plot_viobox_attr: Create violin plot or boxplot for an attribute
In vicstefanou/ViSCA: Cell-Movie Analysis and Visualization

Description Usage Arguments Details Value

Creates the violin plot or boxplot of a numeric attribute of a lineage or division tree. The plot can be created for each colony or generation or for the whole population.

plot_viobox_attr(tree, treeT = c("LT", "DT"), attr, unit = "",
  grouped = c("col", "gen", "pop"), groups = -1, Ngroups, type = c("vio",
  "box"), save = FALSE, savePars = list(w = 2500, h = 2000, res = 300, path
  = getwd(), name = "my_viobox_attr"))

`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
`attr`	The name of the attribute in the `tree`, a character string. It can be any numeric attribute, as returned from `get_attr_names`, except for `"colony"`, `"generation"` and `"frame"`.
`unit`	The unit of `attr`, 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 `attr` is in arbitrary units.
`grouped`	A character string naming the grouping method: `"col"` for grouping by colony `"gen"` for grouping by generation `"pop"` for no grouping (whole population)
`groups`	The IDs of the groups for which to create the violin plot or boxplot, a vector of positive integer values. This argument is ignored in case `grouped = "pop"`. 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"`), a non-zero positive integer value. This argument is ignored in case `grouped = "pop"`.
`type`	A character string naming the type of the plot to be created: `"vio"` for violin plot. The black dot represents the median. `"box"` for boxplot. The black dots represent the outliers (i.e. datapoints out of the 1st/3rd quantile).
`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 `2500`. `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 `300`. `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_viobox_attr"`.

A common plot for all groups specified in groups is generated. Each violin plot or boxplot is created considering all cells that are included in the analysis, as returned from get_cells, except for cells with NA value in attr.

Color denotes the corresponding group.

A dataframe with the following columns:

group is the ID of the group (a positive integer value) or -2 in case grouped = "pop".
Ncells is the number of cells, a positive integer value.

For groups with Ncells < 3, no plot is generated. In case no cells exist, no plot is generated and NULL is returned.

vicstefanou/ViSCA documentation built on May 31, 2019, 10:50 p.m.