BI_boxplot.genedata2: quick way to draw boxplot for multiple markers.

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

Description

boxplot.genedata2 is a plus version of boxplot.genedata.It use the exogenous p values from p.val.matrix from limma package or other differentially analysis tools.

Usage

  boxplot.genedata2(select.genes,
                  design,
                  expr.matrix,
                  p.val.matrix,
                  p.val.col="P.Value",
                  p.val.position=NULL,
                  contrast = "N.status",
                  contrast.list = c("N0","Np"))

Arguments

select.genes	marker names
design	a design object of a expression matrix.
expr.matrix	a expression matrix.
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
contrast	the colname of the group in every facet.
contrast.list	the group in every facet
returndata	whether output the data of boxplot based.

Author(s)

Weibin Huang

Examples

## example
select.genes=co.genes
design=design.x
expr.matrix=expr.x
contrast = "condition"
contrast.list = c("N0","Np")
method = c("t.test", "wilcox.test", "anova", "kruskal.test")[2]
p.val.matrix= p.72305
p.val.col = "P.Value"
boxplot.genedata2(select.genes,
                  design,
                  expr.matrix,
                  p.val.matrix,
                  p.val.col,
                  p.val.position=NULL,
                  contrast,
                  contrast.list)

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