In MassDynamics/MassExpression: MassExpression

knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE, 
                      fig.path = params$output_figure, dev = "svg")

library(dplyr)
library(stringr)
library(MassExpression)
library(plotly)

CompleteIntensityExperiment <- params$listInt$CompleteIntensityExperiment
IntensityExperiment <- params$listInt$IntensityExperiment
design <- colData(IntensityExperiment)

comparisonExperiments <- 
    listComparisonExperiments(CompleteIntensityExperiment)

p=plot_chosen_pca_experiment(CompleteIntensityExperiment, format = "html", 
                             auto_select_features = "de")

if(is.null(p[[1]])){
  text <- "Not enough differentially expressed proteins to produce a PCA plot. At least 4 are required."
}else{
  p[[1]]
}

r if(is.null(p[[1]])) text

MassDynamics/MassExpression documentation built on May 7, 2023, 11:29 a.m.