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Handle input data with single condition #5

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Handle input data with single condition #5

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17 changes: 16 additions & 1 deletion server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -878,6 +878,15 @@ server <- function(input, output, session) {
# diff_all <- test_diff_customized(imputed_data(), type = "manual",
# test = c("SampleTypeTumor"), design_formula = formula(~0+SampleType))
data <- imputed_data()
conditions <- as.character(unique(colData(data)$condition))
validate(need(
length(conditions) >= 2,
paste0(
"Differential expression analysis requires at least 2 conditions. ",
"Only 1 condition ('", conditions[1], "') was detected in the experiment design. ",
"QC plots (PCA, sample correlation, missing values, etc.) are still available."
)
))
if (input$exp == "LFQ" & input$lfq_type == "Spectral Count") {
assay(data) <- log2(assay(data))
} else if (input$exp == "LFQ-peptide" & input$lfq_pept_type == "Spectral Count") {
Expand Down Expand Up @@ -1437,7 +1446,13 @@ server <- function(input, output, session) {
})

cvs_input<-reactive({
plot_cvs(dep(), id="label", scale=!input$cvs_full_range, check.names=F)
data <- imputed_data()
if (input$exp == "LFQ" & input$lfq_type == "Spectral Count") {
assay(data) <- log2(assay(data))
} else if (input$exp == "LFQ-peptide" & input$lfq_pept_type == "Spectral Count") {
assay(data) <- log2(assay(data))
}
plot_cvs(data, id="label", scale=!input$cvs_full_range, check.names=F)
})

num_total <- reactive({
Expand Down