DiagPlots: Produce a comet plot, rocket plot or RDD plot

In tpbilton/GUSbase: Genotyping Uncertainty with Sequencing Data: Base Package

Produce a comet plot, rocket plot or RDD plot

Description

Diagnostic graphs for assessing the validity of the binomial model for read count data generated using high-throughput sequencing technology

Usage

## Method for RA object
RAobj$cometPlot(ploid=2, filename=NULL, cex=1, maxdepth=500, maxSNPs=1e5, res=300, ind=FALSE, ncores=1, ...)

RAobj$rocketPlot(ploid=2, filename=NULL, cex=1, maxdepth=500, maxSNPs=1e5, res=300, scaled=TRUE, ...)

RAobj$RDDPlot(ploid=2, filename=NULL, maxdepth=500, maxSNPs=1e5, ...)


## Stand-alone functions
cometPlot(ref, alt, ploid=2, gfreq=NULL, file=NULL, ind=FALSE, cex=1, maxdepth=500, maxSNPs=1e5, res=300,
          color=NULL, ncores=1, indID=NULL, ...)

rocketPlot(ref, alt, ploid=2, gfreq=NULL, file=NULL, cex=1, maxdepth=500, maxSNPs=1e5, res=300, scaled=TRUE, ...)

RDDPlot(ref, alt, ploid=2, gfreq=NULL, file=NULL, maxdepth=500, maxSNPs=1e5, ...)

Arguments

ref	Integer matrix: Read counts for the reference allele
alt	Integer matrix: Read counts for the alternate allele
ploid	Non-negative integer: The ploidy level of the individuals
gfreq	Numeric matrix: Genotype probabilities for each SNP and individual
ind	Logical: If TRUE, cometPlots are produced for each individual separately
cex	Numeric value: A magnification value for the size of the text and labels on the axes
maxdepth	Postive integer: The maximum depth for the x-axis and y-axis
maxSNPs	Postive integer: The maximum number of SNPs to use in creating the graph
res	Positive numeric value: The resolution of the graph when saving to a file
color	Vector: Color palette used for the heatmap.
ncores	Positive integer: Number of cores to use in the parallelization when constructing comet plots for each individual.
indID	Character vector: Sample IDs corresponding to the rows of the reference and alternative allele matrices
yleg	Positive value: Scaling factor for the vertical height of the legend.
xleg	Positive value: Scaling factor for the horizontal width of the legend.
filename	Character: The name of the file to save the plot to
scaled	Logical: If TRUE, the counts in the rocket plot are scaled

Author(s)

Timothy P. Bilton

Examples

## Read in simulated data in GUSbase package
vcffile <- simDS()$vcf
rafile <- VCFtoRA(vcffile)
radata <- readRA(rafile)

## Produce a comet plot
radata$cometPlot()

## Produce a rocket plot
radata$rocketPlot()

## RDD plot
radata$RDDPlot()

tpbilton/GUSbase documentation built on March 8, 2024, 1:35 p.m.