IsoPlot: Plotting the isoform profiles of a specific gene by groups

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/IsoPlot.R

Description

This function makes a plot with the isoforms of a specific gene splitting the different experimental groups.

Usage

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IsoPlot(get, name, only.sig.iso=FALSE, ylim=NULL, xlab = "Time",  ylab = "Expression value", points=TRUE, cex.main=3,cex.legend=1.5)

Arguments

get

a getDS object a cluster of flat Isoform

name

Name of the specific gen to show in the plot

only.sig.iso

TRUE when the plot is made only with statistically significant isoforms.

ylim

Range of the y axis of the desired plot. If it is NULL it will be computed automatically.

xlab

label for the x axis

ylab

label for the y axis

points

TRUE to plot points and lines. FALSE to plot only lines.

cex.main

graphical parameter magnification to be used for main

cex.legend

graphical parameter magnification to be used for legend

Details

The plot can be made with all the available isoforms or only with the statistilly significant ones.

Value

Plot of isoform profiles of a specific gene by groups.

Author(s)

Maria Jose Nueda, [email protected]

References

Nueda, M.J., Martorell, J., Marti, C., Tarazona, S and Conesa, A. 2017. Identification and visualization of differential isoform expression in RNA-Seq time series. In preparation.

Nueda, M.J., Tarazona, S., Conesa, A. 2014. Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series. Bioinformatics, 30, 2598-602.

Conesa, A., Nueda M.J., Alberto Ferrer, A., Talon, T. 2006. maSigPro: a Method to Identify Significant Differential Expression Profiles in Time-Course Microarray Experiments. Bioinformatics 22, 1096-1102.

See Also

getDS, IsoModel

Examples

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data(ISOdata)
data(ISOdesign)
mdis <- make.design.matrix(ISOdesign)
MyIso <- IsoModel(data=ISOdata[,-1], gen=ISOdata[,1], design=mdis, counts=TRUE)
Myget <- getDS(MyIso)

IsoPlot(Myget,"Gene1005",only.sig.iso=FALSE,cex.main=2,cex.legend=1)

maSigPro documentation built on Nov. 1, 2018, 2:35 a.m.