plotRatioBoxes: plotRatioBoxes Function to boxplot density of ratios between...

In WaltersLab/doseR: doseR

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')

WaltersLab/doseR documentation built on March 2, 2023, 7:01 p.m.