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BASiCS_PlotDE.Rd
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BASiCS_PlotDE.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllGenerics.R, R/BASiCS_PlotDE.R
\name{BASiCS_PlotDE}
\alias{BASiCS_PlotDE}
\alias{BASiCS_PlotDE,BASiCS_ResultsDE-method}
\alias{BASiCS_PlotDE,BASiCS_ResultDE-method}
\alias{BASiCS_PlotDE,missing-method}
\title{Produce plots assessing differential expression results}
\usage{
BASiCS_PlotDE(object, ...)
\S4method{BASiCS_PlotDE}{BASiCS_ResultsDE}(
object,
Plots = c("MA", "Volcano", "Grid"),
Parameters = intersect(c("Mean", "Disp", "ResDisp"), names(object@Results)),
MuX = TRUE,
...
)
\S4method{BASiCS_PlotDE}{BASiCS_ResultDE}(
object,
Plots = c("Grid", "MA", "Volcano"),
Mu = NULL,
TransLogit = FALSE
)
\S4method{BASiCS_PlotDE}{missing}(
GroupLabel1,
GroupLabel2,
ProbThresholds = seq(0.5, 0.9995, by = 0.00025),
Epsilon,
EFDR,
Table,
Measure,
EFDRgrid,
EFNRgrid,
ProbThreshold,
Mu,
TransLogit = FALSE,
Plots = c("Grid", "MA", "Volcano")
)
}
\arguments{
\item{object}{A \linkS4class{BASiCS_ResultsDE} or
\linkS4class{BASiCS_ResultDE} object.}
\item{...}{Passed to methods.}
\item{Plots}{Plots plot to produce? Options: "MA", "Volcano",
"Grid".}
\item{Parameters}{Character vector specifying the parameter(s) to produce
plots for,
Available options are "Mean", (mu, mean expression),
"Disp" (delta, overdispersion) and "ResDisp"
(epsilon, residual overdispersion).}
\item{MuX}{Use Mu (mean expression across both chains) as the X-axis for all
MA plots? Default: TRUE.}
\item{Mu, GroupLabel1, GroupLabel2, ProbThresholds, Epsilon, EFDR, Table, Measure, EFDRgrid, EFNRgrid, ProbThreshold}{Internal arguments.}
\item{TransLogit}{Logical scalar controlling whether a logit transform
is applied to the posterior probability in the y-axis of volcano plots.
As logit(0) and logit(1) are undefined, we clip these values near the range
of the data excluding 0 and 1.}
}
\value{
A plot (possibly several combined using
\code{\link[cowplot]{plot_grid}}).
}
\description{
Produce plots assessing differential expression results
}
\examples{
data(ChainSC)
data(ChainRNA)
Test <- BASiCS_TestDE(Chain1 = ChainSC, Chain2 = ChainRNA,
GroupLabel1 = 'SC', GroupLabel2 = 'P&S',
EpsilonM = log2(1.5), EpsilonD = log2(1.5),
OffSet = TRUE)
BASiCS_PlotDE(Test)
}
\author{
Catalina A. Vallejos \email{[email protected]}
Nils Eling \email{[email protected]}
Alan O'Callaghan
}