Plot PCA by group (one object)

Plot PCA for each group separately, with optional circles around time points and arrows indicating trajectory over time.

Usage

plot_pca_by_group(
  se_obj,
  circle = TRUE,
  arrow = TRUE,
  nrow = 1,
  fontsize = 8,
  assay = 1
)

Arguments

se_obj

A SummarizedExperiment object created by create_input()

circle

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

arrow

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

nrow

Number of rows for arranging the PCA plots (default is 1)

fontsize

Font size for the PCA plots (default is 8)

assay

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

Value

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

Examples

data("example")
plot_pca_by_group(example_obj, circle = TRUE, arrow = TRUE)
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_segment()`).