ggplot_pca: Ggplot a qb_pca object

In ThomasChln/snpclust: SNP Feature Summarization for Unsupervised Clustering

Description

Ggplot a qb_pca object

Usage

ggplot_pca(
  pca,
  group = NULL,
  axes = c(1, 2),
  obs = TRUE,
  obs_sup = FALSE,
  vars = FALSE,
  vars_sup = FALSE,
  pc_variance = TRUE,
  ellipses = FALSE,
  label = NULL,
  link = FALSE,
  alpha_fill = FALSE,
  ellipses_ci = 0.95,
  nas_first = TRUE,
  ...
)

Arguments

pca	pca or qb_pca object (which is fortified)
group	Column index or name of qb_pca$data for the grouping of observations. Default: NULL
axes	Two principal component axes to plot. Default: 1:2
obs	Character identifiers of active observations to use. If TRUE no subset. If FALSE none are used. Default: TRUE
obs_sup	Character identifiers of suppl. observations to use. If TRUE no subset. If FALSE none are used. Default: FALSE
vars	Character identifiers of active variables to use. If TRUE no subset. If FALSE none are used. Default: FALSE
vars_sup	Character identifiers of suppl. variables to use. If TRUE no subset. If FALSE none are used. Default: FALSE
pc_variance	Logical, displays the variance ratio along the axis names
ellipses	Should ellipses be plotted ? Not used if groups is NULL. Default: FALSE
label	name of column to be used for labelling observation. Can be a supplementary variable or "PCx". By default (NULL), no labels are shown.
link	if TRUE a line is drawn between the observations of the same group. This is useful to identify linked observations
alpha_fill	Logical, should also use alpha to discriminate active and additional observations ? Default: FALSE
ellipses_ci	Confidence interval ratio of the ellipses. Not used if ellipses is FALSE. Default: .95
nas_first	Logical, rearranges data frame to put NAs in groups first
...	Passed to draw_pca_vars

Value

ggplot object

Author(s)

tcharlon

ThomasChln/snpclust documentation built on June 11, 2020, 4:27 p.m.