BASiCS_PlotDE: Produce plots assessing differential expression results

In catavallejos/BASiCS: Bayesian Analysis of Single-Cell Sequencing data

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,
  TransLogit = FALSE
)

## 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,
  TransLogit = FALSE,
  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.
TransLogit	Logical scalar controlling whether a logit transform is applied to the posterior probability in the y-axis of volcano plots. As logit(0) and logit(1) are undefined, we clip these values near the range of the data excluding 0 and 1.

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)

catavallejos/BASiCS documentation built on March 27, 2024, 12:49 a.m.