plotVelocityLineplot: Plot cell activity over time

In theMILOlab/cypro: A Toolbox for Analysis of Single Cell Microscopy Data

Plot cell activity over time

Description

Visualizes the percentage of active cells over time.

Usage

plotVelocityLineplot(
  object,
  across = "condition",
  across_subset = NULL,
  phase = NULL,
  threshold = NULL,
  linesize = 1,
  smooth = TRUE,
  smooth_span = 0.25,
  smooth_se = FALSE,
  clrp = "milo",
  verbose = TRUE,
  ...,
  in_shiny = FALSE
)

Arguments

object	A valid cypro object.
across	Character value, character vector or NULL (see details for more). Specifies the grouping variable of interest. Use getGroupingVariableNames() to obtain all variable names that group the cells of your experiment in a certain manner.
across_subset	Character vector, list of character vectors or NULL (see details for more). Specifies the particular groups of interest the grouping variable specified in argument across contains. If set to NULL all of them are chosen. You can prefix groups you are NOT interested in with a '-'. (Saves writing if there are more groups you are interested in than groups you are not interested in.) Use getGroupNames() to obtain all valid input options.
phase	Character or numeric. If character, the ordinal value referring to the phase of interest (e.g. 'first', 'second' etc.). referring to the phase of interest or 'all'. If numeric, the number referring to the phase. If set to NULL takes the phase denoted as default with adjustDefault(). Ignored if the experiment design contains only one phase.
threshold	Numeric value or NULL. If set to NULL (the default) the threshold to consider a cell 'active' is equal to base::mean(speed) + base::sd(speed)
linesize	Numeric value. Denotes the size of the lines drawn.
smooth	Logical. If set to TRUE the values are smoothed.
smooth_span	NUmeric value. Denotes the smoothing span used.
smooth_se	Logical. If set to TRUE the standard error will be displayed.
clrp	Character value. Specifies the color palette to be used to represent groups of discrete variables. Run validColorPalettes() to obtain valid input options.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

theMILOlab/cypro documentation built on April 5, 2022, 2:03 a.m.