Skip to contents

Draws a scores or loadings plot or performs calculations necessary to draw them manually

Source: R/plot.R
plot_pca.Rd

Performs PCA and creates a Scores or Loadings plot. Basically a wrapper around pcaMethods::pca The plot is drawn with ggplot2 and can therefore be easily manipulated afterwards (e.g., changing the theme or the axis labels). Please note that the function is intended to be easy to use and beginner friendly and therefore offers limited ability to fine-tune certain parameters of the resulting plot. If you wish to draw the plot yourself, you can set return_tbl = TRUE. In this case, a tibble is returned instead of a ggplot2 object which you can use to create a plot yourself.

Important Note

plot_pca() depends on the pcaMethods package from Bioconductor. If metamorphr was installed via install.packages(), dependencies from Bioconductor were not automatically installed. When plot_pca() is called without the pcaMethods package installed, you should be asked if you want to install pak and pcaMethods. If you want to use plot_pca() you have to install those. In case you run into trouble with the automatic installation, please install pcaMethods manually. See pcaMethods – a Bioconductor package providing PCA methods for incomplete data for instructions on manual installation.

Usage

plot_pca(
  data,
  method = "svd",
  what = "scores",
  n_pcs = 2,
  pcs = c(1, 2),
  center = TRUE,
  group_column = NULL,
  name_column = NULL,
  return_tbl = FALSE,
  verbose = FALSE
)

Arguments

data

A tidy tibble created by read_featuretable.

method

A character specifying one of the available methods ("svd", "nipals", "rnipals", "bpca", "ppca", "svdImpute", "robustPca", "nlpca", "llsImpute", "llsImputeAll"). If the default is used ("svd") an SVD PCA will be done, in case data does not contain missing values, or a NIPALS PCA if data does contain missing values.

what

Specifies what should be returned. Either "scores" or "loadings".

n_pcs

The number of PCs to calculate.

pcs

A vector containing 2 integers that specifies the PCs to plot. Only relevant if return_tbl = FALSE. The following condition applies: max(pcs) <= n_pcs.

center

Should data be mean centered? See prep for details.

group_column

Either NULL or a column in data (e.g., group_column = Group). If provided, the dots in the scores plot will be colored according to their group. Only relevant if what = "scores".

name_column

Either NULL or a column in data (e.g., name_column = Feature). If provided, feature names are preserved in the resulting tibble. Only relevant if what = "loadings" & return_tbl = TRUE.

return_tbl

A logical. If FALSE, returns a ggplot2 object, if TRUE returns a tibble which can be used to draw the plot manually to have more control.

verbose

Should outputs from pca be printed to the console?

Value

Either a Scores or Loadings Plot in the form of a ggplot2 object or a tibble.

Examples

# Draw a Scores Plot
toy_metaboscape %>%
  impute_lod() %>%
  join_metadata(toy_metaboscape_metadata) %>%
  plot_pca(what = "scores", group_column = Group)


# Draw a Loadings Plot
toy_metaboscape %>%
  impute_lod() %>%
  join_metadata(toy_metaboscape_metadata) %>%
  plot_pca(what = "loadings", name_column = Feature)