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Last data update: 2014.03.03

R: Plots the correlation between injections.

plot_correlation_between_samples

R Documentation

Plots the correlation between injections.

Description

This function plots the Pearson's and Spearman correlation between samples. If decoys are present these are removed before plotting.

Usage

plot_correlation_between_samples(data, column.values = "Intensity", 
Comparison = transition_group_id ~ Condition + BioReplicate, 
fun.aggregate =NULL, ...)

Arguments

`data`	Data frame that is produced by the OpenSWATH/pyProphet workflow
`column.values`	Indicates the columns for which the correlation is assessed. This can be the Intensity or Signal, but also the retention time.
`Comparison`	The comparison for assessing the variability. Default is to assess the variability per transition_group_id over the different Condition and Replicates. Comparison is performed using the dcast() function of the reshape2 package.
`fun.aggregate`	If for the comparison values have to be aggregated one needs to provide the function here.
`...`	further arguments passed to method.

Value

Plots in Rconsole a correlation heatmap and returns the data frame used to do the plotting.

Author(s)

Peter Blattmann

Examples

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(SWATH2stats)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SWATH2stats/plot_correlation_between_samples.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot_correlation_between_samples
> ### Title: Plots the correlation between injections.
> ### Aliases: plot_correlation_between_samples
> 
> ### ** Examples
> 
> data("OpenSWATH_data", package="SWATH2stats")
> data("Study_design", package="SWATH2stats")
> data <- sample_annotation(OpenSWATH_data, Study_design)
> plot_correlation_between_samples(data)
               Var1             Var2     value   method
1    Hela_Control_1   Hela_Control_1 1.0000000  pearson
7    Hela_Control_1   Hela_Control_2 0.9317511  pearson
8    Hela_Control_2   Hela_Control_2 1.0000000  pearson
13   Hela_Control_1   Hela_Control_3 0.9771722  pearson
14   Hela_Control_2   Hela_Control_3 0.9782351  pearson
15   Hela_Control_3   Hela_Control_3 1.0000000  pearson
19   Hela_Control_1 Hela_Treatment_1 0.9850712  pearson
20   Hela_Control_2 Hela_Treatment_1 0.9055501  pearson
21   Hela_Control_3 Hela_Treatment_1 0.9583434  pearson
22 Hela_Treatment_1 Hela_Treatment_1 1.0000000  pearson
25   Hela_Control_1 Hela_Treatment_2 0.8809555  pearson
26   Hela_Control_2 Hela_Treatment_2 0.9689018  pearson
27   Hela_Control_3 Hela_Treatment_2 0.9318751  pearson
28 Hela_Treatment_1 Hela_Treatment_2 0.8636100  pearson
29 Hela_Treatment_2 Hela_Treatment_2 1.0000000  pearson
31   Hela_Control_1 Hela_Treatment_3 0.9325114  pearson
32   Hela_Control_2 Hela_Treatment_3 0.9677573  pearson
33   Hela_Control_3 Hela_Treatment_3 0.9684357  pearson
34 Hela_Treatment_1 Hela_Treatment_3 0.9308194  pearson
35 Hela_Treatment_2 Hela_Treatment_3 0.9750765  pearson
36 Hela_Treatment_3 Hela_Treatment_3 1.0000000  pearson
38   Hela_Control_2   Hela_Control_1 0.7720323 spearman
39   Hela_Control_3   Hela_Control_1 0.8040185 spearman
40 Hela_Treatment_1   Hela_Control_1 0.8573914 spearman
41 Hela_Treatment_2   Hela_Control_1 0.7010402 spearman
42 Hela_Treatment_3   Hela_Control_1 0.7159014 spearman
45   Hela_Control_3   Hela_Control_2 0.8557011 spearman
46 Hela_Treatment_1   Hela_Control_2 0.6365783 spearman
47 Hela_Treatment_2   Hela_Control_2 0.9105590 spearman
48 Hela_Treatment_3   Hela_Control_2 0.8101600 spearman
52 Hela_Treatment_1   Hela_Control_3 0.7442327 spearman
53 Hela_Treatment_2   Hela_Control_3 0.8131283 spearman
54 Hela_Treatment_3   Hela_Control_3 0.9246977 spearman
59 Hela_Treatment_2 Hela_Treatment_1 0.6644153 spearman
60 Hela_Treatment_3 Hela_Treatment_1 0.7413599 spearman
66 Hela_Treatment_3 Hela_Treatment_2 0.8626049 spearman
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>