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Last data update: 2014.03.03

R: Expression plot for selected genes

geneprofile

R Documentation

Expression plot for selected genes

Description

This function generate a plot with many lines. Each line represents a gene. The y-axis is the estimated expression level for the given factor from ANOVA model. The x-axis is for the levels of the give factor, e.g., different strains.

Usage

geneprofile(anovaobj, term, geneidx,
            col="blue", type="b", ylim, xlab, ylab, ...)

Arguments

`anovaobj`	An object of class `maanova`. It should be the result from `fitmaanova`.
`term`	The terms to be plotted.
`geneidx`	The index of genes to be plotted.
`col`	The color to be used in plot.
`type`	The line type.
`ylim`	Y-axis limit.
`xlab`	X-axis label.
`ylab`	Y-axis label.
`...`	Other parameters to be passed to `plot`.

Author(s)

Hao Wu

Examples

# load in data
data(abf1)
# fit the anova model
## Not run: 
fit.fix = fitmaanova(abf1,formula = ~Strain)
# test Strain effect 
test.fix = matest(abf1, fit.fix, term="Strain",n.perm= 1000)
# pick significant genes - pick the genes selected by Fs test
idx <- volcano(test.fix)$idx.Fs
geneprofile(fit.fix, "Strain", idx)
## End(Not run)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(maanova)

Attaching package: 'maanova'

The following object is masked from 'package:base':

    norm

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/maanova/geneprofile.Rd_%03d_medium.png", width=480, height=480)
> ### Name: geneprofile
> ### Title: Expression plot for selected genes
> ### Aliases: geneprofile
> ### Keywords: hplot
> 
> ### ** Examples
> 
> # load in data
> data(abf1)
> # fit the anova model
> ## Not run: 
> ##D fit.fix = fitmaanova(abf1,formula = ~Strain)
> ##D # test Strain effect 
> ##D test.fix = matest(abf1, fit.fix, term="Strain",n.perm= 1000)
> ##D # pick significant genes - pick the genes selected by Fs test
> ##D idx <- volcano(test.fix)$idx.Fs
> ##D geneprofile(fit.fix, "Strain", idx)
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>