incucyte: Incucyte analysis tool

In sebastian-gregoricchio/Rseb: An R-package for NGS data managing and visualization

Incucyte analysis tool

Description

This tool generates confluency plots over time starting from incucyte data.

Usage

incucyte(
  metadata,
  raw.data,
  comparisons = "all",
  error = "SEM",
  normalization.method = "none",
  start.hour = 0,
  plot.days = FALSE,
  show.error.ribbon = TRUE,
  show.error.bars = FALSE,
  show.points = TRUE,
  show.lines = TRUE,
  show.legend = TRUE,
  same.y.scale = TRUE,
  group.order = NULL,
  error.transparency = 0.25,
  point.size = 1,
  line.type = 1,
  line.smooth.span = 0.25,
  colors = NULL,
  skip.head.lines.in.data = 1
)

Arguments

metadata	Path to a table or a data.frame with at least two columns: 'well.ID' and 'group'. The 'well.id' indicates the ID of the wells/columns in the rawData table; the 'group' indicates the name of the group at which each column belongs (wells belonging to the same column will be averaged together). A third column 'color' can be used to indicate the color; notice that each group should have the same color.
raw.data	Path to the rawData table or a data.frame. First column must be 'Elapsed' (the time in hours) and the other columns the wells (e.g., A1, A2, B5, B8, ...).
comparisons	List of vectors containing the groups to be used in each comparison: one vector per comparison. E.g.: list(c("group_A", "group_B"), c("group_B", "group_C", "group_E")). Default: "all".
error	String to indicate the error type. Possible choices: 'SEM', 'SD'. Default: SEM.
normalization.method	String to indicate the normalization method. Possible choices: "none", "division", "subtraction". Default: none. Division: for each group the values are divided by the first timepoint.
start.hour	Number of hours to be excluded from the calculations. Default: 0.
plot.days	Logical value to indicate whether to plotted days instead of hours. Default: FALSE.
show.error.ribbon	Logical value to indicate whether to show the error ribbon. Default: TRUE.
show.error.bars	Logical value to indicate whether to show the error bars. Default: FALSE.
show.points	Logical value to indicate whether to show the individual average points at each time point. Default: TRUE.
show.lines	Logical value to indicate whether to show the interpolation line. Default: TRUE.
show.legend	Logical value to indicate whether to show the color legend. Default: TRUE.
same.y.scale	Logical value to indicate whether the y-axis should show the same limit range. Default: TRUE.
group.order	String vector with the specific order to use for the groups indicated in the metadata (factor levels). Default: NULL.
error.transparency	Number between 0 and 1 indicating the transparency (alpha) to use for the error ribbon. Default: 0.25.
point.size	Number for the point size. Default: 1.
line.type	A vector indicating the line type to use for each group (both numeric and string values accepted). Default: 1 (applied to all the groups).
line.smooth.span	Numeric value of the 'span' for the smoothing of the interpolation line. Default: 0.25.
colors	A vector indicating the color to use for each group (any R color format is accepted). Default: NULL (random colors are generated).
skip.head.lines.in.data	Number of lines to be skipped at the beginning of the raw.data file. Default: 1.

Value

The function returns a list containing:

• metadata: table used for the metadata;

• raw.data: tables used as raw.data;

• analyzed.data: data.frame with the analyzed data (means, n, SEM, SD, groups, ...);

• normalized.data: data.frame with the normalized data used for the plotting;

• plot.list: names list of plots, one plot for each group plus 'all' comparison;

• multiplot: a plot with all the plots in the plot.list .

sebastian-gregoricchio/Rseb documentation built on May 15, 2024, 5:45 a.m.