PlotGeneProgressiveTimecourse {grandR}

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,
  ...
)

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

...

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