show_relative	A logical value indicating whether show relative value.
add_phen_info	A character string of 'phen_info' names.
type_colors	A named vector of colors for types. e.g. c("distributed" = "red")
phen_info_color_list	A list contains named vector of colors for 'phen_info' annotation. e.g. list(gender = c("Male" = "green", "Female" = "red"))
cluster_distance	Method to measure distance, pass to dist.
cluster_method	Method to perform hierarchical clustering, pass to hclust.
bar_width	A numeric vector giving the relative width of bars, ranging from 0 to 1.
sample_name_size	The size of sample names.
legend_side	The position of legend ("top", "bottom", "right", "left").
legend_title	The text for the legend title.
legend_title_size	The size of legend title.
legend_text_size	The size of legend item labels.
dend_width	The relative width of dendrogram, ranging from 0 to 1.
name_width	The relative width of sample names, ranging from 0 to 1.

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