BASiCS_ShowFit: Plotting the trend after Bayesian regression

In BASiCS: Bayesian Analysis of Single-Cell Sequencing data

Description

Plotting the trend after Bayesian regression using a BASiCS_Chain object

Usage

BASiCS_ShowFit(
  object,
  xlab = "log(mu)",
  ylab = "log(delta)",
  pch = 16,
  smooth = TRUE,
  variance = 1.2,
  colour = "dark blue",
  markExcludedGenes = TRUE,
  GenesSel = NULL,
  colourGenesSel = "dark red",
  Uncertainty = TRUE
)

Arguments

object	an object of class BASiCS_Chain
xlab	As in par.
ylab	As in par.
pch	As in par. Default value pch = 16.
smooth	Logical to indicate wether the smoothScatter function is used to plot the scatter plot. Default value smooth = TRUE.
variance	Variance used to build GRBFs for regression. Default value variance = 1.2
colour	colour used to denote genes within the scatterplot. Only used when smooth = TRUE. Default value colour = "dark blue".
markExcludedGenes	Whether or not lowly expressed genes that were excluded from the regression fit are included in the scatterplot. Default value markExcludedGenes = TRUE.
GenesSel	Vector of gene names to be highlighted in the scatterplot. Only used when smooth = TRUE. Default value GenesSel = NULL.
colourGenesSel	colour used to denote the genes listed in GenesSel within the scatterplot. Default value colourGenesSel = "dark red".
Uncertainty	logical indicator. If true, statistical uncertainty around the regression fit is shown in the plot.

Value

A ggplot2 object

Author(s)

Nils Eling [e-mail]

Catalina Vallejos [e-mail]

References

Eling et al (2018). Cell Systems https://doi.org/10.1016/j.cels.2018.06.011

Examples

data(ChainRNAReg)
BASiCS_ShowFit(ChainRNAReg)

BASiCS documentation built on April 16, 2021, 6 p.m.