plot_metagene: Plots the metagene coverage data
In ribosomeprofiling/ribor: An R Interface for Ribo Files

Description Usage Arguments Details Value Examples

The function plot_metagene plots the metagene site coverage, separating by experiment.

plot_metagene(
  x,
  site,
  experiment,
  range.lower,
  range.upper,
  normalize = FALSE,
  title = "Metagene Site Coverage",
  tick = 10
)

`x`	A 'Ribo' object or a data frame generated from `get_metagene`
`site`	"start" or "stop" site
`experiment`	list of experiments
`range.lower`	lower bound of the read length, inclusive
`range.upper`	upper bound of the read length, inclusive
`normalize`	When TRUE, normalizes the data by the total reads.
`title`	title of the generated plot
`tick`	x-axis labeling increment

If a DataFrame is provided as param 'x', then the only additional parameter is the optional title' parameter for the generated plot. If a ribo.object is provided as param 'x', the rest of the parameters listed are necessary.

When given a ribo class object, the plot_metagene function generates a DataFrame by calling the get_tidy_metagene function, so the run times in this case will be mostly comprised of a call to the get_metagene function.

This function uses ggplot in its underlying implementation.

A 'ggplot' of the metagene site coverage

#a potential use case is to directly pass in the ribo object file as param 'x'

#generate the ribo object to directly use
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 the metagene start site coverage for all experiments in 'sample.ribo'
#from read length 2 to 5
plot_metagene(x = sample,
              site = "start",
              range.lower = 2,
              range.upper = 5,
              experiment = experiments)

#Note that the site, range.lower, range.upper, and experiment parameter are only
#necessary if a ribo object is being passed in as param 'x'. If a ribo
#object is passed in, then the param 'experiments' will be set to all of
#the experiments by default.

#If a DataFrame is passed in, then the plot_metagene function
#does not need any other information. All of the elements of the DataFrame
#will be used, assuming that it contains the same column names and number of
#columns as the output from get_tidy_metagene()

#gets the metagene start site coverage from read length 2 to 5
#note that the data must be summed across transcripts and read lengths
#for the plot_metagene function
data <- get_tidy_metagene(sample,
                          site = "start",
                          range.lower = 2,
                          range.upper = 5)

#plot the metagene data
plot_metagene(data)