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

In avastermark19/doseR_0.99.8: doseR

Description

This function plots the expression of the supplied se 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	An se 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 se 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')

avastermark19/doseR_0.99.8 documentation built on May 6, 2019, 12:09 p.m.