diff --git a/.DS_Store b/.DS_Store
new file mode 100644
index 0000000..63d1874
Binary files /dev/null and b/.DS_Store differ
diff --git a/Scripts/delta_list.R b/Scripts/delta_list.R
new file mode 100644
index 0000000..9f299aa
--- /dev/null
+++ b/Scripts/delta_list.R
@@ -0,0 +1,88 @@
+to_matrix <- function(df) {
+  
+  nm <- df[[1]]
+  
+  df %>% select(-1) %>% as.matrix() %>% set_rownames(nm)
+  
+}
+
+my_quick_mass <- function(x) {
+  check_chemform(isotopes = isotopes, x)$monoisotopic_mass
+}
+
+K = my_quick_mass("K")
+Na = my_quick_mass("Na")
+H = my_quick_mass("H")
+C13 = 1.003355
+
+NH3 = my_quick_mass("NH3")
+H2O = my_quick_mass("H2O")
+
+
+delta_list = 
+  c(`Na-H` = Na - H, 
+    `K-H` = K-H,
+    NH3 = NH3,
+    `Na-NH4` = Na - NH3 - H,
+    `K-NH4` = K - NH3 - H,
+    H2O = H2O,
+    C13 = C13,
+    C1H2O2 = my_quick_mass("C1H2O2"),
+    C2H7N1 = my_quick_mass("C2H7N1"),
+    C8H6O3 = my_quick_mass("C8H6O3"),
+    CO2 = my_quick_mass("C1O2"),
+    Bz = my_quick_mass("C7H5O1"),
+    Acetonitrile = my_quick_mass("C2H3N1"),
+    DMSO = my_quick_mass("C2H6O1S1")
+  )
+
+
+d1 <- tibble(
+  adduct = c("H", "Na", "K", "NH4"),
+  delta1 = c(0, Na-H, K-H, NH3)
+)
+
+
+
+d2 <- tibble(
+  gain_loss = c("None", "+DMSO", "+Acetonitrile", "+C2H7N1", "+H2O", "-H2O", "-CO2", "-C1H2O2", "-C8H6O3", "-Bz", "-NH3"),
+  delta2 = c(0, delta_list[c("DMSO", "Acetonitrile", "C2H7N1", "H2O")], -delta_list[c("H2O", "CO2", "C1H2O2", "C8H6O3", "Bz", "NH3")])
+)
+
+d3 <- tibble(
+  isotope = c("M", "M+1", "M+2", "M+3"),
+  delta3 = C13 * c(0:3)
+)
+
+
+format_species <- function(a, gl, iso) {
+  
+  case_when(
+    gl == "None" & iso == "M" ~ sprintf("[%s + %s]", iso, a),
+    gl == "None" & iso != "M" ~ sprintf("[(%s) + %s]", iso, a),
+    gl != "None" & iso == "M" ~ sprintf("[%s + %s] %s", iso, a, gl),
+    TRUE ~ sprintf("[(%s) + %s] %s", iso, a, gl)
+  )
+  
+}
+
+delta_list2 <-
+  expand_grid(
+    adduct = c("H", "Na", "K", "NH4"),
+    gain_loss = c("None", "+DMSO", "+Acetonitrile", "+C2H7N1", "+H2O", "-H2O", "-CO2", "-C1H2O2", "-C8H6O3", "-Bz", "-NH3"),
+    isotope = c("M", "M+1", "M+2", "M+3") 
+  ) %>% 
+  left_join(
+    d1, by = "adduct"
+  ) %>% 
+  left_join(
+    d2, by = "gain_loss"
+  ) %>% 
+  left_join(
+    d3, by = "isotope"
+  ) %>% 
+  filter(!(gain_loss == "-NH3" & adduct == "NH4")) %>% 
+  mutate(
+    name2 = format_species(adduct, gain_loss, isotope),
+    delta  = delta1 + delta2 + delta3
+  )
diff --git a/Scripts/get_network_layout.R b/Scripts/get_network_layout.R
new file mode 100644
index 0000000..58ec930
--- /dev/null
+++ b/Scripts/get_network_layout.R
@@ -0,0 +1,45 @@
+get_network_layout <- function(obj, clust) {
+  
+  #  node_cat, edge_cat, node_size, edge_size
+  
+  node <- obj$node %>% 
+    filter(clust_id == clust)
+  
+  edge <- obj$edge %>% 
+    filter(FEATURE_ID_1 %in% node$FEATURE_ID & FEATURE_ID_2 %in% node$FEATURE_ID)
+  
+  coord <- get_layout(edge)
+  
+  node %<>%
+    left_join(coord, by = "FEATURE_ID")
+  
+  edge %<>%
+    left_join(coord, by = c("FEATURE_ID_1" = "FEATURE_ID")) %>% 
+    left_join(coord, by = c("FEATURE_ID_2" = "FEATURE_ID"), suffix = c("", "end"))
+  
+  deg <- c(edge$FEATURE_ID_1, edge$FEATURE_ID_2) %>% table() %>% {tibble(FEATURE_ID = names(.), Degree = unname(.))}
+  
+  node %<>%
+    left_join(deg, by = "FEATURE_ID")
+  
+  list(
+    edge = edge,
+    node = node
+  )
+
+}
+
+
+
+
+
+  
+  
+
+
+
+  
+  
+
+
+  
diff --git a/Scripts/network_plotter.R b/Scripts/network_plotter.R
new file mode 100644
index 0000000..faf69f5
--- /dev/null
+++ b/Scripts/network_plotter.R
@@ -0,0 +1,71 @@
+
+gg_network_plotter <- function(
+  obj,
+  node_size1 = 10,
+  node_colour_var = "adduct",
+  show_text = F,
+  text_colour_var = "name2",
+  text_size = 8,
+  text_colour = "cyan",
+  edge_colour_var = "Signature",
+  edge_size = 1
+)
+
+{
+  
+  node <- obj$node
+  edge <- obj$edge
+  
+  save(list = ls(), file = "bip.RData")
+  
+  gg <- ggplot() + 
+    geom_segment(
+      mapping = aes(x=x, y=y, xend=xend, yend=yend, colour = !!as.name(edge_colour_var)), 
+      data = edge,
+      size = edge_size
+    ) +
+    
+    geom_point(
+      data = node,
+      mapping=aes(x=x, y=y, fill = !!as.name(node_colour_var)), 
+      shape = 21,
+      size = node_size1,
+    ) +
+    
+    theme_void() +
+    labs(
+      title = "COMPOUND_ID %s MZ %.4f RT %.2f" %>% sprintf(node$COMPOUND_ID[1], node$MZ[1], node$RT[1])
+    )
+
+  if(show_text) {
+    
+    gg <- gg +
+      geom_text(
+        data = node, 
+        mapping=aes(x=x, y=y, label = !!as.name(text_colour_var)), 
+        size = text_size,
+        colour = text_colour,
+      )
+  }
+  
+  
+  return(gg)
+  
+}
+
+
+plot_cluster <- function(obj, clust) {
+  
+  obj %>% 
+    get_network_layout(clust) %>% 
+    gg_network_plotter(show_text = T)
+  
+}
+
+
+
+
+
+
+
+
diff --git a/Scripts/propagate_label.R b/Scripts/propagate_label.R
new file mode 100644
index 0000000..c6968e8
--- /dev/null
+++ b/Scripts/propagate_label.R
@@ -0,0 +1,128 @@
+delta_converter_list <- read_csv("delta_converter_list.csv", show_col_types = FALSE) %>% to_matrix()
+
+my_label_propagation2 <- function(obj) {
+  
+  node <- obj$node %>% 
+    arrange(-mean)
+  
+  edge <- obj$edge
+  
+  # anchor_node: character[1] (FEATURE_ID)
+  anchor_node <- node$FEATURE_ID %>% first()
+  
+  # initiliase tibbles
+  nodelist <- anchor_node
+  done <- character(0)
+  
+  
+  # matrix
+  node_assign <-
+    bind_cols(
+      node %>% select(FEATURE_ID),
+      map_df(as_tibble(delta_converter_list), ~ rep(0L, nrow(node)))
+    ) %>% 
+    to_matrix()
+  
+  # assume principal node is M+H
+  node_assign[anchor_node, "H"] <- 1
+  
+  # neighborhood tibble
+  N <- get_adjacency_tibble(edge)
+  
+  
+  while (length(nodelist) > 0) {
+    
+    new_nodelist <- character(0)
+    
+    # i: character[1]
+    for (i in nodelist) {
+      
+      # print(paste("i", i))
+      
+      # j character[1]
+      for(j in N %>% filter(n1==i) %$% n2 %>% setdiff(done)) {
+        
+        # print(paste("j", j))
+        
+        node_assign[j,] <- node_assign[i,] + convert_delta_code(N %>% filter(n1==i, n2==j) %$% code)
+        
+        new_nodelist <- c(new_nodelist, j)
+      }
+      
+      done <- c(done, i)
+    }
+    
+    done %<>% unique() 
+    
+    nodelist <- new_nodelist %>% unique()
+    
+    
+    
+  }
+  
+  node_assign %<>% 
+    as_tibble(rownames = "FEATURE_ID") %>% 
+    get_species()
+  
+  list(
+    edge = edge,
+    node = node %>% left_join(node_assign %>% select(FEATURE_ID, M, adduct, gain_loss, name2), by = "FEATURE_ID"),
+    decomposition_table = nodelist,
+    anchor_node = anchor_node
+    
+  )
+  
+}
+
+get_species <- function(x) {
+  
+ 
+  x %>% 
+    mutate(
+      adduct = sprintf("_Na_%d__K_%d__H_%d_", Na, K, H) %>% 
+        gsub("_[A-Za-z0-9]+_0_", "", .) %>% 
+        gsub("(_1)|(^_)|(_$)", "", .)  %>% 
+        # sub("H__NH3", "NH4", .) %>% 
+        sub("__H_-([1-9])", "-\\1H", .) %>% 
+        sub("-1H", "-H", .) %>% 
+        gsub("__", "+", .),
+      
+      M = if_else(C13 == 0, "M", sprintf("(M+%d)", C13)),
+      
+      gain_loss = sprintf("_NH3_%d__H2O_%d__FA_%d__C2H7N1_%d__C8H6O3_%d__CO2_%d__Bz_%d__ACN_%d__DMSO_%d_", NH3, H2O, C1H2O2, C2H7N1, C8H6O3, CO2, Bz, Acetonitrile, DMSO) %>% 
+       
+        gsub("_[A-Za-z0-9]+_0_", "", .) %>% 
+        gsub("_([A-Za-z0-9]+)_-([1-9])", "-\\2.\\1", .) %>% 
+        gsub("-1\\.", "-", .) %>% 
+        gsub("(_1)|(^_)|(_$)", "", .)  %>% 
+        gsub("__", "+", .) %>% 
+        gsub("_-", "-", .),
+      
+      name2 = sprintf("[%s + %s] +%s", M, adduct, gain_loss) %>% 
+        gsub("\\+-", "-", .) %>% 
+        gsub("\\+$", "", .) %>% 
+        trimws()
+      
+      
+      ) 
+  
+}
+
+
+
+get_adjacency_tibble <- function(edge) {
+  
+  adj <- get_adjacency_matrix_delta(edge) %>% t()
+  
+  N <- lapply(seq(nrow(adj)), function(i) adj[i,] %>% keep(.!=0)) 
+  
+  tibble(
+    n1 = rownames(adj), 
+    n2 = map(N, ~names(.x)), 
+    code = map(N, ~unname(.x))
+  ) %>% 
+    unnest(c(n2, code))
+  
+}
+
+
diff --git a/cor_cluster_mix.RDS b/cor_cluster_mix.RDS
new file mode 100644
index 0000000..1089330
Binary files /dev/null and b/cor_cluster_mix.RDS differ
diff --git a/data20.RDS b/data20.RDS
new file mode 100644
index 0000000..509d4e5
Binary files /dev/null and b/data20.RDS differ
diff --git a/delta_converter_list.csv b/delta_converter_list.csv
new file mode 100644
index 0000000..f3c7b0d
--- /dev/null
+++ b/delta_converter_list.csv
@@ -0,0 +1,15 @@
+Name,Na,K,H,NH3,H2O,C13,C1H2O2,C2H7N1,C8H6O3,CO2,Bz,Acetonitrile,DMSO
+Na-H,1,0,-1,0,0,0,0,0,0,0,0,0,0
+K-H,0,1,-1,0,0,0,0,0,0,0,0,0,0
+NH3,0,0,0,1,0,0,0,0,0,0,0,0,0
+Na-NH4,1,0,-1,-1,0,0,0,0,0,0,0,0,0
+K-NH4,0,1,-1,-1,0,0,0,0,0,0,0,0,0
+H2O,0,0,0,0,1,0,0,0,0,0,0,0,0
+C13,0,0,0,0,0,1,0,0,0,0,0,0,0
+C1H2O2,0,0,0,0,0,0,1,0,0,0,0,0,0
+C2H7N1,0,0,0,0,0,0,0,1,0,0,0,0,0
+C8H6O3,0,0,0,0,0,0,0,0,1,0,0,0,0
+CO2,0,0,0,0,0,0,0,0,0,1,0,0,0
+Bz,0,0,0,0,0,0,0,0,0,0,1,0,0
+Acetonitrile,0,0,0,0,0,0,0,0,0,0,0,1,0
+DMSO,0,0,0,0,0,0,0,0,0,0,0,0,1
diff --git a/make_data20.R b/make_data20.R
new file mode 100644
index 0000000..7e97a8b
--- /dev/null
+++ b/make_data20.R
@@ -0,0 +1,7 @@
+
+cor_cluster_mix <- readRDS("cor_cluster_mix.RDS")
+
+cl <- cor_cluster_mix$node %>% arrange(-clust_size) %$% clust_id %>% unique() %>% head(100)
+
+purrr::map(cl %>% head(20), ~get_network_layout(cor_cluster_mix, .x) %>% my_label_propagation2()) %>% 
+  saveRDS("data20.RDS")
diff --git a/shiny_uNetwork.R b/shiny_uNetwork.R
new file mode 100644
index 0000000..ea14ad1
--- /dev/null
+++ b/shiny_uNetwork.R
@@ -0,0 +1,386 @@
+rm(list=ls(envir = .GlobalEnv), envir = .GlobalEnv)
+
+library(magrittr)
+library(tidyverse)
+library(igraph)
+library(shiny)
+library(shinythemes)
+library(Matrix)
+library(readxl)
+library(enviPat)
+
+data("isotopes")
+
+
+dir1 <- "Scripts"
+
+for (f in list.files(dir1, pattern = "\\.R$")) {
+  source(file.path(dir1, f))
+  
+}
+
+# source("Scripts/make_network.R")
+# source("Scripts/delta_list.R")
+# source("Scripts/network_plotter.R")
+
+
+# source("Scripts/calc_layout.R")
+# source("Scripts/network_bipartite.R")
+# source("Scripts/convert_to_adjacency.R")
+# 
+assign("colours1", colours() %>% keep(!grepl("^gr[ea]y", .) & !grepl("[0-9]$", .)) %>% sort(), envir = .GlobalEnv)
+
+
+
+ui <- 
+  
+  fluidPage(
+    title = "Feature matrix plotter",
+    sidebarLayout(
+      sidebarPanel(
+        h4("Inputs"),
+        br(),
+        tabsetPanel(
+          tabPanel(
+            title =  "Cluster",
+            br(),
+            
+            uiOutput("select_cluster")
+          ),
+            
+          tabPanel(
+            title =  "Nodes",
+            br(),
+            
+            sliderInput(
+              inputId = "node_size1", 
+              label = "Node size",
+              value = 10,
+              min = 1, 
+              step = 1,
+              max = 20
+            ),
+            
+            
+            selectizeInput(
+              inputId = "node_colour_var",
+              label = "Choose node colour variable",
+              choices = c("adduct", "gain_loss"),
+              selected = c("adduct", "gain_loss")[1],
+              multiple = F,
+              width = "200px"
+            )
+            
+            
+          ), # end node
+          
+          tabPanel(
+            title =  "Edges",
+            br(),
+            
+            sliderInput(
+              inputId = "edge_size", 
+              label = "Edge size (thickness)",
+              value = 1,
+              min = 0.5, 
+              step = 0.5,
+              max = 5
+            ),
+            
+            selectizeInput(
+              inputId = "edge_colour_var",
+              label = "Choose node colour variable",
+              choices = c("Signature", "COR"),
+              selected = c("Signature", "COR")[1],
+              multiple = F,
+              width = "200px"
+            )
+           
+            
+          ), # end edge
+          
+          tabPanel(
+            title =  "Label",
+            br(),
+            
+            radioButtons(
+              inputId = "show_text", 
+              label = "Show labels",
+              choices = c("yes", "no"),
+              selected = "yes",
+              inline = T
+            ),
+            
+            sliderInput(
+              inputId = "text_size", 
+              label = "Label size",
+              value = 5,
+              min = 1, 
+              step = 0.5,
+              max = 10
+            ),
+            
+            selectizeInput(
+              inputId = "text_var",
+              label = "Choose node colour variable",
+              choices = c("FEATURE_ID", "name2"),
+              selected = "name2",
+              multiple = F,
+              width = "200px"
+            ),
+            
+            selectizeInput(
+              inputId = "text_colour",
+              label = "Label colour",
+              choices = colours1,
+              selected = "black",
+              multiple = F,
+              width = "200px"
+            )
+            
+            
+          ), # end text
+          
+          tabPanel(
+            title =  "Canvas",
+            br(),
+            
+            sliderInput(
+              inputId = "plot_width", 
+              label = "Plot width (pixels)",
+              value = 600,
+              min = 500, 
+              step = 100,
+              max = 1500
+            ),
+            
+            sliderInput(
+              inputId = "plot_height", 
+              label = "Plot height (pixels)",
+              value = 600,
+              min = 500, 
+              step = 100,
+              max = 1500
+            )
+            
+          ), # end canvas
+            
+
+            
+            tabPanel(
+              title =  "Pdf",
+              br(),
+            
+            sliderInput(
+              inputId = "plot_width_cm", 
+              label = "Pdf plot widht (cm)",
+              value = 12,
+              min = 10, 
+              step = 1,
+              max = 20
+            ),
+            
+            sliderInput(
+              inputId = "plot_height_cm", 
+              label = "Pdf plot height (cm)",
+              value = 12,
+              min = 10, 
+              step = 1,
+              max = 20
+            ),
+            
+            br(),
+            
+            downloadButton("download_plot", "Save plot as pdf")
+            
+            ), # end pdf
+          
+          tabPanel(
+            title =  "Layout",
+            br(),
+            
+            # selectizeInput(
+            #   inputId = "layout_method",
+            #   label = "Igraph layout algorithm",
+            #   choices = igraph_layout_algos,
+            #   selected = "layout_nicely",
+            #   multiple = F,
+            #   width = "200px"
+            # ),
+            
+            
+            br(),
+            
+            # fileInput(
+            #   inputId = "matrix_infile",
+            #   label = "Upload feature matrix"
+            # ),
+            
+            br(),
+            
+            actionButton("recalc_layout", "Recalculate layout")
+            
+          ) # end layout
+            
+        )
+        
+        
+        
+      ), 
+      mainPanel(
+        br(),
+        
+        uiOutput("main_header"),
+        
+        br(),
+        uiOutput("bipartite_plot_wrapper"),
+        
+        br(),
+        
+        tableOutput("plot_click")
+        
+      )
+    )
+    
+    
+  )
+
+
+server <- function(input, output, session) {
+  
+  my_plot <- reactiveValues()
+  
+  my_data <- readRDS("data20.RDS")
+  
+  
+  output$select_cluster <- renderUI({
+    
+    req(my_data)
+    
+    ch <- names(my_data)
+    
+    nm <- sprintf("%s (%s)", ch, map_int(my_data, ~nrow(.x$node)))
+      map_int(my_data, ~nrow(.x$node))
+    
+    selectizeInput(
+      inputId = "cluster",
+      label = "Choose cluster",
+      choices = ch %>% set_names(nm),
+      selected = ch[1],
+      multiple = F,
+      width = "200px"
+    )
+
+  })
+  
+  observeEvent(
+    input$cluster,
+    {
+      my_plot$data <- my_data[[input$cluster]]
+    }
+  )
+  
+  output$bipartite_plot_wrapper <- renderUI({
+    
+    plotOutput(
+      "bipartite_plot", 
+      click = "plot_click",
+      dblclick ="plot_dbl_click",
+      hover = "plot_hover",
+      brush = "plot_brush",
+      height = ifelse(is.null(input$plot_height), 600, input$plot_height),
+      width = ifelse(is.null(input$plot_width), 600, input$plot_width)
+    )
+  })
+  
+  
+  
+  
+  output$bipartite_plot <- renderPlot({
+    
+    req(my_plot$data)
+    
+    my_plot$gg <-
+      gg_network_plotter(
+        my_plot$data,
+        node_size1 = input$node_size1,
+        node_colour_var = input$node_colour_var,
+        show_text = input$show_text == "yes",
+        text_colour_var = input$text_var,
+        text_size = input$text_size,
+        text_colour = input$text_colour,
+        edge_colour_var = input$edge_colour_var,
+        edge_size = input$edge_size
+      )
+    
+    my_plot$gg
+    
+  })
+  
+  output$plot_click <- renderTable({
+    
+    req(input$plot_click)
+    
+    nearPoints(
+      my_plot$data$node,
+      input$plot_click,
+      maxpoints = 1,
+      threshold = 300
+    ) 
+  })
+  
+  # observeEvent(
+  #   input$plot_dbl_click,
+  #   {
+  #     my_plot$highlight_nodes <- NA
+  #   })
+  
+  output$plot_hover <- renderTable({
+    
+    req(input$plot_hover)
+    
+      nearPoints(
+        my_plot$data$node,
+        input$plot_hover,
+        maxpoints = 1,
+        threshold = 100
+      ) 
+    
+  })
+  
+  output$download_plot  <- downloadHandler(
+      
+      filename = "fbf_bipartite_plot.pdf",
+      content = function(file) {
+            ggsave(file, height = input$plot_height_cm, width = input$plot_width_cm, units = "cm")
+      }
+    )
+    
+  
+  onStop(function() {
+    
+    env = parent.env(environment())
+    
+    ls(envir = env) %>%
+      ## .. excluding e.g. session" and "output"
+      setdiff(c("session", "output", "my_pref_update")) %>%
+      ## object in a list
+      mget(envir = env) %>% 
+      ## keep only reactive values
+      subset(., subset = sapply(., is.reactivevalues)) %>% 
+      ## convert reactive values
+      sapply(function(z) isolate(reactiveValuesToList(z)), simplify=F) %>% 
+      ## assign to global environment
+      list2env(envir = .GlobalEnv)
+    
+    
+    cat("Session stopped\n")
+    cat("Type `save(list=ls(), file='tmp.RData')` to save state variables in your current working directory\n")
+    cat("Find out what current working directory by typing `getwd()`\n")
+  })
+  
+  
+}
+
+
+shinyApp(ui, server)
\ No newline at end of file