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",
      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 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 1.99.1 Index]