PlotGeneTotalVsNtr: Gene plot comparing total RNA vs the NTR

In grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Gene plot comparing total RNA vs the NTR

Description

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

Usage

PlotGeneTotalVsNtr(
  data,
  gene,
  slot = DefaultSlot(data),
  columns = NULL,
  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
slot	the slot of the grandR object to get the data from
columns	which columns (i.e. samples or cells) to show (see details)
log	show the x axis (total RNA) 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 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

a ggplot object.

See Also

GetData, PlotGeneOldVsNew,PlotGeneGroupsPoints,PlotGeneGroupsBars

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