update

.gitignore

@@ -1,2 +1,5 @@
 .DS_Store
 .Rproj.user
+.Rhistory
+.RData
+temp.R

app.R

@@ -1,4 +1,4 @@
-#.libPaths('/Users/chenjiawen/Desktop/Rlibs-4.0')
+.libPaths('/Users/chenjiawen/Desktop/Rlibs-4.0')
 library(shiny)
 library(bslib)
 library(dplyr)
@@ -21,8 +21,9 @@ library(readr)
 
 
 alter_method_name = function(method_vector){
-  input_name = c('Binspect','MoranI','SpaGene','RayleighSelection','scGCO','Spanve','HRG','SINFONIA',
-                 'SpaGCN','SpaGFT','SPARK','SPARKX','singleCellHaystack','nnsvg','SOMDE','SpatialDE','SpatialDE2_test_stat','HEARTSVG','Sepal','BSP',
+  input_name = c('Binspect','BinSpect','MoranI',"Moran's I",'SpaGene','RayleighSelection','scGCO','Spanve','HRG','SINFONIA',
+                 'SpaGCN','SpaGFT','SPARK','SPARKX','SPARK-X','singleCellHaystack','singlecellHaystack',
+                 'nnsvg','nnSVG','SOMDE','SpatialDE','SpatialDE2_test_stat','HEARTSVG','Sepal','sepal','BSP',
                  'SpatialDE2')
   # check if all method in input_name
   input = unique(method_vector)
@@ -33,7 +34,9 @@ alter_method_name = function(method_vector){
   }
   method_vector = case_when(
     method_vector == 'Binspect' ~ 'Binspect',
+    method_vector == 'BinSpect' ~ 'Binspect',
     method_vector == 'MoranI' ~ 'Moran\'s I',
+    method_vector == 'Moran\'s I' ~ 'Moran\'s I',
     method_vector == 'SpaGene' ~ 'SpaGene',
     method_vector == 'RayleighSelection' ~ 'RayleighSelection',
     method_vector == 'scGCO' ~ 'scGCO',
@@ -44,14 +47,18 @@ alter_method_name = function(method_vector){
     method_vector == 'SpaGFT' ~ 'SpaGFT',
     method_vector == 'SPARK' ~ 'SPARK',
     method_vector == 'SPARKX' ~ 'SPARK-X',
+    method_vector == 'SPARK-X' ~ 'SPARK-X',
     method_vector == 'singleCellHaystack' ~ 'singleCellHaystack',
+    method_vector == 'singlecellHaystack' ~ 'singleCellHaystack',
     method_vector == 'nnsvg' ~ 'nnSVG',
+    method_vector == 'nnSVG' ~ 'nnSVG',
     method_vector == 'SOMDE' ~ 'SOMDE',
     method_vector == 'SpatialDE' ~ 'SpatialDE',
     method_vector == 'SpatialDE2_test_stat' ~ 'SpatialDE2',
     method_vector == 'SpatialDE2' ~ 'SpatialDE2',
     method_vector == 'HEARTSVG' ~ 'HEARTSVG',
     method_vector == 'Sepal' ~ 'Sepal',
+    method_vector == 'sepal' ~ 'Sepal',
     method_vector == 'BSP' ~ 'BSP',
     TRUE ~ method_vector
   )
@@ -97,7 +104,8 @@ ui <- navbarPage(
           checkboxInput("show_anno", "Show annotation", FALSE),
           selectizeInput('anno_name','Annotation column',c(''), selected = '',multiple=FALSE),
           hr(), # Add a horizontal rule
-          checkboxInput("show_gene_exp", "Show gene expression (take a while to load the data)", FALSE),
+          #checkboxInput("show_gene_exp", "Show gene expression (take a while to load the data)", FALSE),
+          input_task_button("show_gene_exp", "Show gene expression (take a while to load the data)"), 
           selectizeInput('gene_name','Gene',c(''), selected = '',multiple=TRUE),
           tags$style(type = 'text/css',".selectize-input { word-wrap : break-word;}.selectize-dropdown {word-wrap : break-word;} "),
           tags$style(htmltools::HTML("
@@ -142,6 +150,7 @@ ui <- navbarPage(
           numericInput("digits", "Number of digits", value = 2, min = 0, max = 20)
         ),
         mainPanel(
+          tableOutput("SVG_message"),
           DTOutput("dataset_table")
         )
       )
@@ -170,7 +179,8 @@ ui <- navbarPage(
 server <- function(input, output, session) {
   
   
-  slide_data = reactive({
+  slide_data = eventReactive(
+    input$show_gene_exp,{
     req(input$slide_name)
     slide_name0 = input$slide_name
     tech = (meta_file %>% filter(slide==slide_name0))$tech
@@ -226,11 +236,10 @@ server <- function(input, output, session) {
 
   output$scatter <- renderPlot(
     {
-      if(input$show_gene_exp){
         data = slide_data()
         data = data %>% select(xaxis,yaxis,input$gene_name)
         data = reshape2::melt(data,id.vars = c('xaxis','yaxis'))
-        print(data)
+        #print(data)
         p <- ggplot(data)+geom_point(aes(x=xaxis,y=yaxis,color=value),size = input$point_size)+
           theme_article()+scale_y_reverse()+scale_color_viridis_c(name='Gene expression')+
           facet_wrap(~variable)+
@@ -239,9 +248,6 @@ server <- function(input, output, session) {
                 axis.ticks = element_blank())+
           coord_fixed()
         p
-      }else{
-        NULL
-      }
     },
     res = 100
   )
@@ -315,10 +321,32 @@ server <- function(input, output, session) {
     },
     res = 100
   )
-
+  
+  output$SVG_message = renderTable({
+    req(input$atlas_slide_name)
+    req(input$atlas_method)
+    SVG_table_rank = fread("rank_threshold.csv")
+    #print(input$atlas_method)
+    method_message = SVG_table_rank%>%
+      mutate(Method_alter = alter_method_name(Method)) %>%
+      filter(Method_alter==input$atlas_method)
+    #paste0('Method: ', method_message$Method_alter, ' Order: ', method_message$`Rank order`,
+    #       ' Rank Variable Name: ', method_message$`Rank Variable Name`, 
+    #       ' SVG Threshold Name: ', method_message$`SVG Threshold Name`, 
+    #       ' Threshold Value: ', method_message$`Threshold Value`)\
+    method_message = method_message %>% select(-Method,-Language) %>% select(Method_alter,everything())
+    colnames(method_message) = c('Method','Rank order','Rank Variable Name','SVG Threshold Name','Threshold Value')
+    method_message
+  }) 
+  
   output$dataset_table <- renderDT({
-    file_name = paste0(input$atlas_slide_name,'.csv')
-    output_table = fread(file_name)
+    req(input$atlas_slide_name)
+    req(input$atlas_method)
+    output_table = request(paste0('https://huggingface.co/datasets/jiawennnn/STimage-benchmark-data/resolve/main/SVG/',input$atlas_method,'/',input$atlas_slide_name,'_organized.csv')) |> 
+      req_perform()|>
+      resp_body_string() |>   # get text body as string
+      read_csv(show_col_types = FALSE) %>% as.data.table()
+    colnames(output_table)[1:3] = c('Gene','.SVG','.SVG_rank')
     # round the numeric columns to specified digits
     num_cols = sapply(output_table, is.numeric)
     output_table[, (which(num_cols)) := lapply(.SD, round, digits = input$digits), .SDcols = which(num_cols)]
@@ -326,4 +354,4 @@ server <- function(input, output, session) {
   })
 }
 
-shinyApp(ui, server)
+shinyApp(ui, server)