plot_variation_vs_total {SWATH2stats} | R Documentation |
This function plots the total variation and the variation within replicates for a given value. If decoys are present these are removed before plotting.
plot_variation_vs_total(data, column.values = "Intensity", Comparison1 = transition_group_id ~ BioReplicate + Condition, Comparison2 = transition_group_id + Condition ~ BioReplicate, fun.aggregate = NULL, label=TRUE, ...)
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. |
... |
further arguments passed to method. |
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.
Peter Blattmann
data("OpenSWATH_data", package="SWATH2stats") data("Study_design", package="SWATH2stats") data <- sample_annotation(OpenSWATH_data, Study_design) plot_variation_vs_total(data)