merge_cells: Merge two cells
In vicstefanou/ViSCA: Cell-Movie Analysis and Visualization

Description Usage Arguments Details Value Prerequisites See Also

Merges two cells from the same or different lineage trees.

1 2	merge_cells(LT1, LT2 = NULL, cell1, cell2, cell_list, col_list, Ncols, pixelR, matFolder, matFileName, exeFolder, mcrFolder, show = TRUE)

`LT1`	The lineage tree where the cell specified in `cell1` belongs, an object of class `"igraph"`.
`LT2`	The lineage tree where the cell specified in `cell12` belongs, an object of class `"igraph"`. When the default value `NULL` is used, `cell2` belongs to the `LT`.
`cell1`	The label of the first cell in the `LT1` to be merged, a character string. It can be any non-root cell, as returned from `get_cells`.
`cell2`	The label of the second cell in the `LT2` (or `LT1` in case `LT2 = NULL`) to be merged, a character string. It can be any valid candidate merge cell, as returned from `get_cand_merge_cells`.
`cell_list`	A list containing all the cell instants of the movie.
`col_list`	A list containing all the colony instants of the movie.
`Ncols`	Number of colonies in the movie, a non-zero positive integer value.
`pixelR`	The pixel ratio in units of length, a non-zero positive numeric value.
`matFolder`	A character string naming the absolute path of the directory where the `.mat` file generated by BaSCA is saved (excluding the last `"/"`). The default value is the current working directory `getwd()`. NOTE: The components should be separated by `"/"` on Windows.
`matFileName`	A character string naming the `.mat` file generated by BaSCA (including the suffix `".mat"`). The filename is relative to the `matFolder`.
`exeFolder`	A character string naming the absolute path of the installation folder of the MATLAB executable (excluding the last `"/"`). NOTE: The components should be separated by `"/"` on Windows.
`mcrFolder`	A character string naming the absolute path of the installation folder of the Matlab Compiler Runtime (MCR) (excluding the last `"/"`). NOTE: The components should be separated by `"/"` on Windows.
`show`	A logical value (`TRUE` or `FALSE`) indicating whether `view_cell` will be called for `cell1` and `cell2` before the merge operation and the resulting cell after the merge operation. This capability is useful in order to see the result of the function. The default value is `TRUE`.

After the merge operation, cell1 is replaced in both LT1 and cell_list by the resulting cell. Daughter branches of cell2 are extracted from LT2 (or LT1 in case LT2 = NULL), with successive calls of extract_branch. These motherless branches (lineage trees) are added as daughter branches to cell1, with successive calls of add_branch, until cell1 has two daughters. Finally, cell2 is deleted from LT2 (or LT1 in case LT2 = NULL) with extract_branch.

A named list with the following components:

`LT1`	The updated LT1 with `cell1` replaced and the possible daughter branches added/replaced, an object of class `"igraph"`.
`LT2`	The updated LT2 with `cell2` and its daughter branches deleted, an object of class `"igraph"`. `NULL` is returned in case LT2 was anywise `NULL` or if it ended up with no cells.
`cell_list`	The updated cell_list with `cell1` replaced.
`branches`	A list with the remaining motherless branches. Each branch (element of the list) is an object of class `"igraph"`.