plot.Assessment {AssessORF} | R Documentation

## Plot Assessment Objects

### Description

The `plot` method for `Assessment` objects

### Usage

    ## S3 method for class 'Assessment'
    plot(x, y = NULL, related_MinConStart = 0.8, ...)

### Arguments

`x` | An object of class `Assessment` and of either subclass `DataMap` or subclass `Results`.
`y` | An optional object of class `Assessment` and of either subclass `DataMap` or subclass `Results`. Its subclass must be different than the subclass of `x`
`related_MinConStart` | Minimum value of the conservation to coverage ratio needed to call a start conserved. Must range from 0 to 1. Lower values allow more conserved starts through. Recommended to use default value.
`...` | Further plotting parameters.

### Details

If only `x` is specified and `x` is of subclass `DataMap`, an interactive genome viewer showing how the proteomics data and evolutionary conservation data maps to the central genome is plotted.

If only `x` is specified and `x` is of subclass `Results`, a bar chart describing the number of genes in each category is plotted.

If both `x` and `y` are specified, an interactive genome viewer showing how the proteomics data, evolutionary evolutionary conservation data, and gene set map to the central genome is plotted.

### Value

Invisibly returns the input object `x`

### See Also

`Assessment-class`, `locator`

### Examples

    currMapObj <- readRDS(system.file("extdata",
                                      "MGAS5005_PreSaved_DataMapObj.rds",
                                      package = "AssessORF"))

    currResObj <- readRDS(system.file("extdata",
                                      "MGAS5005_PreSaved_ResultsObj_Prodigal.rds",
                                      package = "AssessORF"))

    plot(currMapObj)

    plot(currResObj)

    plot(currMapObj, currResObj)

    plot(currResObj, currMapObj)

[Package AssessORF version 1.0.2 Index]