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Plot PCA by group (list of objects)

Source: R/plot_pca_by_group.R
plot_pca_by_group_list.Rd

Plot PCA by group, input is a list of SummarizedExperiment objects, with each object corresponding to a group

Usage

plot_pca_by_group_list(
  se_obj_list,
  circle = TRUE,
  arrow = TRUE,
  nrow = 1,
  fontsize = 8,
  assay = 1
)

Arguments

se_obj_list

A list of SummarizedExperiment objects, such as output of split_groups()

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")
example_obj_list <- split_groups(example_obj)
plot_pca_by_group_list(example_obj_list)
#> 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()`).