GEO_boxplot.DE: quick way to draw a boxplot for specified contrast via...

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

boxplot.DE() is based on boxplot.genedata2 and a quick way to draw a boxplot for specified contrast via DesignEset object.

Usage

boxplot.DE(DesignEset1,
           contrast,
           select,
           p.val.matrix=sig.exprs,
           p.val.col="P.Value",
           p.val.position=NULL)

boxplot.DE2(DesignEset1,
            cut.n=11,
            contrast,
            p.val.matrix=sig.exprs,
            p.val.col="P.Value",
            p.val.position=NULL,
            names="test1",
            width = 12,height = 8)

Arguments

DesignEset1	a DesignEset object.It is always be one after lucky::AnnotateDesignEset()
contrast	the group in every facet
select	marker names
p.val.matrix	a result object containing p.val
p.val.col	colnames of p value in the p.val.matrix
p.val.position	the position of significant symbol in the plot

Author(s)

Weibin Huang

Examples

## example
library(lucky)
data(test-DesignEset1)
contrast=c("Np","N0")
data(test-sig.exprs)
p.val.matrix=sig.exprs
select <- rownames(sig.exprs)[1:10]
p.val.col="P.Value"
boxplot.DE(test-DesignEset1,
           contrast,
           select,
           p.val.matrix=sig.exprs,
           p.val.col,
           p.val.position=NULL)

boxplot.DE2(test-DesignEset1,
            cut.n=11,
            contrast,
            p.val.matrix=sig.exprs,
            p.val.col="P.Value",
            p.val.position=NULL)

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.