BASiCS_DiagPlot: Create diagnostic plots of MCMC parameters

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

Create diagnostic plots of MCMC parameters

Description

Plot parameter values and effective sample size. See effectiveSize for more details on this diagnostic measure.

Usage

BASiCS_DiagPlot(
  object,
  Parameter = "mu",
  Measure = c("ess", "geweke.diag", "rhat"),
  x = NULL,
  y = NULL,
  LogX = isTRUE(x %in% c("mu", "delta")),
  LogY = isTRUE(y %in% c("mu", "delta")),
  Smooth = TRUE,
  HLine = TRUE,
  na.rm = TRUE
)

BASiCS_diagPlot(...)

Arguments

object	an object of class BASiCS_Summary
Parameter	Name of the parameter to be plotted. Default Parameter = 'mu'
Measure	Character scalar specifying the diagnostic measure to plot. Current options are effective sample size, the Geweke diagnostic criterion, and the rhat diagnostic.
x, y	Optional MCMC parameter values to be plotted on the x or y axis, respectively. If neither is supplied, Parameter will be plotted on the x axis and effective sample size will be plotted on the y axis as a density plot.
LogX, LogY	A logical value indicating whether to use a log10 transformation for the x or y axis, respectively.
Smooth	A logical value indicating whether to use smoothing (specifically hexagonal binning using geom_hex).
HLine	Numeric scalar or vector indicating threshold value(s) to be displayed as a dashed line on the plot when DrawHLine = TRUE. Alternatively, can be set to FALSE to disable line drawing, or TRUE to use the default thresholds.
na.rm	Logical value indicating whether NA values should be removed before calculating effective sample size.
...	Unused.

Value

A ggplot object.

Author(s)

Alan O'Callaghan

See Also

BASiCS_Chain

Examples

# Built-in example chain
data(ChainSC)

# Point estimates versus effective sample size
BASiCS_DiagPlot(ChainSC, Parameter = "mu")
# Effective sample size as colour, mu as x, delta as y.
BASiCS_DiagPlot(ChainSC, x = "mu", y = "delta")

# Point estimates versus Geweke diagnostic
BASiCS_DiagPlot(ChainSC, Parameter = "mu", Measure = "geweke.diag")

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