diff --git a/my_header.R b/my_header.R
index 2fa892c..ddec019 100644
--- a/my_header.R
+++ b/my_header.R
@@ -124,7 +124,7 @@ install.packages("data.table")
 
 if (!require("PerformanceAnalytics")){
   install.packages("PerformanceAnalytics", dependencies = T)
-  library(PerformaceAnalytics)
+  library(PerformanceAnalytics)
 }
 
 if (!require ("GGally")){
diff --git a/scripts/Header_TT.R b/scripts/Header_TT.R
index 935f5ec..767d647 100755
--- a/scripts/Header_TT.R
+++ b/scripts/Header_TT.R
@@ -134,7 +134,7 @@ if(!require("data.table")) {
 
 if (!require("PerformanceAnalytics")){
   install.packages("PerformanceAnalytics", dependencies = T)
-  library(PerformaceAnalytics)
+  library(PerformanceAnalytics)
 }
 
 if (!require ("GGally")){
diff --git a/scripts/functions/logoP_msa.R b/scripts/functions/logoP_msa.R
index a120d20..d613df0 100644
--- a/scripts/functions/logoP_msa.R
+++ b/scripts/functions/logoP_msa.R
@@ -40,35 +40,40 @@
 ###########################################
 #LogoPlotMSA <- function(msaSeq_mut # chr vector
 #                        , msaSeq_wt # chr vector
-LogoPlotMSA <- function(unified_msa
-                        , logo_type = c("EDLogo") #"bits_pfm", "probability_pfm", "bits_raw", "probability_raw")
-                        , EDScore_type =  c("log") # see if this relevant, or source function should have it!
-                        , bg_prob = NULL
-                        , my_logo_col = "chemistry" 
-                        , plot_positions
-                        , y_breaks
-                        , x_lab_mut = "nsSNP position"
-                        , y_lab_mut
-                        , x_ats = 13 # text size
-                        , x_tangle = 90 # text angle
-                        , x_axis_offset = 0 # dist b/w y-axis and plot start
-                        , x_axis_offset_filtered = 0
-                        , y_axis_offset = 0
-                        , y_axis_increment = 1
-                        , y_ats = 13
-                        , y_tangle = 0
-                        , x_tts = 13 # title size
-                        , y_tts = 13
-                        , leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
-                        , leg_dir = "horizontal" #can be vertical or horizontal
-                        , leg_ts = 16 # leg text size
-                        , leg_tts = 16 # leg title size
+LogoPlotMSA <- function(# unified_msa # <- not needed any more because we have 'target' now
+  target = 'embb'
+  , logo_type = c("EDLogo") #"bits_pfm", "probability_pfm", "bits_raw", "probability_raw")
+  , EDScore_type =  c("log") # see if this relevant, or source function should have it!
+  , bg_prob = NULL
+  , my_logo_col = "chemistry" 
+  , plot_positions
+  , y_breaks
+  , x_lab_mut = ""
+  , y_lab_mut
+  , x_ats = 10 # text size
+  , x_tangle = 90 # text angle
+  , x_axis_offset = 0 # dist b/w y-axis and plot start
+  , x_axis_offset_filtered = 0
+  , y_axis_offset = 0
+  , y_axis_increment = 1
+  , y_ats = 10
+  , y_tangle = 0
+  , x_tts = 10 # title size
+  , y_tts = 10
+  , leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
+  , leg_dir = "horizontal" #can be vertical or horizontal
+  , leg_ts = 14 # leg text size
+  , leg_tts = 14 # leg title size
+  , ...
 )
 
 {
   # FIXME: Hack!
   # msaSeq_mut=unified_msa[[1]]
   # msaSeq_wt=unified_msa[[2]]
+  
+  unified_msa = get(paste0(target, "_unified_msa"))
+  
   msaSeq_mut=unified_msa[['msa_seq']]
   msaSeq_wt=unified_msa[['wt_seq']]
   
@@ -79,6 +84,51 @@ LogoPlotMSA <- function(unified_msa
   names(data_ed)
   #"pfm_mutM" "pfm_mut_scaledM" "combED_mutM" "pfm_wtM" "pfm_wt_scaledM" "combED_wtM"
   
+  #merged_df3 for current target (unfortunatly i can't think of an easy way to get this from unified_msa)
+  contig_df=data.frame(position=1:max(nchar(unified_msa$wt_seq)))
+  plot_df = get(paste0(target, "_merged_df3"))
+
+  # generate the tile columns
+  #plot_df=cbind(embb_merged_df3)
+  plot_df$col_aa = ifelse(plot_df[["position"]]%in%active_aa_pos,
+                          "transparent", "transparent")
+  plot_df$bg_all = plot_df$col_aa
+  plot_df$bg_all = ifelse(plot_df[["position"]]%in%aa_pos_drug,
+                          "drug", plot_df$bg_all)
+  plot_df$col_bg1 = plot_df$bg_all
+  plot_df$col_bg1 = ifelse(plot_df[["position"]]%in%aa_pos_lig1,
+                           "lig1", plot_df$col_bg1)
+  plot_df$col_bg2 = plot_df$col_bg1
+  plot_df$col_bg2 = ifelse(plot_df[["position"]]%in%aa_pos_lig2,
+                           "lig2", plot_df$col_bg2)
+  plot_df$col_bg3 = plot_df$col_bg2
+  plot_df$col_bg3 =  ifelse(plot_df[["position"]]%in%aa_pos_lig3
+                            , "lig3", plot_df$col_bg3)
+  
+  plot_df = generate_distance_colour_map(plot_df, debug=FALSE)
+  
+  # copy only the tile columns to the contiguous DF
+
+  contig_df$ligand_distance = plot_df$ligand_distance[match(contig_df$position, plot_df$position)]
+  contig_df_map = generate_distance_colour_map(contig_df, debug=TRUE)
+  contig_df$ligD_colours = contig_df_map$ligD_colours[match(contig_df$position, contig_df_map$position)]
+  
+  #contig_df$ligD_colours = plot_df$ligD_colours[match(contig_df$position, plot_df$position)]
+  contig_df$bg_all = plot_df$bg_all[match(contig_df$position, plot_df$position)]
+  contig_df$col_bg1 = plot_df$col_bg1[match(contig_df$position, plot_df$position)]
+  contig_df$col_bg2 = plot_df$col_bg2[match(contig_df$position, plot_df$position)]
+  contig_df$col_bg3 = plot_df$col_bg3[match(contig_df$position, plot_df$position)]
+  contig_df=replace_na(
+    contig_df,
+    list(
+      ligD_colours='transparent', 
+      bg_all = 'transparent', 
+      col_bg1 = 'transparent',
+      col_bg2 = 'transparent',
+      col_bg3 = 'transparent'
+    )
+  )
+  
   if (logo_type == "EDLogo"){
     msa_method    = "custom"
     y_label       = "Enrichment Score"
@@ -416,13 +466,13 @@ LogoPlotMSA <- function(unified_msa
           
     ) +
     scale_y_discrete(expand = c(0,0)) +
-    ylab("") + xlab("Wild-type position")
+    ylab("") + xlab("")
   
   if (missing(plot_positions)){
     
     # No y-axis needed
     ed_wt_logo_P = p1# + 
-  }else{
+  } else {
     
     ed_wt_logo_P = p1 +
       scale_x_discrete(expand = c(0, 0),
@@ -430,13 +480,27 @@ LogoPlotMSA <- function(unified_msa
                        #labels = i_extract,
                        limits = factor(i_extract)
       )
+    
+    #plot_df=plot_df[plot_df$position %in% plot_positions,]
+    contig_df=contig_df[contig_df$position %in% plot_positions,]
+    anno_bar = position_annotation(
+      contig_df,
+      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,
+      generate_colours = FALSE
+    )
+    
   }
   cowplot::plot_grid(ed_mut_logo_P
                      , ed_wt_logo_P
-                     , nrow = 2
+                     , anno_bar
+                     , ncol = 1
                      , align = "v"
                      #, axis='lr'
-                     , rel_heights = c(3/4, 1/4))
+                     , rel_heights = c(3/4, 1/4,1/10))
   
 }
 #LogoPlotMSA(unified_msa)
diff --git a/scripts/functions/position_annotation.R b/scripts/functions/position_annotation.R
index fb5775e..1290f6b 100644
--- a/scripts/functions/position_annotation.R
+++ b/scripts/functions/position_annotation.R
@@ -4,6 +4,7 @@
 position_annotation=function(plot_df,
                              bg="transparent",
                              reorder_position = FALSE, # enable to reorder according to plot_df$pos_count
+                             generate_colours = TRUE, #set FALSE if you want to generate all the colour columns elsewhere
                              aa_pos_drug=1:100,
                              active_aa_pos=1:100,
                              aa_pos_lig1=1:100,
@@ -32,36 +33,38 @@ position_annotation=function(plot_df,
   #plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
   # plot_df$col_aa = ifelse(plot_df[["position"]]%in%active_aa_pos,
   #                         "brown", "transparent")
-  plot_df$col_aa = ifelse(plot_df[["position"]]%in%active_aa_pos,
-                          "transparent", "transparent")
-  
-  plot_df$bg_all = plot_df$col_aa
-  plot_df$bg_all = ifelse(plot_df[["position"]]%in%aa_pos_drug,
-                          "drug", plot_df$bg_all)
-  
-  plot_df$col_bg1 = plot_df$bg_all
-  plot_df$col_bg1 = ifelse(plot_df[["position"]]%in%aa_pos_lig1,
-                           "lig1", plot_df$col_bg1)
-  
-  plot_df$col_bg2 = plot_df$col_bg1
-  plot_df$col_bg2 = ifelse(plot_df[["position"]]%in%aa_pos_lig2,
-                           "lig2", plot_df$col_bg2)
-  
-  
-  plot_df$col_bg3 = plot_df$col_bg2
-  plot_df$col_bg3 =  ifelse(plot_df[["position"]]%in%aa_pos_lig3
-                            , "lig3", plot_df$col_bg3)
-  
-  # the call to generate_distance_colour_map should probably be
-  # wherever the outer DF is built, and not here.
-  plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
   
+  if (generate_colours){
+    plot_df$col_aa = ifelse(plot_df[["position"]]%in%active_aa_pos,
+                            "transparent", "transparent")
+    
+    plot_df$bg_all = plot_df$col_aa
+    plot_df$bg_all = ifelse(plot_df[["position"]]%in%aa_pos_drug,
+                            "drug", plot_df$bg_all)
+    
+    plot_df$col_bg1 = plot_df$bg_all
+    plot_df$col_bg1 = ifelse(plot_df[["position"]]%in%aa_pos_lig1,
+                             "lig1", plot_df$col_bg1)
+    
+    plot_df$col_bg2 = plot_df$col_bg1
+    plot_df$col_bg2 = ifelse(plot_df[["position"]]%in%aa_pos_lig2,
+                             "lig2", plot_df$col_bg2)
+    
+    
+    plot_df$col_bg3 = plot_df$col_bg2
+    plot_df$col_bg3 =  ifelse(plot_df[["position"]]%in%aa_pos_lig3
+                              , "lig3", plot_df$col_bg3)
+    
+    # the call to generate_distance_colour_map should probably be
+    # wherever the outer DF is built, and not here.
+    plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
+  }
   heat_bar = ggplot(plot_df) + # THIS STUPID FUCKING FACTOR THING
     
     # scale_x_discrete("Position", labels=factor(plot_df$position)) +
     theme_nothing() +
     theme(#axis.text.x = element_text(angle = 90, size = 6),
-          title = element_blank()
+      title = element_blank()
     ) + # enable for alignment debug
     labs(x = NULL, y = NULL) +
     
@@ -77,87 +80,87 @@ position_annotation=function(plot_df,
     }
   #end of distance-heat-bar
   #NULL,
-    if(reorder_position) {
-      pos_tiles = ggplot(plot_df) +
-        #scale_x_discrete("Position", labels=factor(plot_df$position)) +
-        scale_color_manual(values = c(
-          "brown"="brown",
-          "drug"=drug_colour,
-          "transparent"="transparent",
-          "lig1"=lig1_colour,
-          "lig2"=lig2_colour,
-          "lig3"=lig3_colour
-        ),
-        #expand=c(0,0)
-        ) +
-        scale_fill_manual(values = c(
-          "brown"="brown",
-          "drug"=drug_colour,
-          "transparent"="transparent",
-          "lig1"=lig1_colour,
-          "lig2"=lig2_colour,
-          "lig3"=lig3_colour
-        ),
-        #expand=c(0,0)
-        ) +
-        theme_nothing() +
-        theme(plot.background = element_rect(fill = bg, colour=NA),
-              #plot.margin = margin(t=0,b=0),
-              panel.background = element_rect(fill = bg, colour=NA),
-              legend.position = "none"
-        ) +
-        labs(x = NULL, y= NULL) +
+  if(reorder_position) {
+    pos_tiles = ggplot(plot_df) +
+      #scale_x_discrete("Position", labels=factor(plot_df$position)) +
+      scale_color_manual(values = c(
+        "brown"="brown",
+        "drug"=drug_colour,
+        "transparent"="transparent",
+        "lig1"=lig1_colour,
+        "lig2"=lig2_colour,
+        "lig3"=lig3_colour
+      ),
+      #expand=c(0,0)
+      ) +
+      scale_fill_manual(values = c(
+        "brown"="brown",
+        "drug"=drug_colour,
+        "transparent"="transparent",
+        "lig1"=lig1_colour,
+        "lig2"=lig2_colour,
+        "lig3"=lig3_colour
+      ),
+      #expand=c(0,0)
+      ) +
+      theme_nothing() +
+      theme(plot.background = element_rect(fill = bg, colour=NA),
+            #plot.margin = margin(t=0,b=0),
+            panel.background = element_rect(fill = bg, colour=NA),
+            legend.position = "none"
+      ) +
+      labs(x = NULL, y= NULL) +
       geom_tile(aes(y = 1,x=reorder(position,-pos_count), fill = bg_all, colour = bg_all)
       ) +
-        geom_tile(aes(y = 2, x=reorder(position,-pos_count), fill = col_bg1, colour = col_bg1)
-        ) +
-        geom_tile(aes(y = 3, x=reorder(position,-pos_count), fill = col_bg2, colour = col_bg2)
-        ) +
-        geom_tile(aes(y = 4, x=reorder(position,-pos_count), fill = col_bg3, colour = col_bg3)
-        )
-      
-    } else {
-      pos_tiles = ggplot(plot_df) +
-        #scale_x_discrete("Position", labels=factor(plot_df$position)) +
-        scale_color_manual(values = c(
-          "brown"="brown",
-          "drug"=drug_colour,
-          "transparent"="transparent",
-          "lig1"=lig1_colour,
-          "lig2"=lig2_colour,
-          "lig3"=lig3_colour
-        ),
-        #expand=c(0,0)
-        ) +
-        scale_fill_manual(values = c(
-          "brown"="brown",
-          "drug"=drug_colour,
-          "transparent"="transparent",
-          "lig1"=lig1_colour,
-          "lig2"=lig2_colour,
-          "lig3"=lig3_colour
-        ),
-        #expand=c(0,0)
-        ) +
-        theme_nothing() +
-        theme(plot.background = element_rect(fill = bg, colour=NA),
-              #plot.margin = margin(t=0,b=0),
-              panel.background = element_rect(fill = bg, colour=NA),
-              legend.position = "none"
-        ) +
-        labs(x = NULL, y= NULL) +
+      geom_tile(aes(y = 2, x=reorder(position,-pos_count), fill = col_bg1, colour = col_bg1)
+      ) +
+      geom_tile(aes(y = 3, x=reorder(position,-pos_count), fill = col_bg2, colour = col_bg2)
+      ) +
+      geom_tile(aes(y = 4, x=reorder(position,-pos_count), fill = col_bg3, colour = col_bg3)
+      )
+    
+  } else {
+    pos_tiles = ggplot(plot_df) +
+      #scale_x_discrete("Position", labels=factor(plot_df$position)) +
+      scale_color_manual(values = c(
+        "brown"="brown",
+        "drug"=drug_colour,
+        "transparent"="transparent",
+        "lig1"=lig1_colour,
+        "lig2"=lig2_colour,
+        "lig3"=lig3_colour
+      ),
+      #expand=c(0,0)
+      ) +
+      scale_fill_manual(values = c(
+        "brown"="brown",
+        "drug"=drug_colour,
+        "transparent"="transparent",
+        "lig1"=lig1_colour,
+        "lig2"=lig2_colour,
+        "lig3"=lig3_colour
+      ),
+      #expand=c(0,0)
+      ) +
+      theme_nothing() +
+      theme(plot.background = element_rect(fill = bg, colour=NA),
+            #plot.margin = margin(t=0,b=0),
+            panel.background = element_rect(fill = bg, colour=NA),
+            legend.position = "none"
+      ) +
+      labs(x = NULL, y= NULL) +
       geom_tile(aes(y = 1, x=factor(position), fill = bg_all, colour = bg_all)
       ) +
-        geom_tile(aes(y = 2, x=factor(position), fill = col_bg1, colour = col_bg1)
-        ) +
-        geom_tile(aes(y = 3, x=factor(position), fill = col_bg2, colour = col_bg2)
-        ) +
-        geom_tile(aes(y = 4, x=factor(position), fill = col_bg3, colour = col_bg3)
-        )
-    }
-# tile thingies end  
-
-    heat_legend=get_legend(heat_bar)
+      geom_tile(aes(y = 2, x=factor(position), fill = col_bg1, colour = col_bg1)
+      ) +
+      geom_tile(aes(y = 3, x=factor(position), fill = col_bg2, colour = col_bg2)
+      ) +
+      geom_tile(aes(y = 4, x=factor(position), fill = col_bg3, colour = col_bg3)
+      )
+  }
+  # tile thingies end  
+  
+  heat_legend=get_legend(heat_bar)
   out_plot=cowplot::plot_grid(
     heat_bar,
     NULL,