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Get Principal components analysis.

getPCA.Rd

Given a table containing data, it performs the Principal components analysis.

Usage

getPCA(
  df,
  v,
  s = NULL,
  f = NULL,
  dfv = NULL,
  sv = NULL,
  fv = NULL,
  labels_on_loading = TRUE,
  col_pal = NULL,
  col_pal_fv = NULL,
  PC_to_plot = c("PC1", "PC2"),
  ellipses_on_score = TRUE,
  ellipses_on_loading = FALSE
)

Arguments

df

dataframe. Containing data to plot.

v

character. The names of the columns of df containing numerical data (ideally, they should be already centered and scaled!!).

s

NULL or a character of length 1. The name of the column of df containing the sample names. Pass it only if you want sample names on the score plot.

f

NULL or character of length 1. The name of the column of df containing the factor variable. Pass it only if you want colored points and ellipses on the score plot.

dfv

NULL or a dataframe. The first column must contain v. To this dataframe the lodgings table will be added.

sv

NULL or character. The name of the column of dfv containing the names you want to put on the loading plot. Pass it only if you want those names on the loading plot.

fv

NULL or character. The name of the column of dfv containing the factor variable. Pass it only if you want colored points and ellipses on the loading plot.

labels_on_loading

logical. Even if dfv and/or sv are NULL, if this argument is set to TRUE, the loading plot will report v as labels.

col_pal

a character vector containing colors for f. If NULL, colors from the pals package will be used (see function build_long_vector_of_colors).

col_pal_fv

a character vector containing colors for fv. If NULL, colors from the pals package will be used (see function build_long_vector_of_colors).

PC_to_plot

character of length 2. The principal components to plots on the score and loading plots.

ellipses_on_score

logical. If you specified f and this is TRUE, ellipses will be added to the score plot.

ellipses_on_loading

logical. If you specified fv and this is TRUE, ellipses will be added to the score plot.

Value

A list with 4 objects:

  • df_with_scores_table: the df with additional columns containing the scores.

  • dfv_with_loadings_table: the dfv with additional columns containing containing the loadings.

  • score_plot: a ggplot object with the score plot.

  • loading_plot: a ggplot object with the loading plot.