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 1.99.1 Index]