plotExpr: plotExpr Function to generate a boxplot (expression) for a...

In avastermark19/doseR_development: Test Package of doseR

Description

This function boxplots the expression of the supplied countData object. plotExpr is a generic function used to produce boxplot summaries of various expression data. The function invokes particular plottings which depend on the selected grouping and treatment.

Usage

plotExpr(cD, groupings, mode_mean, treatment, LOG2, clusterby_grouping, ...)

Arguments

cD	A countData object, an object for which a summary is desired.
groupings	A grouping (annotation column), e.g. groupings="something".
mode_mean	Boolean, Calculate RowMeans or RowMedians.
treatment	list, indicating which treatments (columns) to be plotted.
LOG2	Boolean, Calculate LOG2.
clusterby_grouping	Boolean, Cluster boxplots by grouping (or treatment).
...	Passthrough arguments to boxplot (additional arguments affecting the summary produced).

Details

This function boxplots the expression of the supplied countData object, based on a selected annotation column and selected treatments.

Value

Returns an invisible data frame containing values and labels.

Author(s)

AJ Vaestermark, JR Walters.

References

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

avastermark19/doseR_development documentation built on May 6, 2019, 4:31 p.m.