PlotGeneProgressiveTimecourse: Plot progressive labeling timecourses

In grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Plot progressive labeling timecourses

Description

Plot the abundance of new and old RNA and the fitted model over time for a single gene.

Usage

PlotGeneProgressiveTimecourse(
  data,
  gene,
  slot = DefaultSlot(data),
  time = Design$dur.4sU,
  type = c("nlls", "ntr", "lm"),
  exact.tics = TRUE,
  show.CI = FALSE,
  return.tables = FALSE,
  rescale = TRUE,
  ...
)

Arguments

data	a grandR object
gene	the gene to be plotted
slot	the data slot of the observed abundances
time	the labeling duration column in the column annotation table
type	how to fit the model (see FitKinetics)
exact.tics	use axis labels directly corresponding to the available labeling durations?
show.CI	show confidence intervals; one of TRUE/FALSE (default: FALSE)
return.tables	also return the tables used for plotting
rescale	for type=ntr or type=chase, rescale all samples to the same total value?
...	given to the fitting procedures

Details

For each Condition there will be one panel containing the values and the corresponding model fit.

Value

either a ggplot object, or a list containing all tables used for plotting and the ggplot object.

See Also

FitKineticsGeneNtr, FitKineticsGeneLeastSquares, FitKineticsGeneLogSpaceLinear

grandR documentation built on April 4, 2025, 2:27 a.m.