plot_variation_vs_total {SWATH2stats} | R Documentation

## Plots the total variation versus variation within replicates

### Description

This function plots the total variation and the variation within replicates for a given value. If decoys are present these are removed before plotting.

### Usage

    plot_variation_vs_total(data, column.values = "Intensity",
    Comparison1 = transition_group_id  ~ BioReplicate + Condition,
    Comparison2 = transition_group_id + Condition ~ BioReplicate,
    fun.aggregate = NULL, label=FALSE,
    title = "coefficient of variation - total versus within replicates",
    boxplot = TRUE,...)

### Arguments

`data` | Data table that is produced by the OpenSWATH/pyProphet workflow
`column.values` | Indicates the columns for which the variation is assessed. This can be the Intensity or Signal, but also the retention time.
`Comparison1` | The comparison for assessing the total variability. Default is to assess the variability per transition_group_id over the combination of Replicates and different Conditions.
`Comparison2` | The comparison for assessing the variability within the replicates. Default is to assess the variability per transition_group_id and Condition over the different Replicates.
`fun.aggregate` | If depending on the comparison values have to be aggregated one needs to provide the function here.
`label` | Option to print value of median cv.
`title` | Option to define title of plot.
`boxplot` | Option to add boxplot.
`...` | further arguments passed to method.

### Value

Plots in Rconsole a violin plot comparing the total variation with the variation within replicates. In addition it returns the data frame from which the plotting is done and a table with the calculated mean, median and mode of the cv for the total or replicate data.

### Author(s)

Peter Blattmann

### Examples

    data("OpenSWATH_data", package="SWATH2stats")
    data("Study_design", package="SWATH2stats")
    data <- sample_annotation(OpenSWATH_data, Study_design)
    plot_variation_vs_total(data)

[Package SWATH2stats version 1.17.5 Index]