BASiCS_showFit {BASiCS}R Documentation

Plotting the trend after Bayesian regression

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", ...)

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".

...

Additional parameters for plotting.

Value

A ggplot2 object

Author(s)

Nils Eling eling@ebi.ac.uk

Catalina Vallejos cnvallej@uc.cl

References

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

Examples

data(ChainRNAReg)
BASiCS_showFit(ChainRNAReg)


[Package BASiCS version 1.6.0 Index]