plot.Assessment: Plot Assessment Objects

In DRK248/AssessORF: Assess Gene Predictions Using Proteomics and Evolutionary Conservation

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)

DRK248/AssessORF documentation built on Jan. 30, 2020, 7:05 p.m.