Style code (GHA)

bigomics · Sep 11, 2023 · 6274642 · 6274642
1 parent 523f975
commit 6274642
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Showing 5 changed files with 42 additions and 42 deletions.
diff --git a/components/board.connectivity/R/connectivity_plot_connectivityHeatmap.R b/components/board.connectivity/R/connectivity_plot_connectivityHeatmap.R
@@ -99,7 +99,7 @@ connectivity_plot_connectivityHeatmap_server <- function(id,
         }
         F <- F[order(-rowMeans(F**2, na.rm = TRUE)), , drop = FALSE]
         F <- scale(F, center = FALSE)
-        
+
         list(
           F = F,
           score = rho2
@@ -124,42 +124,41 @@ connectivity_plot_connectivityHeatmap_server <- function(id,
         )
       }
 
-      reverse_negative <- function(F, k=1) {
-          ## reverse sign of negative profiles
-          fsign <- sign(cor(F, F[,k])[,1])    
-          F2 <- t( t(F) * fsign)
-          ii <- which(fsign < 0)
-          if(length(ii)) {
-              reverse_contrast_name <- function(s) {
-                  prefix <- sub(":.*","",s)
-                  if(prefix==s) {
-                      prefix=NULL
-                  } else {
-                      prefix <- paste0(prefix,":")
-                  }
-                  vs.name <- sub(".*[:]","",s)
-                  vs.name2 <- strsplit(vs.name, split="_vs_")[[1]]
-                  paste0(prefix,paste(rev(vs.name2),collapse="_vs_"))
-              }
-              rev.name <- sapply(colnames(F2)[ii], reverse_contrast_name )
-              colnames(F2)[ii] <- rev.name
+      reverse_negative <- function(F, k = 1) {
+        ## reverse sign of negative profiles
+        fsign <- sign(cor(F, F[, k])[, 1])
+        F2 <- t(t(F) * fsign)
+        ii <- which(fsign < 0)
+        if (length(ii)) {
+          reverse_contrast_name <- function(s) {
+            prefix <- sub(":.*", "", s)
+            if (prefix == s) {
+              prefix <- NULL
+            } else {
+              prefix <- paste0(prefix, ":")
+            }
+            vs.name <- sub(".*[:]", "", s)
+            vs.name2 <- strsplit(vs.name, split = "_vs_")[[1]]
+            paste0(prefix, paste(rev(vs.name2), collapse = "_vs_"))
           }
-          F2
+          rev.name <- sapply(colnames(F2)[ii], reverse_contrast_name)
+          colnames(F2)[ii] <- rev.name
+        }
+        F2
       }
-
-      create_iheatmap <- function(F, score, maxfc = 20, maxgenes = 60) {
 
+      create_iheatmap <- function(F, score, maxfc = 20, maxgenes = 60) {
         sel <- 1:min(NCOL(F), maxfc)
         F <- F[, sel, drop = FALSE]
         score <- score[colnames(F)]
         F <- head(F, maxgenes)
-        if(input$reverse_neg) {
-            F <- reverse_negative(F, k=1)
-            score <- abs(score)
+        if (input$reverse_neg) {
+          F <- reverse_negative(F, k = 1)
+          score <- abs(score)
         }
         ii <- order(rowMeans(F, na.rm = TRUE))
         F <- F[ii, ]
-        
+
         plt <- iheatmapr::main_heatmap(
           data = t(F),
           layout = list(margin = list(r = 0))

diff --git a/components/board.connectivity/R/connectivity_plot_connectivityMap.R b/components/board.connectivity/R/connectivity_plot_connectivityMap.R
@@ -403,7 +403,7 @@ connectivity_plot_connectivityMap_server <- function(id,
         plt <- plt %>%
           plotly::layout(
             showlegend = FALSE,
-            margin = list(l = 0, r = 0, b = 0, t = 0)            
+            margin = list(l = 0, r = 0, b = 0, t = 0)
           ) %>%
           plotly::hide_colorbar()
         return(plt)

diff --git a/components/board.connectivity/R/connectivity_server.R b/components/board.connectivity/R/connectivity_server.R
@@ -71,14 +71,14 @@ ConnectivityBoard <- function(
       meta2 <- pgx$gset.meta$meta
       has.contrast <- ct %in% names(meta1) && ct %in% names(meta2)
       shiny::req(has.contrast)
-      
+
       if (!has.contrast) {
         dbg("[ConnectivityBoard:getCurrentContrast] ERROR! ct = ", ct)
         dbg("[ConnectivityBoard:getCurrentContrast] ERROR! names(gx.meta) = ", names(meta1))
         dbg("[ConnectivityBoard:getCurrentContrast] ERROR! names(gset.meta) = ", names(meta2))
         return(NULL)
       }
-      
+
       fc <- meta1[[ct]]$meta.fx
       names(fc) <- rownames(meta1[[ct]])
       gs <- meta2[[ct]]$meta.fx
@@ -87,16 +87,16 @@ ConnectivityBoard <- function(
       list(name = ct, fc = fc, gs = gs)
     })
 
-##    observeEvent({
-##        getCurrentContrast()
-##        input$genelist_ntop
-##    },{
+    ##    observeEvent({
+    ##        getCurrentContrast()
+    ##        input$genelist_ntop
+    ##    },{
     observe({
       contr <- getCurrentContrast()
       shiny::req(contr)
       ntop <- as.integer(input$genelist_ntop)
       top50 <- head(names(sort(abs(contr$fc), decreasing = TRUE)), ntop)
-      top50 <- paste(top50, collapse = " ")      
+      top50 <- paste(top50, collapse = " ")
       updateTextAreaInput(session, "genelist", value = top50)
     })
 
@@ -269,8 +269,8 @@ ConnectivityBoard <- function(
       }
 
       scores <- as.data.frame(all.scores[[ct]])
-      dbg("[getConnectivityScores] dim.scores=",dim(scores))
-      
+      dbg("[getConnectivityScores] dim.scores=", dim(scores))
+
       if (input$abs_score == FALSE) {
         ## put sign back!!!
         scores$score <- scores$score * sign(scores$rho)

diff --git a/components/board.connectivity/R/connectivity_table_foldchange.R b/components/board.connectivity/R/connectivity_table_foldchange.R
@@ -68,7 +68,7 @@ connectivity_table_foldchange_server <- function(id,
         fillContainer = TRUE,
         options = list(
           dom = "lfrtip",
-          #dom = "lrtip",
+          # dom = "lrtip",
           pageLength = 99999,
           scrollX = TRUE,
           scrollY = height,

diff --git a/components/board.connectivity/R/connectivity_ui.R b/components/board.connectivity/R/connectivity_ui.R
@@ -59,10 +59,11 @@ ConnectivityInputs <- function(id) {
         "Paste a list of genes that defines your signature. By default, the top50 most (absolute) differentially expressed genes (by logFC) are chosen for the selected comparison."
       ),
       shiny::radioButtons(
-                 ns("genelist_ntop"),
-                 "ngenes:", choices = c(10,50,100),
-                 sel = 50, inline = TRUE
-             ),
+        ns("genelist_ntop"),
+        "ngenes:",
+        choices = c(10, 50, 100),
+        sel = 50, inline = TRUE
+      ),
       br(),
       withTooltip(
         shiny::actionButton(ns("recalc"), "recalculate"),