| 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)