@Sara01 Welcome to Community!
Check out Using downloadHandler and R Studio 'Export as pdf' (cairo_pdf) for a working example . This is example is using base plot and not ggplot2.
Given ggplot2 plot objects can be saved, I would update the code to do something like:
plot_obj <- reactive({
pca_output <- pca_objects()$pca_output
eig = (pca_output$sdev)^2
variance <- eig*100/sum(eig)
cumvar <- paste(round(cumsum(variance),1), "%")
eig_df <- data.frame(eig = eig,
PCs = colnames(pca_output$x),
cumvar = cumvar)
ggplot(eig_df, aes(reorder(PCs, -eig), eig)) +
geom_bar(stat = "identity", fill = "white", colour = "black") +
geom_text(label = cumvar, size = 4,
vjust=-0.4) +
theme_bw(base_size = 14) +
xlab("PC") +
ylab("Variances") +
ylim(0,(max(eig_df$eig) * 1.1))
})
output$plot2 <- renderPlot({
plot_obj()
})
output$downloadPdf <- downloadHandler(
filename = function(){paste(input$dataset, '.pdf', sep = '')},
content = function(file){
ggsave(file, plot_obj())
},
contentType = "application/pdf"
)