plot_metagene {ribor} | R Documentation

## Plots the metagene coverage data

### Description

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

### Usage

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

### Arguments

`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

### Details

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.

### Value

A 'ggplot' of the metagene site coverage

### Examples

    #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)

[Package ribor version 1.4.0 Index]