GraphsBox: Boxplots

In AlzbetaG/Metabol: The statistical analysis of metabolomic data

Description

Display 5 variants of boxplots in PDF files for every variable (metabolite) in data table separately.

Usage

GraphsBox(data, name, groupnames, tsf = "clr", QCs = FALSE,
  newlabs = FALSE, pair = FALSE, long = FALSE)

Arguments

data	Data table with variables (metabolites) in columns. Samples in rows are sorted according to specific groups.
name	A character string or expression indicating a name of data set. It occurs in names of every output.
groupnames	A character vector defining specific groups in data. Every string must be specific for each group and they must not overlap.
tsf	Data transformation must be defined by "clr" (default), "log", "log10", "PQN", "lnPQN", "pareto" or "none". See Details.
QCs	logical. If FALSE (default) quality control samples (QCs) are automatically distinguished and skipped.
newlabs	logical. If FALSE (default) standard names are used. If vector of characters then the new names of points in boxplots are drawn.
pair	logical. If TRUE then the paired boxplots are drawn. Deaful is FALSE.
long	logical. Used for long group names. If TRUE, labels of x-axis are written vertically. Deaful is FALSE.

Details

Data transformation: with "clr" clr trasformation is used (see References), with "log" natural logarithm is used, with "log10" decadic logarithm is used, with "pareto" data are only scaled by Pareto scaling, with "PQN" probabilistic quotient normalization is done, with "lnPQN" natural logarithm of PQN transformed data is done, with "none" no tranformation is done.

Up to twenty different groups can be distinguished in data (including QCs).

Value

Boxplot graphs.

Excel file with medians and differences of these medians of all groups in data.

References

Aitchison, J. (1986) The Statistical Analysis of Compositional Data Monographs on Statistics and Applied Probability. Chapman & Hall Ltd., London (UK). p. 416.

Examples

data=metabol
name="Metabolomics"    #name of the project
groupnames=c("Con","Pat","QC")
GraphsBox(data,name,groupnames)

AlzbetaG/Metabol documentation built on May 31, 2019, 12:39 a.m.