Plots for Principal Component Analysis (PCA)

Visualization for glystats::gly_pca() results (glystats_pca_res object). Possible types of plots:

• "screeplot": Scree plot to see the contribution of each PC.

• "individual" (default): Plot samples as individuals.

• "variables": Plot loadings for variables.

• "biplot": Biplot showing both samples and variables.

Usage

# S3 method for class 'glystats_pca_res'
autoplot(object, type = "individual", groups = NULL, group_col = NULL, ...)

Arguments

object

A glystats_pca_res object.

type

The type of plot, one of "screeplot", "individual", "variables", or "biplot".

groups

A factor or character vector specifying group membership for each sample. If provided, the plot will be colored by group. Only applicable to "individual" and "biplot" types. Passed to the habillage paramter of factoextra::fviz_pca_ind() or factoextra::fviz_pca_biplot().

group_col

A character string specifying where to find the group information. If you uses glystats::gly_pca() on a glyexp::experiment() to get the result, sample information has already been added to the result. In this case, you can specify the column name in the sample information tibble to be used for coloring. If not provided, this function will try "group".

...

Other arguments passed to factoextra functions.

• For "screeplot", see factoextra::fviz_screeplot().

• For "individual", see factoextra::fviz_pca_ind().

• For "variables", see factoextra::fviz_pca_var().

• For "biplot", see factoextra::fviz_pca_biplot().

Value

A ggplot object.

See also

factoextra::fviz_screeplot(), factoextra::fviz_pca_ind(), factoextra::fviz_pca_var(), factoextra::fviz_pca_biplot()