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. For the predicted gene categories, bars are colored by the correctness of that category, where dark green represents "definitely correct", light green represents "likely correct", white represents "no evidence", dark red represents "definitely incorrect", light red represents "likely incorrect", and grey represents "potentially incorrect". For the two categories that come from ORFs without predicted genes, dark blue represents "likely missing" and light blue represents "potentially missing".

If both `x` and `y` are specified, an interactive genome viewer showing how the proteomics data, 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 1.2.0 Index]