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

plot-BASiCS_Summary-methodR Documentation

'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 cnvallej@uc.cl

Nils Eling eling@ebi.ac.uk

Examples


help(BASiCS_MCMC)


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