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

Description Usage Arguments Details Value Author(s) References Examples

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

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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

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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.