pav_pca: pav_pca

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

Description

pav_pca

Usage

pav_pca(
  pav_obj,
  center = T,
  scale = F,
  rank = NULL,
  add_phen_info = NULL,
  phen_info_color_list = NULL,
  axis_text_size = NULL,
  axis_title_size = NULL,
  legend_side = "right",
  legend_text_size = NULL,
  legend_title_size = NULL
)

Arguments

pav_obj	A PAV object.
center	A logical value indicating whether the variables should be shifted to be zero centered, pass to prcomp.
scale	A logical value indicating whether the variables should be scaled to have unit variance before the analysis takes place, pass to prcomp.
rank	A number specifying the maximal rank, pass to prcomp.
add_phen_info	A character string of 'phen_info' names.
phen_info_color_list	A list contains named vector of colors for 'phen_info' annotation. e.g. list(gender = c("Male" = "green", "Female" = "red"))
axis_text_size	The size of tick labels on axis.
axis_title_size	The size of axis title.
legend_side	The position of legend ("top", "bottom", "right", "left").
legend_text_size	The size of legend item labels.
legend_title_size	The size of legend title.

xiaonui/vPan documentation built on Dec. 23, 2021, 6:17 p.m.