plotAllTracks: Plot cell migration

In kueckelj/celltracer: An Analysis-Toolbox for High-Throughput Cell Imaging Data

Usage

plotAllTracks(
  object,
  across = "condition",
  across_subset = NULL,
  time_subset = NULL,
  phase = "all",
  phase_cluster = "first_tmt",
  n_cells = 100,
  color_to = NULL,
  linetype = "solid",
  linesize = 0.75,
  clrp = "milo",
  ...,
  verbose = TRUE
)

Arguments

object	A valid cell tracer object.
across	Character value. Denotes the discrete variable in the data.frame across which the variables of interest are to be analyzed or displayed. Valid input options can be obtained via getAcrossOptions().
across_subset	Character vector. The groups of interest that the across- variable contains. Valid input options can be obtained via getVariableValues().
time_subset	Numeric value. Refers to the time up to which the migration is plotted. If set to NULL the entire timespan is used.
phase	Character value. Refers to the phase of the experiment. Valid inputs are: 'before_tmt' Uses the data that refers to the time before the treatment. 'first_tmt' Uses the data that refers tot the time after the treatment. 'entire' Uses the complete data of the entire timespan. Note: This argument is ignored if the experiment set up did not include any treatment or the treatment started right from the beginning.
phase_cluster	Character value. Refers to the phase of the experiment from which to take the clustering variables. Valid inputs are: 'before_tmt' Uses the data that refers to the time before the treatment. 'first_tmt' Uses the data that refers tot the time after the treatment. Note: This argument is ignored if the experiment set up did not include any treatment or the treatment started right from the beginning.
n_cells	Numeric calue. Determines the number of cells that are randomly chosen from every group to be displayed. Useful to keep plots insightful and aesthetically pleasing.
color_to	Character value. The variable that is to be displayed or highlighted by the dots color.
linetype	Character value. Valid options are 'solid', 'twodash', 'longdash', 'dotted' and 'dotdash'.
linesize	Numeric value. Denotes the size of the lines drawn.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

Value

A ggplot.

kueckelj/celltracer documentation built on June 2, 2021, 6:37 a.m.