label_milestones {dynwrap} R Documentation

## Label milestones either manually (label_milestones) or using marker genes (label_milestones_markers)

### Description

label_milestones can be used to manually assign labels to a milestone using their identifiers

### Usage

label_milestones(trajectory, labelling)

label_milestones_markers(
trajectory,
markers,
expression_source = "expression",
n_nearest_cells = 20
)

is_wrapper_with_milestone_labelling(trajectory)

get_milestone_labelling(trajectory, label_milestones = NULL)


### Arguments

 trajectory The trajectory as created by infer_trajectory() or add_trajectory() labelling Named character vector containing for a milestone a new label markers List containing for each label a list of marker genes expression_source The expression source n_nearest_cells The number of nearest cells to use for extracting milestone expression label_milestones How to label the milestones. Can be TRUE (in which case the labels within the trajectory will be used), "all" (in which case both given labels and milestone_ids will be used), a named character vector, or FALSE

### Details

label_milestones_markers will assign a label to a milestone if its marker profile most closely resembles a given profile

### Value

label_milestones: A trajectory object with milestone_labelling, a named vector where milestone identifiers are mapped to their labels

get_milestone_labelling: A named vector giving a mapping between milestones and their labels. If certain milestones were not given a label, this vector will give the identifiers themselves.

### Examples

trajectory <- example_trajectory

# manual labelling
trajectory <- label_milestones(
trajectory,
labelling = c("milestone_begin" = "Let's go")
)
get_milestone_labelling(trajectory)

# marker gene labelling
trajectory <- label_milestones_markers(
trajectory,
markers = list(A_high = "A")
)
get_milestone_labelling(trajectory)

is_wrapper_with_milestone_labelling(trajectory)



[Package dynwrap version 1.2.2 Index]