BASiCS_PlotDE: Produce plots assessing differential expression results

In BASiCS: Bayesian Analysis of Single-Cell Sequencing data

Description

Produce plots assessing differential expression results

Usage

BASiCS_PlotDE(object, ...)

## S4 method for signature 'BASiCS_ResultsDE'
BASiCS_PlotDE(
  object,
  Plots = c("MA", "Volcano", "Grid"),
  Parameters = intersect(c("Mean", "Disp", "ResDisp"), names(object@Results)),
  MuX = TRUE,
  ...
)

## S4 method for signature 'BASiCS_ResultDE'
BASiCS_PlotDE(object, Plots = c("Grid", "MA", "Volcano"), Mu = NULL)

## S4 method for signature 'missing'
BASiCS_PlotDE(
  GroupLabel1,
  GroupLabel2,
  ProbThresholds = seq(0.5, 0.9995, by = 0.00025),
  Epsilon,
  EFDR,
  Table,
  Measure,
  EFDRgrid,
  EFNRgrid,
  ProbThreshold,
  Mu,
  Plots = c("Grid", "MA", "Volcano")
)

Arguments

object	A BASiCS_ResultsDE or BASiCS_ResultDE object.
...	Passed to methods.
Plots	Plots plot to produce? Options: "MA", "Volcano", "Grid".
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).
MuX	Use Mu (mean expression across both chains) as the X-axis for all MA plots? Default: TRUE.
Mu, GroupLabel1, GroupLabel2, ProbThresholds, Epsilon, EFDR, Table, Measure, EFDRgrid, EFNRgrid, ProbThreshold	Internal arguments.

Value

A plot (possibly several combined using plot_grid).

Author(s)

Catalina A. Vallejos [e-mail]

Nils Eling [e-mail]

Alan O'Callaghan

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)

BASiCS documentation built on April 16, 2021, 6 p.m.