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plot_variation_pca() is a GGplot2 implementation for plotting the variability in normalized values by PCA analysis, generating two facets. The left facet is a plot of CVs for each normalization method. The right facet is a plot of the 95%CI in abundance, essentially the conservative dynamic range. The goal is to select a normalization method that minimizes CVs while also retaining the dynamic range.

Usage

plot_variation_pca(data = NULL, ...)

Arguments

data

tidyproteomics data object

...

passthrough for ggsave see plotting

Value

a (tidyproteomics data-object | ggplot-object)

Examples

library(dplyr, warn.conflicts = FALSE)
library(tidyproteomics)
hela_proteins %>%
  normalize(.method = c("linear", "loess", "randomforest")) %>%
  plot_variation_pca()
#>  Normalizing quantitative data
#>  ... using linear regression
#>  ... using linear regression [219ms]
#> 
#>  ... using loess regression
#>  ... using loess regression [1.3s]
#> 
#>  ... using randomforest regression
#>  ... using randomforest regression [41.2s]
#> 
#>  Selecting best normalization method
#>  Selecting best normalization method ... done
#> 
#>   ... selected randomforest