createFLT: Create cells' FLT
In vicstefanou/ViSCA: Cell-Movie Analysis and Visualization

Description Usage Arguments Details Value See Also

Creates the cells' Forest of Lineage Trees (FLT) given a list containing all the cell instants of the movie.

1	createFLT(cell_list, Ncols)

`cell_list`	A list containing all the cell instants of the movie.
`Ncols`	Number of colonies in the movie, a non-zero positive integer value.

Apart from the cell instants of the movie contained in the cell_list, FLT nodes include an imaginary main root cell as well as imaginary root cells for each colony. Colonies' root cells are daughters of the main root cell. Cell instants of the first frame of the movie are daughters of the corresponding colony's root cell. The imaginary root cells are used to facilitate the tree representation of the movie and the colony tracking and are automatically excluded from the analysis.

Each node of the FLT has as attributes all numeric and boolean values existing as components in the corresponding element of the cell_list. The imaginary root cells have value -1 in all numeric attributes and value FALSE in all boolean attributes. The following character string values also form attributes of each FLT node:

"name" is the label of the cell in the FLT, a non-zero positive integer number stored as a character string. Value "1" corresponds to the main root cell. Values "1+<i>" correspond to the colonies' root cells, where "<i>" is the colony ID. The rest values correspond to the cell instants in the cell_list (1-1 correspondence).
"cellName", as in the cell_list. Value "root" is used for the main root cell. Values "colony<i>" are used for the colonies' root cells, where "<i>" is the colony ID.
"colId", as in the cell_list, but here stored as a character string. Value "-1" is used for the imaginary root cells.

NOTE: This attribute is stored iff it exists as component in the elements of the cell_list.

A named list with the following components:

`LTmain`	The main part of the overall FLT, a connected lineage tree containing the imaginary root cells (object of class `"igraph"`). Attribute `"colony"` in the `LTmain` depicts the starting colony of each cell instant (i.e. the colony of the corresponding colony's root cell from which a cell instant emanated). This approach is necessary in order to keep track of merging colonies.
`branches`	A list with the motherless branches of the overall FLT. Each branch (element of the list) is a connected lineage tree (object of class `"igraph"`). Motherless branches arise from tracking errors, in case a cell instant (root of the branch) fails to be connected to any cell instant of the previous frame, or when a cell instant (root of the branch) just entered the field of view.