BASiCS_PlotDE {BASiCS}R Documentation

Produce plots assessing differential expression results

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

Which 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 cnvallej@uc.cl

Nils Eling eling@ebi.ac.uk

Alan O'Callaghan a.b.o'callaghan@sms.ed.ac.uk

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)

[Package BASiCS version 2.0.0 Index]