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

In mjnueda/maSigPro: Significant Gene Expression Profile Differences in Time Course Gene Expression Data

Description

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

Usage

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, [e-mail]

References

Nueda, M.J., Martorell, J., Marti, C., Tarazona, S., Conesa, A. 2018. Identification and visualization of differential isoform expression in RNA-seq time series. Bioinformatics. 34, 3, 524-526.

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

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)

mjnueda/maSigPro documentation built on Dec. 11, 2020, 12:21 a.m.