plot_tree: Plot a tree
In vicstefanou/ViSCA: Cell-Movie Analysis and Visualization

Description Usage Arguments Details See Also

Plots a lineage or division tree.

plot_tree(tree, treeT = c("LT", "DT"), attrC = "", unitC = "",
  NC = NULL, attrS = "", cellsC = "", colorCol = FALSE, Ncols,
  showLabels = FALSE, sizeLabel = 0.1, circular = TRUE,
  showLegends = TRUE, sizeL = 1, sizeV = 0.5, sizeE = 0.1,
  save = FALSE, savePars = list(w = 6000, h = 6000, res = 600, path =
  getwd(), name = "my_tree"))

`tree`	The connected 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
`attrC`	The name of the attribute in the `tree` by which the cells will be colored, a character string. It can be any numeric or boolean attribute, as returned from `get_attr_names`. Coloring is applied to all non-root cells, as returned from `get_cells`, except for cells with `NA` value in this attribute which are colored gray. Any existing imaginary root cells are always colored white. When the default value `""` (the empty character) is used, nodes' color is the default.
`unitC`	The unit of `attrC`, a character string. It should be in the format `"<string>,<number>"`, where `",<number>"` represents the power and is optional (e.g. `"m"` for meters and `"cm,3"` for cubic centimeters). The default value is the empty character `""`, which implies that `attrC` is in arbitrary units. This argument is ignored in case `attrC = ""`.
`NC`	Number of colonies in the movie (if `attrC = "colony"`) or number of generations in the movie (if `attrC = "generation"`), a non-zero positive integer value. This argument is ignored in case `attrC != "colony"` and `attrC != "generation"`.
`attrS`	The name of the attribute in the `tree` by which the cells will be shaped, a character string. It can be any boolean attribute, as returned from `get_attr_names`. Cells are represented by dots or squares if their value in this attribute is `TRUE` or `FALSE`, respectively. When the default value `""` (the empty character) is used, nodes' shape is the default.
`cellsC`	The labels of the cells in the `tree` which will be colored red, a vector of character strings. They can be any cells, as returned from `get_cells`. The default value is the empty character `""`, which stands for no cell.
`colorCol`	A logical value (`TRUE` or `FALSE`) indicating whether the edges of the tree will be colored based on the colony or not, respectively. The value `TRUE` can be used only if `tree` contains the imaginary main root cell. When the default value `FALSE` is used, edges' color is the default.
`Ncols`	Number of colonies in the movie, a non-zero positive integer value. This argument is ignored in case `colorCol = FALSE`.
`showLabels`	A logical value (`TRUE` or `FALSE`) indicating whether the labels of the cells will be shown on the plot or not, respectively. The default value is `FALSE`.
`sizeLabel`	Size of cell labels, a non-zero positive numeric value. The default value is `0.1`. This argument is ignored in case `showLabels = FALSE`.
`circular`	A logical value (`TRUE` or `FALSE`) indicating whether the tree will be plotted in circular or classical tree layout, respectively. The default value is `FALSE`.
`showLegends`	A logical value (`TRUE` or `FALSE`) indicating whether the explanatory legends and title will be shown on the plot or not, respectively. The default value is `FALSE`.
`sizeL`	Size of explanatory legends and title, a non-zero positive numeric value. The default value is `1`. This argument is ignored in case `showLegends = FALSE`.
`sizeV`	Size of vertices, a non-zero positive numeric value. The default value is `0.5`.
`sizeE`	Width of edges, a non-zero positive numeric value. The default value is `0.1`.
`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 `6000`. `h` The height of the image file in pixels, a non-zero positive integer value. The default value is `6000`. `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 `600`. `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_tree"`.