diff --git a/msa/global.R b/msa/global.R
index c4c8907..1ee5bcd 100644
--- a/msa/global.R
+++ b/msa/global.R
@@ -42,8 +42,13 @@ source(paste0(load_dir,"LSHTM_analysis/scripts/Header_TT.R"))
 load_target_globals=function(target){
   cat(paste0("Reloading Target: ", target))
   source(paste0(load_dir, "LSHTM_analysis/config/", target, ".R")) # load per-target config file
-  
+  invisible(assign(paste0(target, "_aa_pos_drug"), aa_pos_drug, envir = .GlobalEnv))
+  invisible(assign(paste0(target, "_active_aa_pos"), active_aa_pos, envir = .GlobalEnv))
+  invisible(assign(paste0(target, "_aa_pos_lig1"), aa_pos_lig1, envir = .GlobalEnv))
+  invisible(assign(paste0(target, "_aa_pos_lig2"), aa_pos_lig2, envir = .GlobalEnv))
+  invisible(assign(paste0(target, "_aa_pos_lig3"), aa_pos_lig3, envir = .GlobalEnv))
   invisible(assign(paste0(target, "_merged_df3"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-merged_df3.csv")), envir = .GlobalEnv))
+  
   invisible(assign(paste0(target, "_merged_df2"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-merged_df2.csv")), envir = .GlobalEnv))
   invisible(assign(paste0(target, "_corr_df_m3_f"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-corr_df_m3_f.csv")), envir = .GlobalEnv))
   invisible(assign(paste0(target, "_lin_lf"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-lin_lf.csv")), envir = .GlobalEnv))
@@ -96,24 +101,7 @@ load_msa_global=function(gene){
 
 #### Local Functions ####
 
-
-# FIXME: passing in the per-plot params is broken
-lin_sc=function(x, all_lineages = F, ...){
-  lf_var = get(paste0(x,"_lin_lf"))
-  wf_var = get(paste0(x,"_lin_wf"))
-  cowplot::plot_grid(lin_count_bp_diversity(wf_var, all_lineages, ...), lin_count_bp(lf_var, all_lineages, ...))
-}
-
-
-options(shiny.port = 8000)
-options(shiny.host = '0.0.0.0') # This means "listen to all addresses on all interfaces"
-options(shiny.launch.browser = FALSE)
-options(width=120)
-options(DT.options = list(scrollX = TRUE))
-
-
 ################ STATIC GLOBALS ONLY ##############
-# never quite sure where "outdir" gets set :-|
 
 # using dataframes instead of lists lets us avoid use of map()
 plot_functions_df=data.frame(
@@ -254,6 +242,13 @@ lapply(c(
 
 #### Shiny UI #####
 if(interactive()){
+  
+  options(shiny.port = 8000)
+  options(shiny.host = '0.0.0.0') # This means "listen to all addresses on all interfaces"
+  options(shiny.launch.browser = FALSE)
+  options(width=120)
+  options(DT.options = list(scrollX = TRUE))
+  
   ui <- dashboardPage(
     #dashboardHeader(title = paste0(gene, "/", drug)),
     dashboardHeader(title = "Sequence Alignment"),
@@ -328,6 +323,7 @@ if(interactive()){
         # C O M P A T I B I L I T Y
         #gene=input$switch_target
         #drug=target_map[[gene]]
+        target = input$switch_target
         merged_df3=cbind(get(paste0(input$switch_target, '_merged_df3')))
         
         position_max=max(merged_df3[['position']])
@@ -341,7 +337,6 @@ if(interactive()){
         # merged_df3$n=NULL
         # 
         mutable_df3 = cbind(merged_df3)
-        unified_msa = get(paste0(input$switch_target, '_unified_msa'))
         # 
         # # re-sort the dataframe according to position count
         sorted_df = cbind(merged_df3)
@@ -366,13 +361,7 @@ if(interactive()){
         
         #input$stability_snp_param
         
-        updateSliderInput(
-          session, 
-          "display_position_range",
-          min = position_min,
-          max = position_max
-          #, value = c(position_min, position_min+150)
-        )
+
         updateSliderInput(
           session,
           "display_position_full_range",
@@ -380,43 +369,23 @@ if(interactive()){
           max = position_max #, 
           # value = c(position_min, position_min+150)
         )
-        updateNumericInput(session, "selected_logop_snp_position", min = position_min, max = position_max, value = position_min)
-        updateNumericInput(session, "selected_logop_ed_position", min = position_min, max = position_max, value = position_min)
-        updateNumericInput(session, "corr_lig_dist", min = min_ligand_distance, max = max_ligand_distance, value = min_ligand_distance)
-        
-        stability_colname      = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"stability_colname"]
-        outcome_colname        = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"outcome_colname"]
-        
-        display_position_range = input$display_position_range
-        plot_min=display_position_range[1]
-        plot_max=display_position_range[2]
-        
+
         display_position_full_range = input$display_position_full_range
         full_range_min=display_position_full_range[1]
         full_range_max=display_position_full_range[2]
         
         logoplot_colour_scheme = input$logoplot_colour_scheme
-        omit_snp_count = input$omit_snp_count
-        
-        print(paste0('Plotting positions between: ', plot_min, ' and ', plot_max))
-        
-        subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
-        
-        subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
-        subset_sorted_df=sorted_df[(sorted_df$position>=plot_min & sorted_df$position <=plot_max),]
-        
-        
-        
+
         #### LogoPlotMSA/Logo Plot ED ####
         output$LogoPlotMSA = renderPlot(
-          LogoPlotMSA(target=input$switch_target,
+          LogoPlotMSA(target=target,
                       plot_positions=full_range_min:full_range_max,
                       my_logo_col = logoplot_colour_scheme,
-                      aa_pos_drug = aa_pos_drug,
-                      active_aa_pos = active_aa_pos,
-                      aa_pos_lig1 = aa_pos_lig1,
-                      aa_pos_lig2 = aa_pos_lig2,
-                      aa_pos_lig3 = aa_pos_lig3
+                      aa_pos_drug = paste0(target,"_aa_pos_drug"),
+                      active_aa_pos = paste0(target,"_active_aa_pos"),
+                      aa_pos_lig1 = paste0(target,"_aa_pos_lig1"),
+                      aa_pos_lig2 = paste0(target,"_aa_pos_lig2"),
+                      aa_pos_lig3 = paste0(target,"_aa_pos_lig3")
           )
         )
       }
diff --git a/msa/server.R b/msa/server.R
index 542fe34..a401d5f 100644
--- a/msa/server.R
+++ b/msa/server.R
@@ -9,6 +9,7 @@ function(input, output, session) {
       # C O M P A T I B I L I T Y
       #gene=input$switch_target
       #drug=target_map[[gene]]
+      target = input$switch_target
       merged_df3=cbind(get(paste0(input$switch_target, '_merged_df3')))
       
       position_max=max(merged_df3[['position']])
@@ -22,15 +23,14 @@ function(input, output, session) {
       # merged_df3$n=NULL
       # 
       mutable_df3 = cbind(merged_df3)
-      unified_msa = get(paste0(input$switch_target, '_unified_msa'))
       # 
       # # re-sort the dataframe according to position count
       sorted_df = cbind(merged_df3)
       sorted_df = sorted_df %>% arrange(pos_count)
       
       # 
-      outdir = paste0("~/git/Data/", drug, '/output/')
-      indir  = paste0("~/git/Data/", drug , "/input/")
+      outdir = paste0(load_dir, "Data/", drug, '/output/')
+      indir  = paste0(load_dir, "Data/", drug , "/input/")
       # 
       # source("~/git/LSHTM_analysis/scripts/plotting/logo_data_msa.R") # probably unnecessary...
       
@@ -47,13 +47,7 @@ function(input, output, session) {
       
       #input$stability_snp_param
       
-      updateSliderInput(
-        session, 
-        "display_position_range",
-        min = position_min,
-        max = position_max
-        #, value = c(position_min, position_min+150)
-      )
+      
       updateSliderInput(
         session,
         "display_position_full_range",
@@ -61,45 +55,30 @@ function(input, output, session) {
         max = position_max #, 
         # value = c(position_min, position_min+150)
       )
-      updateNumericInput(session, "selected_logop_snp_position", min = position_min, max = position_max, value = position_min)
-      updateNumericInput(session, "selected_logop_ed_position", min = position_min, max = position_max, value = position_min)
-      updateNumericInput(session, "corr_lig_dist", min = min_ligand_distance, max = max_ligand_distance, value = min_ligand_distance)
-      
-      stability_colname      = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"stability_colname"]
-      outcome_colname        = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"outcome_colname"]
-      
-      display_position_range = input$display_position_range
-      plot_min=display_position_range[1]
-      plot_max=display_position_range[2]
       
       display_position_full_range = input$display_position_full_range
       full_range_min=display_position_full_range[1]
       full_range_max=display_position_full_range[2]
       
       logoplot_colour_scheme = input$logoplot_colour_scheme
-      omit_snp_count = input$omit_snp_count
-      
-      print(paste0('Plotting positions between: ', plot_min, ' and ', plot_max))
-      
-      subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
-      
-      subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
-      subset_sorted_df=sorted_df[(sorted_df$position>=plot_min & sorted_df$position <=plot_max),]
-      
-      
       
       #### LogoPlotMSA/Logo Plot ED ####
       output$LogoPlotMSA = renderPlot(
-        LogoPlotMSA(target=input$switch_target,
+        LogoPlotMSA(target=target,
                     plot_positions=full_range_min:full_range_max,
                     my_logo_col = logoplot_colour_scheme,
-                    aa_pos_drug = aa_pos_drug,
-                    active_aa_pos = active_aa_pos,
-                    aa_pos_lig1 = aa_pos_lig1,
-                    aa_pos_lig2 = aa_pos_lig2,
-                    aa_pos_lig3 = aa_pos_lig3
+                    aa_pos_drug = paste0(target,"_aa_pos_drug"),
+                    active_aa_pos = paste0(target,"_active_aa_pos"),
+                    aa_pos_lig1 = paste0(target,"_aa_pos_lig1"),
+                    aa_pos_lig2 = paste0(target,"_aa_pos_lig2"),
+                    aa_pos_lig3 = paste0(target,"_aa_pos_lig3")
         )
       )
     }
   )
+  
+  #### EOF Shiny Server ####
+  
+  
+  
 }
\ No newline at end of file