plotRatioBoxes {doseR} | R Documentation

## plotRatioBoxes Function to boxplot density of ratios between two treatments (using groupings from an annotation column) within a SummarizedExperiment object.

### Description

This function plots the expression of the supplied object, representing ratios between a pair of selected treatments as a boxplot for each group in the selected annotation column.

### Usage

    plotRatioBoxes(se, groupings= NULL, treatment1=NULL, treatment2=NULL,
    mode_mean=TRUE, LOG2=TRUE, ...)

### Arguments

`se` | A SummarizedExperiment object.
`groupings` | A grouping (annotation column), e.g. groupings="something".
`treatment1` | Symbol, treatment 1.
`treatment2` | Symbol, treatment 2.
`mode_mean` | Boolean, Calculate RowMeans or RowMedians.
`LOG2` | Boolean, Calculate LOG2.
`...` | Passthrough arguments to boxplot (additional arguments affecting the summary produced).

### Details

This function boxplots expression of the supplied object using ratios of treatment1/treatment2.

### Value

Returns an invisible data frame containing the values.

### Author(s)

AJ Vaestermark, JR Walters.

### References

The "doseR" package, 2018 (in press).

### Examples

    data(hmel.se)
    plotRatioBoxes(se, groupings='annotation.ZA', treatment1 = 'Male',
    treatment2 = 'Female')

[Package doseR version 1.2.0 Index]