aggregateTrackedCells: Aggregate trackedCells Objects

In ocbe-uio/cellmigRation: Track Cells, Analyze Cell Trajectories and Compute Migration Statistics

Description

Aggregate two or more trackedCells-class objects together. Input objects must carry information of cell tracks (otherwise an error will be raised). All tracks form the different experiments/images are returned in a large data.frame. A new unique ID is assigned to specifically identify each cell track from each image/experiment.

Usage

aggregateTrackedCells(
  x,
  ...,
  meta_id_field = c("tiff_file", "experiment", "condition", "replicate")
)

Arguments

x	a trackedCells-class object where cells have already been tracked
...	one or more trackedCells-class object(s) where cells have already been tracked
meta_id_field	string, can take one of the following values, c("tiff_file", "experiment", "condition", "replicate"). Indicates the meta-data column used as unique ID for the image/experiment. Can be abbreviated. Defaults to "tiff_file".

Details

each trackedCells-class object passed to this function requires a unique identifier (such as a unique tiff_file name). Any of the metadata columns can be used as unique ID for an image/experiment. The function will raise an error if non-unique identifiers are found across the input objects.

Value

An aggregate data.frame including all cells that were tracked over two or more images/experiments. The data.frame includes the following columns: "new.ID", "frame.ID", "X", "Y", "cell.ID", "tiff_name", "experiment", "condition", "replicate". The "new.ID" uniquely identifies a cell in a given image/experiment.

Author(s)

Damiano Fantini, [e-mail]

References

https://www.data-pulse.com/dev_site/cellmigration/

Examples

# Please, see the package vignette
# for an example of how to use this function.
# A pseudo-code example is shown below
# Let x0, x1, x2, ... be trackedCells-class objects
# with a non-empty tracks slot.
x0 <- get(data(TrackCellsDataset))
x0 <- setCellsMeta(x0, experiment = "my_exp_01", condition = "CTRL")
x1 <- setCellsMeta(x0, experiment = "my_exp_01", condition = "DMSO")
x2 <- setCellsMeta(x0, experiment = "my_exp_01", condition = "DRUG")
y <- aggregateTrackedCells(x0, x1, x2, meta_id_field = "condition")
utils::head(y, 50)

ocbe-uio/cellmigRation documentation built on Dec. 16, 2021, 10:59 p.m.