plot_length_distribution: Plots the length distribution
In mjgeng/ribor: An R Interface for Ribo Files

Description Usage Arguments Details Value See Also Examples

The function plot_length_distribution can take either a DataFrame or a "Ribo" object to generate a line graph of the length distributions from range.lower to range.upper.

plot_length_distribution(
  x,
  region,
  experiment,
  range.lower,
  range.upper,
  fraction = FALSE,
  title = "Length Distribution"
)

`x`	A 'Ribo' object or a DataFrame generated from `get_region_counts`
`region`	the region of interest
`experiment`	a list of experiment names
`range.lower`	a lower bounds for a read length range
`range.upper`	an upper bounds for a read length range
`fraction`	logical value that, if TRUE, presents the count as a fraction of the total reads in the given ranges
`title`	a title for the generated plot

The param 'fraction' will plot the fractions of each length relative to the total sum of the read length range provided by param 'range.lower' and 'range.upper'. When fraction is set to FALSE, the total count of each read length is plotted.

When given a "Ribo" object, plot_length_distribution calls get_region_counts to retrieve the necessary information for plotting.

The user can instead provide a DataFrame with the same structure as the output of the get_region_counts function where the 'transcript' parameter is set to FALSE and 'length' parameters is the default value of TRUE. This also means that the many of the remaining parameters of the plot_length_distribution function are not necessary. The run time becomes substantially faster when plot_region_counts is given the direct DataFrame to plot. Note that there is no manipulation by this function on the DataFrame. This responsibility is given to the user and allows for more control.

A 'ggplot' of the length distribution

get_region_counts to generate a DataFrame that can be provided as input, Ribo to create a ribo.object that can be provided as input

#ribo object use case

#generate the ribo object
file.path <- system.file("extdata", "sample.ribo", package = "ribor")
sample <- Ribo(file.path)

#specify experiments of interest
experiments <- c("Hela_1", "Hela_2", "WT_1")

plot_length_distribution(x = sample,
                         region = "CDS",
                         range.lower = 2,
                         range.upper = 5,
                         experiment = experiments,
                         fraction = TRUE)


#DataFrame use case
#obtains the region counts at each individual read length, summed across every transcript
region.counts <- get_length_distribution(ribo.object = sample,
                                         region      = "CDS",
                                         range.lower = 2,
                                         range.upper = 5,
                                         experiment  = experiments)

#the param 'length' must be set to FALSE and param 'transcript' must be set
#to TRUE to use a DataFrame
plot_length_distribution(region.counts)