plot-BASiCS_Summary-method: 'plot' method for BASiCS_Summary objects

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

'plot' method for BASiCS_Summary objects

Description

'plot' method for BASiCS_Summary objects

Usage

## S4 method for signature 'BASiCS_Summary,ANY'
plot(
  x,
  Param = "mu",
  Param2 = NULL,
  Genes = NULL,
  Cells = NULL,
  Batches = NULL,
  RegressionTerms = NULL,
  xlab = "",
  ylab = "",
  xlim = "",
  ylim = NULL,
  pch = 16,
  col = "blue",
  bty = "n",
  SmoothPlot = TRUE,
  ...
)

Arguments

x	A BASiCS_Summary object.
Param	Name of the slot to be used for the plot. Possible values: 'mu', 'delta', 'phi', 's', 'nu', 'theta', 'beta', 'sigma2' and 'epsilon'.
Param2	Name of the second slot to be used for the plot. Possible values: 'mu', 'delta', 'epsilon', 'phi', 's' and 'nu' (combinations between gene-specific and cell-specific parameters are not admitted).
Genes	Specifies which genes are requested. Required only if Param = 'mu', 'delta' or 'epsilon'.
Cells	Specifies which cells are requested. Required only if Param = 'phi', 's' or 'nu'
Batches	Specifies which batches are requested. Required only if Param = 'theta'
RegressionTerms	Specifies which regression coefficients are requested. Required only if Param = 'beta'
xlab	As in par.
ylab	As in par.
xlim	As in par.
ylim	As in par.
pch	As in par.
col	As in par.
bty	As in par.
SmoothPlot	Logical parameter. If TRUE, transparency will be added to the color of the dots.
...	Other graphical parameters (see par).

Value

A plot object

Author(s)

Catalina A. Vallejos [e-mail]

Nils Eling [e-mail]

Examples

help(BASiCS_MCMC)

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