RlaPlots: RLA plots

In NormalizeMets: Analysis of Metabolomics Data

Description

Produces within group and across group relative log abundance plots to visualise a metabolomics data matrix. See De Livera et al. 2012, 2013, and 2015 for details.

Usage

RlaPlots(featuredata, groupdata, minoutlier = 0.5, type = c("ag", "wg"),
  saveplot = FALSE, plotname = "RLAPlot", savetype = c("png", "bmp",
  "jpeg", "tiff", "pdf"), interactiveplot = TRUE, interactiveonly = TRUE,
  saveinteractiveplot = FALSE, interactivesavename = "interactiveRlaPlot",
  cols = NULL, cex.axis = 0.7, las = 2, keeporder = FALSE,
  ylim = NULL, oma = c(3, 3, 3, 5) + 0.1, xlabel = "Samples",
  showlegend = TRUE, ...)

Arguments

featuredata	featuredata A data frame in the featuredata format. This is a dataframe with metabolites in columns and samples in rows. Unique sample names should be provided as row names. See NormalizeMets Vignette for details.
groupdata	A data frame or a vector with group names.
minoutlier	A number indicating which samples names to show, samples names will only be shown for samples with a median reading greater than the number entered.
type	A character string indicating whether within group ("wg") or across group ("ag") RLA plots need to be plotted.
saveplot	A logical indication whether to save the plot produced.
plotname	Name of the output file if the file is to be saved.
savetype	The required format for the plot to be saved in. Threre is a choice of "png","bmp","jpeg","tiff","pdf" type files.
interactiveplot	A boolean indicator whether to make an interactive plot.
interactiveonly	A boolean indicating whether only an interactive plot should be returned.
saveinteractiveplot	A boolean indicating whether to save the interactive plot as an html file.
interactivesavename	A character string to be used as the filename for saving the interactive plot.
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.
keeporder	A logical indicator whether to keep the original sample order or group them by groupdata.
ylim	A vector containing y-axis limits.
oma	A vector giving the size of the outer margins.
xlabel	Label for the x-axis
showlegend	A logical indicator whether to display a legend for the plot.
...	Other graphical parameters. See par.

Author(s)

Alysha M De Livera, Gavriel Olshansky

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., and Speed, T.P. 2013. Statistical Analysis of Metabolomics Data. Methods in Molecular Biology (Clifton, N.J.) 1055 (Jan): 291-307.

De Livera, A. M,. Aho-Sysi M., Laurent J., Gagnon-Bartch J., Sandra, C, Simpson, J.A., and Speed, T. P. 2015. Statistical Methods for Handling Unwanted Variation in Metabolomics Data. Analytical Chemistry 87 (7). American Chemical Society: 3606-3615.

Examples

    data(mixdata)
    
    RlaPlots(mixdata$featuredata, mixdata$sampledata[,1], 
    ylim = c(-2, 2), cols = c("green","purple"),cex.axis = 0.8)
    

NormalizeMets documentation built on May 1, 2019, 10:26 p.m.