Add 4 conditions on manhattan plots

ladyson1806 · Jan 19, 2024 · e554663 · e554663
1 parent e8fec9d
commit e554663
Showing 1 changed file with 69 additions and 27 deletions.
diff --git a/code/shiny_apps/piQTL_manhattan/app.R b/code/shiny_apps/piQTL_manhattan/app.R
@@ -26,36 +26,55 @@ ui <- fluidPage(
       br(),
       column(
         width = 8,
-        plotlyOutput(outputId = "MTX_manhattanplot")
+        plotlyOutput(outputId = "Drug_MTX_manhattanplot")
         ),
 
       column(
         width = 4,
-        plotlyOutput(outputId = "MTX_qqplot")
+        plotlyOutput(outputId = "Drug_MTX_qqplot")
       ),
 
-      # column(
-      #   width = 3,
-      #   plotlyOutput(outputId = "MTX_volcanoplot")
-      # ),
+      br(),
+      br(),
+
+      h3("Drug + noMTX"),
+      column(
+        width = 8,
+        plotlyOutput(outputId = "Drug_noMTX_manhattanplot")
+      ),
 
+      column(
+        width = 4,
+        plotlyOutput(outputId = "Drug_noMTX_qqplot")
+      ),  
+
       br(),
       br(),
+
       h3("noDrug + MTX"),
       column(
         width = 8,
-        plotlyOutput(outputId = "noMTX_manhattanplot")
+        plotlyOutput(outputId = "noDrug_MTX_manhattanplot")
       ),
 
       column(
         width = 4,
-        plotlyOutput(outputId = "noMTX_qqplot")
+        plotlyOutput(outputId = "noDrug_MTX_qqplot")
+      ),
+
+      br(),
+      br(),
+
+      h3("noDrug + noMTX"),
+      column(
+        width = 8,
+        plotlyOutput(outputId = "noDrug_noMTX_manhattanplot")
       ),
 
-      # column(
-      #   width = 3,
-      #   plotlyOutput(outputId = "noMTX_volcanoplot")
-      # )   
+      column(
+        width = 4,
+        plotlyOutput(outputId = "noDrug_noMTX_qqplot")
+      )   
     )
   )
 )
@@ -66,45 +85,68 @@ library(manhattanly)
 
 server <- function(input, output) {
 
-  MTX_datasetInput <- reactive({
+  Drug_MTX_datasetInput <- reactive({
     PPI <- input$ppi
     DRUG <- input$drug
     infile = glue('https://raw.githubusercontent.com/ladyson1806/public_hosting/main/piQTL_mapping/formatted_for_manhattan/{PPI}_MTX_{DRUG}_avg_logratio_Fitness_minus_ref.csv')
     read.csv(infile)
   })
+
+  Drug_noMTX_datasetInput <- reactive({
+    PPI <- input$ppi
+    DRUG <- input$drug
+    infile = glue('https://raw.githubusercontent.com/ladyson1806/public_hosting/main/piQTL_mapping/formatted_for_manhattan/{PPI}_noMTX_{DRUG}_avg_logratio_Fitness_minus_ref.csv')
+    read.csv(infile)
+  })
 
-  noMTX_datasetInput <- reactive({
+  noDrug_MTX_datasetInput <- reactive({
     PPI <- input$ppi
     DRUG <- input$drug
     infile = glue('https://raw.githubusercontent.com/ladyson1806/public_hosting/main/piQTL_mapping/formatted_for_manhattan/{PPI}_MTX_noDrug_avg_logratio_Fitness_minus_ref.csv')
 
     read.csv(infile)
   })
+
+  noDrug_noMTX_datasetInput <- reactive({
+    PPI <- input$ppi
+    DRUG <- input$drug
+    infile = glue('https://raw.githubusercontent.com/ladyson1806/public_hosting/main/piQTL_mapping/formatted_for_manhattan/{PPI}_noMTX_noDrug_avg_logratio_Fitness_minus_ref.csv')
+
+    read.csv(infile)
+  })
 
 
-  output$MTX_manhattanplot <- renderPlotly({
-    manhattanly(MTX_datasetInput(), chr='CHR', snp="SNP", gene="GENE", labelChr=c(1:16,"MT"), suggestiveline = -log10(1e-04), genomewideline=F, title=glue('{input$ppi} with {input$drug}' ))
+  output$Drug_MTX_manhattanplot <- renderPlotly({
+    manhattanly(Drug_MTX_datasetInput(), chr='CHR', snp="SNP", gene="GENE", labelChr=c(1:16,"MT"), suggestiveline = -log10(1e-04), genomewideline=F, title=glue('{input$ppi} with {input$drug}' ))
   })
 
-  output$MTX_qqplot <- renderPlotly({
-    qqly(MTX_datasetInput(), chr='CHR', snp="SNP", gene="GENE")
+  output$Drug_MTX_qqplot <- renderPlotly({
+    qqly(Drug_MTX_datasetInput(), chr='CHR', snp="SNP", gene="GENE")
   })
 
-  output$MTX_volcanoplot <- renderPlotly({
-    volcanoly(MTX_datasetInput(), genomewideline=-log10(1e-04))
+  output$Drug_noMTX_manhattanplot <- renderPlotly({
+    manhattanly(Drug_noMTX_datasetInput(), chr='CHR', snp="SNP", gene="GENE", labelChr=c(1:16,"MT"), suggestiveline = -log10(1e-04), genomewideline=F, title=glue('{input$ppi} withss {input$drug}'))
   })
 
-  output$noMTX_manhattanplot <- renderPlotly({
-    manhattanly(noMTX_datasetInput(), chr='CHR', snp="SNP", gene="GENE", labelChr=c(1:16,"MT"), suggestiveline = -log10(1e-04), genomewideline=F, title=glue('{input$ppi} without {input$drug}'))
+  output$Drug_noMTX_qqplot <- renderPlotly({
+    qqly(Drug_noMTX_datasetInput(), chr='CHR', snp="SNP", gene="GENE")
+  })
+
+  output$noDrug_MTX_manhattanplot <- renderPlotly({
+    manhattanly(noDrug_MTX_datasetInput(), chr='CHR', snp="SNP", gene="GENE", labelChr=c(1:16,"MT"), suggestiveline = -log10(1e-04), genomewideline=F, title=glue('{input$ppi} without {input$drug}'))
   })
 
-  output$noMTX_qqplot <- renderPlotly({
-    qqly(noMTX_datasetInput(), chr='CHR', snp="SNP", gene="GENE")
+  output$noDrug_MTX_qqplot <- renderPlotly({
+    qqly(noDrug_MTX_datasetInput(), chr='CHR', snp="SNP", gene="GENE")
+  })
+
+  output$noDrug_noMTX_manhattanplot <- renderPlotly({
+    manhattanly(noDrug_noMTX_datasetInput(), chr='CHR', snp="SNP", gene="GENE", labelChr=c(1:16,"MT"), suggestiveline = -log10(1e-04), genomewideline=F, title=glue('{input$ppi} without {input$drug}'))
   })
 
-  # output$noMTX_volcanoplot <- renderPlotly({
-  #   volcanoly(noMTX_datasetInput(), genomewideline=-log10(1e-04))
-  # })
+  output$noDrug_noMTX_qqplot <- renderPlotly({
+    qqly(noDrug_noMTX_datasetInput(), chr='CHR', snp="SNP", gene="GENE")
+  })
 
 }