plot_Ncells: Plot cell counts
In vicstefanou/ViSCA: Cell-Movie Analysis and Visualization

Description Usage Arguments Details Value

Calculates and plots the number of cells (cell counts) in a lineage or division tree. Cell counts can be plotted for each colony, generation or frame.

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plot_Ncells(tree, treeT = c("LT", "DT"), grouped = c("col", "gen", "frame"),
  groups = -1, Ngroups, save = FALSE, savePars = list(w = 4000, h = 2000,
  res = 250, path = getwd(), name = "my_Ncells"))

`tree`	The lineage or division tree, an object of class `"igraph"`.
`treeT`	A character string naming the type of `tree`: `"LT"` if `tree` is a lineage tree `"DT"` if `tree` is a division tree
`grouped`	A character string naming the grouping method: `"col"` for grouping by colony `"gen"` for grouping by generation `"frame"` for grouping by frame, which is acceptable in case `treeT = "LT"`.
`groups`	The IDs of the groups for which to plot the cell counts, a vector of positive integer values. The default value `-1` stands for all existing groups in the `tree`.
`Ngroups`	Number of colonies in the movie (if `grouped = "col"`) or number of generations in the movie (if `grouped = "gen"`) or number of frames in the movie (if `grouped = "frame"`), a non-zero positive integer value.
`save`	A logical value (`TRUE` or `FALSE`) indicating whether the generated plot will be saved in a `.png` file or displayed in the Plots Pane of RStudio, respectively. The default value is `FALSE`.
`savePars`	A named list specifying the parameters of the generated image file. This argument is ignored in case `save = FALSE`. Elements of the list are the following: `w` The width of the image file in pixels, a non-zero positive integer value. The default value is `4000`. `h` The height of the image file in pixels, a non-zero positive integer value. The default value is `2000`. `res` The resolution of the image file in pixels per inch (ppi), a non-zero positive integer value. The smaller this value, the larger the plot area in inches, and the smaller the text relative to the graph itself. The default value is `250`. `path` A character string naming the directory where the image file will be saved (excluding the last `"/"`). If it does not contain an absolute path, the image file will be saved relative to the current working directory `getwd()`. The default value is the current working directory `getwd()`. NOTE: The components should be separated by `"/"` on Windows. `name` The image file name, a character string. The suffix `".png"` is added automatically. The default value is `"my_Ncells"`.

A common plot for all groups specified in groups is generated. Cell counts are calculated considering all cells that are included in the analysis, as returned from get_cells.

Color denotes the corresponding group.

A dataframe with the following columns: