Problems with DESeq2 'design' parameter using Shiny/rhandsontable
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hinkel2 • 0
@hinkel2-16914
Last seen 2.6 years ago

Hi all!

I want to create a shiny app for DESeq2 analysis. My main thought is to upload count matrix, extract colnames/experiments and provide an editable table to user in order to assign conditions to respective experiment (-> colData). After adjustment, user has to click a button in order to start DESeq2. However, when I click the button, I get following error:

Warning: Error in DESeqDataSet: the design formula contains an ordered factor. The internal steps do not work on ordered factors as a formula. Instead you should provide a matrix to the 'design' slot or to the 'full' argument of DESeq(), constructed using model.matrix.

I also checked whether values$new was transformed into a dataframe using hot _ to _ r(), and indeed it was. I can also present it as a dataframe in shiny using renderTable() (not shown in code), suggesting that transformation to dataframe from rhandsontable object worked

Does someone see why especially the design-part does not work or how I could solve this? Thanks in advance!

# server part
server <- function(input, output) {
  values <- reactiveValues(df_data = NULL)

  # general data input
  observeEvent(input$file, {
    if (is.null(input$file$datapath))
      return(NULL)

      values$count <- read.csv(input$file$datapath, row.names = 1)
      values$df_data <- data.frame(experiment_name = colnames(values$count),
                      condition = rep(" information",length(colnames(values$count))))
  })

 #render table
  output$x1 <- renderRHandsontable({
    if(is.null(values$df_data))
      return(NULL)

    rhandsontable(values$df_data) %>%
      hot_col(col = c("experiment_name","condition"), allowInvalid = TRUE, strict=FALSE)
  })

  #save edits/update (button click)!
  observeEvent(input$saveBtn,{
    values$new <- as.data.frame(hot_to_r(input$x1))

    values$de <- DESeqDataSetFromMatrix(countData = values$count,
                                        colData = values$new,
                                        design = ~condition)
  })
}
deseq2 shiny design rhandsontable hot_to_r() • 621 views
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@mikelove
Last seen 4 hours ago
United States

Can you show me the condition column of colData? Is it an ordered factor? Is there reason to have it an ordered factor?

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Hi Michael!

I checked for condition column before (values$df_data) and after (values$new) user edit if it is a factor and used renderText() to get output (corresponding ui-part not shown):

output$df_data <- renderText({
 is.factor(values$df_data$condition)
})

output$x2 <- renderText({
 is.factor(values$new$condition)
})

For both, the result is 'TRUE', but I don't know why. The following just shows me the factor vector with numbers (if i only have one condition, I get n times 1 and so on):

output$df_data <- renderText({
  values$df_data$condition
})

output$x2 <- renderText({
  values$new$condition
})

I actually did not expect it be a factor when I created the data frame at the top of 'server' function. Even if I use as.character() as wrapper around 'experiment_name' and/or 'condition', I still get a factor:

values$df_data <- data.frame(experiment_name = as.character(colnames(values$count)),
                                   condition = as.character(rep(" information",
                                               length(colnames(values$count)))))
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Can you print out colData(dds)$condition?

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0
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Assuming you mean DESeqDataSetFromMatrix(...) with 'dds', I printed it out using renderText():

output$x2 <- renderText({
colData(DESeqDataSetFromMatrix(countData = values$count,
                                 colData = values$new,
                                  design = ~condition))$condition
})

resulting in the same error:

Error in DESeqDataSet: the design formula contains an ordered factor. The internal steps do not work on ordered factors as a formula. Instead you should provide a matrix to the 'design' slot or to the 'full' argument of DESeq(), constructed using model.matrix.

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0
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Oops, I mean, can you print out values$new?

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renderTable() (renderText() won't work because it cannot concat table to string):

output$x2 <- renderTable({
values$new
})

OR

output$x2 <- renderTable({
values$new$experiment_name
})

OR

output$x2 <- renderTable({
values$new$condition
})

will print out the correctly edited table in the shiny app. So in general data storage and editing seems to work, but can - for some reason - not be accessed using '~condition'.

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0
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Hmm, I can't help much more I guess on this one, because for debugging, you would want to know what the input you are providing to DESeq2.

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