This can also perform dimensionality reduction of

The projected expression state with RNA velocity, only if

`dimred`

is a function and`pair_with_velocity=TRUE`

The trajectory, by projecting the milestones and some "waypoints" to the reduced space, only if

`dataset`

contains a trajectory

```
add_dimred(
dataset,
dimred,
dimred_milestones = NULL,
dimred_segment_progressions = NULL,
dimred_segment_points = NULL,
project_trajectory = TRUE,
connect_segments = FALSE,
pair_with_velocity = !is.null(dataset$expression_future),
expression_source = "expression",
...
)
```is_wrapper_with_dimred(dataset)

get_dimred(
dataset,
dimred = NULL,
expression_source = "expression",
return_other_dimreds = FALSE
)

dataset

A dataset created by `wrap_data()`

or `wrap_expression()`

dimred

Can be

A function which will perform the dimensionality reduction, see

`dyndimred::list_dimred_methods()`

A matrix with the dimensionality reduction, with cells in rows and dimensions (

*comp_1*,*comp_2*, ...) in columns

dimred_milestones

An optional dimensionality reduction of the milestones. A matrix with milestones in rows and components (*comp_1*, *comp_2*, ...) in columns

This will be automatically calculated if `project_trajectory = TRUE`

dimred_segment_progressions, dimred_segment_points

An optional set of points along the trajectory with their dimensionality reduction. `dimred_segment_progressions`

is a dataframe containing the *from* and *to* milestones, and their *progression*. `dimred_segment_points`

is a matrix with points (the same number as in `dimred_segment_progressions`

) in rows and components (*comp_1*, *comp_2*, ...) in columns. Both objects have the same number of rows.

These will be automatically calculated if `project_trajectory = TRUE`

project_trajectory

Whether to also project the trajectory. Only relevant if dataset contains a trajectory, and dimred_segment_progressions and dimred_segment_points are not provided

connect_segments

Whether to connect segments between edges

pair_with_velocity

Can perform dimensionality reduction if `dimred`

is a function.

expression_source

The source of expression, can be "counts", "expression", an expression matrix, or another dataset which contains expression

...

extra information to be stored in the wrapper

return_other_dimreds

Whether or not to return also the milestone dimreds and the segment dimreds, if available.

A dataset object with *dimred*, which is a numeric matrix with cells in rows and the different components in columns.

If the dataset contained a trajectory, and

`project_trajectory=TRUE`

(default),*dimred_milestones*,*dimred_segment_progressions*and*dimred_segment_points*will also be present. These are described in`project_trajectory()`

.

`dyndimred::list_dimred_methods()`

, `project_trajectory()`

```
# NOT RUN {
if (requireNamespace("dyndimred", quietly = TRUE)) {
dataset <- example_dataset
dataset <- add_dimred(
dataset,
dyndimred::dimred_landmark_mds
)
head(dataset$dimred)
}
# }
```

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