plot_growth_attr_cell: Plot single-cell growth curve of an attribute

In vicstefanou/ViSCA: Cell-Movie Analysis and Visualization

Description

Plots the raw (and fitted) single-cell growth curve (time-series data) of a numeric attribute for a set of given cells in a division tree.

Usage

plot_growth_attr_cell(DT, LT, attr, unit = "", cells = "all",
  model = c("", "lin", "exp", "both"), frameR, save = FALSE,
  savePars = list(w = 1500, h = 1000, res = 150, path = getwd(), name =
  "my_growth_attr_cell"))

Arguments

DT	The division tree where the cells specified in cells belong, an object of class "igraph".
LT	The corresponding lineage tree of the DT, an object of class "igraph".
attr	The name of the attribute in the LT, a character string. It can be any numeric attribute, as returned from get_attr_names, except for "colony", "generation", "frame" and "age".
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.
cells	The labels of the cells in the DT whose growth curve will be plotted, a vector of character strings. They can be any non-root cells, as returned from get_cells. The default value "all" stands for all cells in the DT.
model	A character string naming the optional fitted growth curve(s) to be plotted, if the corresponding parameters have been already successfully estimated using add_attr_growth_fit_pars: "" (the empty string) for plotting just the raw growth curve "lin" for plotting the fitted linear model "exp" for plotting the fitted exponential model "both" for plotting both fitted linear and exponential model
frameR	Frame rate of the movie in frames per minute, a non-zero positive numeric value. This argument is ignored in case model = "".
save	A logical value (TRUE or FALSE) indicating whether the generated plot(s) will be saved in .png file(s) or displayed in the Plots Pane of RStudio, respectively. The default value is FALSE.
savePars	A named list specifying the parameters of each 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 1500. h The height of the image file in pixels, a non-zero positive integer value. The default value is 1000. 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 150. 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_growth_attr_cell".

Details

A separate plot for each cell specified in cells is generated.

x-axis represents the life of the cell in frames, starting from its birth (value 1).

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