BASiCS_PlotDE {BASiCS} | R Documentation |
Produce plots assessing differential expression results
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") )
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. |
A plot (possibly several combined using
plot_grid
).
Catalina A. Vallejos cnvallej@uc.cl
Nils Eling eling@ebi.ac.uk
Alan O'Callaghan
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)