RlaPlots: RLA plots

Description Usage Arguments Details Author(s) References Examples

View source: R/RlaPlots.r

Description

Produces within group and across group relative log abundance plots to visualise a metabolomics data matrix.

Usage

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RlaPlots(inputdata, type = c("ag", "wg"), cols = NULL,
    cex.axis = 0.8, las = 2, ylim = c(-2, 2), oma = c(7, 4, 4, 2) + 0.1, ...)

Arguments

inputdata

A log transformed data frame in the input data format. See metabolomics for details.

type

A character string indicating whether within group ("wg") or across group ("ag") RLA plots need to be plotted.

cols

A character string with colours to be used for the box plots.

cex.axis

The magnification to be used for x- and y-labels relative to the current setting of cex.

las

A numeric in 0, 1, 2, 3 denoting the style of axis labels. See par.

ylim

A vector containing y-axis limits.

oma

A vector giving the size of the outer margins.

...

Other graphical parameters. See par.

Details

Across group RLA plots is obtained by standardising the metabolites by removing the median from each metabolite across all groups. The boxplots of these scaled metabolites can be used to compare the behaviour of metabolites in the samples between groups.This gives a visual inspection of variation in the data across groups.

For within group RLA plots, each metabolite is scaled by removing the median within each group. Boxplots of these can be used to visualise the tightness of the replicates within groups, and should have a median close to zero and low variation around the median.

See De Livera et al. 2012a and 2012b for further details.

Author(s)

Alysha M De Livera, Jairus B Bowne

References

De Livera, A. M., Dias, D. A., De Souza, D., Rupasinghe, T., Pyke, J., Tull, D., Roessner, U., McConville, M., Speed, T. P. (2012a) Normalising and integrating metabolomics data. Analytical Chemistry 84(24): 10768-10776.

De Livera, A.M., Olshansky, M., Speed, T. P. (2012b) Statistical analysis of metabolomics data. Methods in Molecular Biology In press.

Examples

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    data(treated)
    treated.log <- LogTransform(treated)$output 
    
    #Across group RLA plot for comparing samples across groups
    RlaPlots(treated.log, ylim = c(-5, 5))
    
    #Within group RLA plot for comparing the replicates
    RlaPlots(treated.log, "wg", ylim = c(-3, 3), cols = c("green","purple"))

metabolomics documentation built on May 29, 2017, 3:32 p.m.