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)

## PCA
p=plot_chosen_pca_experiment(CompleteIntensityExperiment, format = "html")
p[[1]] 
#%>% layout(
    #legend = list(
    #  orientation = 'h', x = 0.3, y = -0.1)
    #)