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I am trying to create a shiny board for my scRNA seq data. I have saved my seurat objects adn I use following code as below:

library(shiny)
library(shinythemes)
library(Seurat)
library(uwot)


set_1 <- readRDS("/temp2/data/mydataB10.rds")
set_2 <- readRDS("/temp2/data/mydataB5.rds")

ui <- fluidPage(
    
    # Application title
    titlePanel("scRNAseq data browser"),
    
    fluidRow(
        column(4,
               
               sidebarPanel(
                   radioButtons("dataset", label = h3("Dataset"),
                                choices = list("sample1" = "set_1", "sample2" = "set_2"),
                                selected = "set_1"),
                   helpText("Enter gene names in CAPS.  Gene names must be exact."),
                   textInput("gene2", label = "Gene Name", value = "GAPDH")
                   
               )
        ),
        column(8,
               column(6, 
                      mainPanel(
                          plotOutput("dimPlot1", width = "150%"),
                          plotOutput("genePlot2", width = "150%")
                      )
               )
        )
    )
)


server <- function(input, output, session) {
    
    datasetInput <- reactive({
        df <- (input$dataset)
            })
    
    output$dimPlot1 <- renderPlot({
        DimPlot(datasetInput(), reduction = "umap")
    })
    
    output$genePlot2 <- renderPlot({
        FeaturePlot(datasetInput(), features = (input$gene2), reduction = "umap")
    })
    
}

shinyApp(ui, server)  

That error that I get on the section where image needs to be displayed is "Subscript out of bound".

Following dataset can be downloaded and used as an example curl -Lo pbmc_10k_v3.rds https://www.dropbox.com/s/3f3p5nxrn5b3y4y/pbmc_10k_v3.rds?dl=1

Can anyone help in fixing this shiny script so that it works.

Many thanks.

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Not easy to reproduce your error but here is my guess. This is a string, you can check it:

input$dataset
class(input$dataset)

This is a simple solution. If you want to call out the dataset depending on input, use a list:

set_1 <- readRDS("/temp2/data/mydataB10.rds")
set_2 <- readRDS("/temp2/data/mydataB5.rds")
data_list = list(set_1=set_1,set_2=set_2)

Then in the server :

datasetInput <- reactive({
        df <- data_list[[input$dataset]]
            })
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  • $\begingroup$ It worked, thank you:) $\endgroup$
    – Angelo
    Dec 3 '20 at 11:04

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