R: Gene plot for snapshot timecourse data

PlotGeneSnapshotTimecourse {grandR}

R Documentation

Gene plot for snapshot timecourse data

Description

Plot the total RNA expression vs the new-to-total RNA ratio for a gene

Usage

PlotGeneSnapshotTimecourse(
  data,
  gene,
  time = Design$dur.4sU,
  mode.slot = DefaultSlot(data),
  columns = NULL,
  average.lines = TRUE,
  exact.tics = TRUE,
  log = TRUE,
  show.CI = FALSE,
  aest = NULL,
  size = 2
)

Arguments

`data`	the grandR object to get the data to be plotted from
`gene`	the gene to plot
`time`	the times to show on the x axis (see details)
`mode.slot`	the mode.slot of the grandR object to get the data from
`columns`	which columns (i.e. samples or cells) to show (see details)
`average.lines`	add average lines?
`exact.tics`	use axis labels directly corresponding to the available temporal values?
`log`	show the y axis in log scale
`show.CI`	show confidence intervals; one of TRUE/FALSE (default: FALSE)
`aest`	parameter to set the visual attributes of the plot
`size`	the point size used for plotting; overridden if size is defined via aest

Details

The x axis of this plot will show a temporal dimension. The time parameter defines a name in the Coldata table containing the temporal values for each sample.

The value of the aest parameter must be an Aesthetic mapping as generated by aes.

The table used for plotting is the table returned by GetData with coldata set to TRUE, i.e. you can use all names from the Coldata table for aest.

By default, aest is set to aes(color=Condition,shape=Replicate) (if both Condition and Replicate are names in the Coldata table).

Columns can be given as a logical, integer or character vector representing a selection of the columns (samples or cells). The expression is evaluated in an environment having the Coldata, i.e. you can use names of Coldata as variables to conveniently build a logical vector (e.g., columns=Condition=="x").

Value