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Plot PCA by group

Source: R/plot_pca_by_group.R
plot_pca_by_group.Rd

Plot PCA for each group separately, with optional circles around time points and arrows indicating trajectory over time. Accepts either a SummarizedExperiment object or a list of them (from split_groups()).

Usage

plot_pca_by_group(
  se_obj,
  circle = TRUE,
  arrow = TRUE,
  pc1 = 1,
  pc2 = 2,
  nrow = 1,
  fontsize = 8,
  assay = 1,
  legend_pos = "right"
)

Arguments

se_obj

A SummarizedExperiment object, or a named list of them (e.g. from split_groups()).

circle

Logical, whether to draw ellipses around samples of each time point (default: TRUE).

arrow

Logical, whether to draw arrows indicating the trajectory over time (default: TRUE).

pc1

Principal component for the x-axis (default: 1).

pc2

Principal component for the y-axis (default: 2).

nrow

Number of rows for arranging the plots (default: 1).

fontsize

Base font size (default: 8).

assay

Assay index to use, where 1 is the original data and 2 is normalised to time 0 (if available) (default: 1).

legend_pos

Legend position (default: "right").

Value

A series of PCA plots showing the distribution of samples in each group, coloured by Time.

Examples

data(example_obj)
plot_pca_by_group(example_obj, circle = TRUE, arrow = TRUE)
#> Warning: Using size for a discrete variable is not advised.
#> Warning: Using size for a discrete variable is not advised.
#> Warning: Using size for a discrete variable is not advised.
#> Warning: Using size for a discrete variable is not advised.


# Also accepts a list from split_groups()
example_obj_list <- split_groups(example_obj)
plot_pca_by_group(example_obj_list)
#> Warning: Using size for a discrete variable is not advised.
#> Warning: Using size for a discrete variable is not advised.
#> Warning: Using size for a discrete variable is not advised.
#> Warning: Using size for a discrete variable is not advised.