PlotIndiv integration in shinyapps

Support
1

Dear mixOmics team,

I’m trying to display a plotIndiv graph in a shiny dashboard tabPanel.
I declare a function to load and parse my dataset, compute a PCA to finaly plot individuals (mixOmics pca and plotIndiv).
Independently, this function works well, but when is integrated in shiny it doesn’t.

Any tricks ? Thanks.

Xavier.

Ubuntu 18.04
R4.0.5
Rstudio

2

Hi @xgrand,

Are you sure you set up the shiny input/output correctly? This does work just fine for me using the following app:

library(shiny)
library(mixOmics)

# Define UI for application that draws a histogram
ui <- fluidPage(
    titlePanel("plotIndiv"),
    sidebarLayout(
        sidebarPanel(
            numericInput('pc1', 'First PC', value=1,
                         min=1, max=5, step=1),
            numericInput('pc2', 'Second PC', value=2,
                         min=1, max=5, step=1)
        ),
        mainPanel(plotOutput("plotIndiv"))
    )
)

server <- function(input, output) {

    output$plotIndiv <- renderPlot({
        data(multidrug)
        comp <- c(input$pc1, input$pc2)
        pca.res <- pca(multidrug$ABC.trans, ncomp = 5, scale = TRUE)
        # biplot(pca.res, group = multidrug$cell.line$Class, legend.title = 'Class')
        # samples representation
        plotIndiv(pca.res, comp = comp, ind.names = multidrug$cell.line$Class,
                  group = as.numeric(as.factor(multidrug$cell.line$Class)))
        
    })
}

# Run the application 
shinyApp(ui = ui, server = server)

Can you check and see if it works on your machine as well?

Best,

Al

3

Yes, it was something like input/output setup. Many thanks !
Xavier.