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. (I think this should be sum, yesno?)
`label` | Option to print value of median cv.
`title` | Title of plot. Default: "cv across conditions"
`boxplot` | Logical. If boxplot should be plotted. Default: TRUE
`...` | Arguments passed through, currently unused.

### 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)
     var_summary <- plot_variation_vs_total(data)
     }

[Package SWATH2stats version 1.20.1 Index]