Cosmetic changes for the logs

cengenproject · Oct 12, 2022 · 4a65f0d · 4a65f0d
1 parent 2b82e41
commit 4a65f0d
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Showing 2 changed files with 33 additions and 19 deletions.
diff --git a/server.R b/server.R
@@ -1,5 +1,5 @@
-#### CenGenAPP 2018-2020
-#### Report bugs to: gabrielsantperebaro@gmail.com
+#### CeNGEN-app 2018-2022
+#### Report bugs at https://github.com/cengenproject/CengenApp/issues
 
 
 
@@ -8,6 +8,7 @@ server <- function(input, output) {
   ### Gene expression by cell type Panel ----
 
   observeEvent(input$TCell, {
+    cat("--> thresholded gene expression TCell\n")
     withProgress(message = "Obtaining information...", value = 0, {
 
       load_as_needed("L4.all.TPM.raw_th")
@@ -75,6 +76,7 @@ server <- function(input, output) {
   })
 
   observeEvent(input$TGene, {
+    cat("--> thresholded gene expression TGene\n")
 
     load_as_needed("L4.all.TPM.raw_th")
     load_as_needed("ths")
@@ -179,6 +181,7 @@ server <- function(input, output) {
   })
 
   observeEvent( list(input$Tgene_name_batch, input$Tgene_cut_batch) , {
+    cat("--> thresholded gene expression Tgene_name_batch/Tgene_cut_batch\n")
 
     load_as_needed("L4.all.TPM.raw_th")
     load_as_needed("ths")
@@ -244,6 +247,7 @@ server <- function(input, output) {
   ### Find markers based on percentage of expression Panel ----
 
   observeEvent(input$Filter, {
+    cat("--> find markers Filter\n")
 
     load_as_needed("pcttable")
 
@@ -321,6 +325,7 @@ server <- function(input, output) {
   ### Enriched Genes by cell type Panel ----
 
   observeEvent(input$Markers, {
+    cat("--> enriched genes Markers\n")
 
     load_as_needed("markers")
 
@@ -350,7 +355,9 @@ server <- function(input, output) {
         }
       )
   })
+
   observeEvent(input$Markers2, {
+    cat("--> enriched genes Markers2\n")
 
     load_as_needed("markersAllcells")
 
@@ -380,8 +387,7 @@ server <- function(input, output) {
 
   ### Find Differential Expression between Cell Types Panel ----
   observeEvent(input$DEXButton, {
-
-    cat("Testing DE of ", input$batch1, " vs ", input$batch2, "\n")
+    cat("--> testing DE of ", input$batch1, " vs ", input$batch2, "\n")
 
     b1 <- unlist(strsplit(input$batch1, split = ","))
     b1 <- gsub(" ", "", as.character(b1))
@@ -534,7 +540,8 @@ server <- function(input, output) {
 
   ### Heatmaps of gene expression Panel ----
 
-  observeEvent(input$PlotHeatmap, {
+  observeEvent(input$PlotHeatmapFromList, {
+    cat("--> heatmap PlotHeatmapFromList\n")
 
     load_as_needed("med.scaled.long")
     load_as_needed("L4.TPM.raw.scaled.long")
@@ -696,7 +703,8 @@ server <- function(input, output) {
 
   ### From file
 
-  observeEvent(input$PlotHeatmap2, {
+  observeEvent(input$PlotHeatmapFromFile, {
+    cat("--> heatmap PlotHeatmapFromFile\n")
 
     load_as_needed("med.scaled.long")
     load_as_needed("L4.TPM.raw.scaled.long")

diff --git a/ui.R b/ui.R
@@ -1,5 +1,8 @@
-#### CenGenAPP 2018-2020
-#### Report bugs to: [email protected]
+#### CeNGEN-app 2018-2022
+#### Report bugs at https://github.com/cengenproject/CengenApp/issues
+
+
+cat("############# Loading libraries #################\n")
 
 require(shiny)
 library(shinyjs)
@@ -22,15 +25,18 @@ library(qs)
 library(Matrix)
 library(limma)
 
+cat("############## Setting options ##################\n")
+
 options(repos = BiocManager::repositories())
 options(shiny.maxRequestSize = 400 * 1024 ^ 2)
 
-source("Functions.R")
-
-
 options(scipen = 0)
 options(digits = 2)
 
+cat("############ End initializations ################\n")
+
+
+source("Functions.R")
 utr <-
   c(
     "WBGene00023498",
@@ -113,7 +119,7 @@ ui <- fluidPage(
               choices = c(1:4, "Unfiltered", "All Cells Unfiltered"),
               selected = 2
             ),
-            actionButton("TCell", "Expressed genes", icon = icon("hand-o-right"))
+            actionButton("TCell", "Expressed genes", icon = icon("hand-point-right"))
 
           ),
           #column(width = 1, offset = 0, style='padding:5px;'),
@@ -130,7 +136,7 @@ ui <- fluidPage(
               choices = c(1:4, "Unfiltered", "All Cells Unfiltered"),
               selected = 2
             ),
-            actionButton("TGene", "Which cell types", icon = icon("hand-o-right"))
+            actionButton("TGene", "Which cell types", icon = icon("hand-point-right"))
           ),
           column(
             2,
@@ -206,7 +212,7 @@ ui <- fluidPage(
               label = "Minimum percentage of cells expressing the gene",
               value = 65
             ),
-            actionButton("Filter", "Run query", icon = icon("hand-o-right"))
+            actionButton("Filter", "Run query", icon = icon("hand-point-right"))
 
           ),
           #column(width = 1, offset = 0, style='padding:5px;'),
@@ -343,7 +349,7 @@ ui <- fluidPage(
               selected = c("RME_DV","RME_LR"),
               multiple = TRUE
             ),
-            actionButton("DEXButton", "Calculate DEX", icon = icon("hand-o-right"))
+            actionButton("DEXButton", "Calculate DEX", icon = icon("hand-point-right"))
 
           ),
           column(
@@ -400,8 +406,8 @@ ui <- fluidPage(
 
 
         actionButton(
-          "PlotHeatmap","Plot heatmap from list",
-          icon = icon("hand-o-right")
+          "PlotHeatmapFromList","Plot heatmap from list",
+          icon = icon("hand-point-right")
 
 
         ),
@@ -415,9 +421,9 @@ ui <- fluidPage(
           )),
           #column(3,actionButton("resetFile", "Clear uploaded file")),
           column(3,   actionButton(
-            "PlotHeatmap2",
+            "PlotHeatmapFromFile",
             "Plot heatmap from file",
-            icon = icon("hand-o-right")
+            icon = icon("hand-point-right")
           ))
         ),