plotRatioDensity: plotRatioDensity Function to plot density of ratios between...

In WaltersLab/doseR: doseR

plotRatioDensity Function to plot density of ratios between two treatments (using groupings from an annotation column) within an object.

Description

This function plots the expression of the supplied object, using ratios between a pair of selected treatments.

Usage

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

Arguments

se	A SummarizedExperiment object.
groupings	A grouping (annotation); groupings="annotation.ZA"
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 plots expression of the supplied object using ratios of treatment1/treatment2.

Value

Returns an invisible data frame containing the x-values and corresponding density for each applicable annotation column entry.

Author(s)

AJ Vaestermark, JR Walters.

References

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

Examples

data(hmel.se)
plotRatioDensity(se, groupings='annotation.ZA', treatment1 = 'Male',
treatment2 = 'Female',lty=1,type="l")

WaltersLab/doseR documentation built on June 24, 2024, 2:51 a.m.