diff --git a/scripts/plotting/plotting_thesis/linage_bp_dist.R b/scripts/plotting/plotting_thesis/linage_bp_dist.R
new file mode 100644
index 0000000..38d2d05
--- /dev/null
+++ b/scripts/plotting/plotting_thesis/linage_bp_dist.R
@@ -0,0 +1,172 @@
+#!/usr/bin/env Rscript  
+
+#########################################################
+# TASK: Lineage plots [merged_df2]
+# Count
+# Diversity
+# Average stability dist
+# Avergae affinity dist: optional
+#########################################################
+#=======
+# output
+#=======
+# outdir_images = paste0("~/git/Writing/thesis/images/results/"
+#                        , tolower(gene), "/")
+# cat("plots will output to:", outdir_images)
+#########################################################
+
+#===============
+#Quick numbers checks
+#===============
+nsample_lin = merged_df2[merged_df2$lineage%in%c("L1", "L2", "L3", "L4"),]
+
+if ( all(table(nsample_lin$sensitivity)== table(nsample_lin$mutation_info_labels)) ){
+  cat("\nTotal no. of samples belonging to L1-l4 for", gene,":", nrow(nsample_lin)
+      , "\nCounting R and S samples")
+  if( sum(table(nsample_lin$sensitivity)) ==  nrow(nsample_lin) ){
+    cat("\nPASSNumbers cross checked:")
+    print(table(nsample_lin$sensitivity))
+  }
+}else{
+  stop("Abort: Numbers mismatch. Please check")
+}
+########################################################################
+###################################################
+#                  Lineage barplots               #
+###################################################
+
+#===============================
+# lineage sample and SNP count
+#===============================
+lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']]
+             , all_lineages = F
+             , x_categ = "sel_lineages"
+             , y_count = "p_count"
+             , use_lineages = c("L1", "L2", "L3", "L4")
+             , bar_fill_categ = "count_categ"
+             , display_label_col = "p_count"
+             , bar_stat_stype = "identity"
+             , d_lab_size = 8
+             , d_lab_col = "black"
+             , my_xats = 25 # x axis text size
+             , my_yats = 25 # y axis text sized_lab_size
+             , my_xals = 25 # x axis label size
+             , my_yals = 25 # y axis label size
+             , my_lls  = 25 # legend label size
+             , bar_col_labels =  c("SNPs", "Total Samples")
+             , bar_col_values = c("grey50", "gray75")
+             , bar_leg_name = ""
+             , leg_location = "top"
+             , y_log10 = F
+             , y_scale_percent = FALSE
+             , y_label = c("Count")
+             )
+
+#===============================
+# lineage SNP diversity count
+#===============================
+lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']]
+                              , x_categ = "sel_lineages"
+                              , y_count = "snp_diversity"
+                              #, all_lineages = F
+                              , use_lineages = c("L1", "L2", "L3", "L4")
+                              , display_label_col = "snp_diversity_f"
+                              , bar_stat_stype = "identity"
+                              , x_lab_angle = 90
+                              , d_lab_size =9
+                              , my_xats = 25 # x axis text size
+                              , my_yats = 25 # y axis text size
+                              , my_xals = 25 # x axis label size
+                              , my_yals = 25 # y axis label size
+                              , my_lls  = 25 # legend label size
+                              , y_log10 = F
+                              , y_scale_percent = F
+                              , leg_location = "top"
+                              , y_label = "Percent" #"SNP diversity"
+                              , bp_plot_title = "nsSNP diversity"
+                              , title_colour = "black" #"chocolate4"
+                              , subtitle_text = NULL
+                              , sts = 20
+                              , subtitle_colour = "#350E20FF")
+
+#=============================================
+# Output plots: Lineage count and Diversity
+#=============================================
+# lineage_bp_CL =  paste0(outdir_images
+#                         ,tolower(gene)
+#                         ,"_lineage_bp_CL_Tall.svg")
+# 
+# cat("Lineage barplots:", lineage_bp_CL)
+# svg(lineage_bp_CL, width = 8, height = 15)
+# 
+# cowplot::plot_grid(lin_countP, lin_diversityP
+#                      #, labels = c("(a)", "(b)", "(c)", "(d)")
+#                       , nrow = 2
+#                      # , ncols = 2
+#                       , labels = "AUTO"
+#                       , label_size = 25)
+# 
+# dev.off()
+########################################################################
+
+
+###################################################
+#                   Stability dist                #
+###################################################
+# scaled_cols_stability = c("duet_scaled"       
+#                           , "deepddg_scaled"   
+#                           , "ddg_dynamut2_scaled"
+#                           , "foldx_scaled"
+#                           , "avg_stability_scaled")
+
+my_xlabel = paste0("Average stability ", "(", stability_suffix, ")"); my_xlabel
+#plotdf = merged_df2[merged_df2$lineage%in%c("L1", "L2", "L3", "L4"),]
+
+linP_dm_om = lineage_distP(merged_df2
+                           , with_facet = F
+                           , x_axis = "avg_stability_scaled"
+                           , y_axis = "lineage_labels"
+                           , x_lab = my_xlabel
+                           , use_lineages = c("L1", "L2", "L3", "L4")
+                           #, fill_categ = "mutation_info_orig", fill_categ_cols = c("#E69F00", "#999999")
+                           , fill_categ = "sensitivity"
+                           , fill_categ_cols = c("red", "blue")
+                           , label_categories = c("Resistant", "Sensitive")
+                           , leg_label = "Mutation group"
+                           , my_ats = 22 # axis text size
+                           , my_als = 22 # axis label size
+                           , my_leg_ts = 22
+                           , my_leg_title = 22
+                           , my_strip_ts = 22
+                           , alpha = 0.56
+)
+
+linP_dm_om
+
+###################################################
+#                 Affinity dist [OPTIONAL]        #
+###################################################
+# scaled_cols_affinity = c("affinity_scaled" 
+#                          , "mmcsm_lig_scaled" 
+#                          , "mcsm_ppi2_scaled" 
+#                          , "mcsm_na_scaled"
+#                          , "avg_affinity_scaled")
+
+# lineage_distP(merged_df2
+#               , with_facet = F
+#               , x_axis = "avg_affinity_scaled"
+#               , y_axis = "lineage_labels"
+#               , x_lab = my_xlabel
+#               , use_lineages = c("L1", "L2", "L3", "L4")
+#               #, fill_categ = "mutation_info_orig", fill_categ_cols = c("#E69F00", "#999999")
+#               , fill_categ = "sensitivity"
+#               , fill_categ_cols = c("red", "blue")
+#               , label_categories = c("Resistant", "Sensitive")
+#               , leg_label = "Mutation group"
+#               , my_ats = 22 # axis text size
+#               , my_als = 22 # axis label size
+#               , my_leg_ts = 22
+#               , my_leg_title = 22
+#               , my_strip_ts = 22
+#               , alpha = 0.56
+# )
diff --git a/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R b/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R
index 1b8c5ce..00f3adc 100644
--- a/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R
+++ b/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R
@@ -1,5 +1,10 @@
 #!/usr/bin/env Rscript  
 
+###########################################
+# TASK: generate plots for lineage
+# Individual plots in 
+#lineage_bp_both.R
+#linage_dist_ens_stability.R
 ###########################################
 my_label_size = 25
 
diff --git a/scripts/plotting/plotting_thesis/linage_dist_ens_stability.R b/scripts/plotting/plotting_thesis/linage_dist_ens_stability.R
deleted file mode 100644
index 2071b59..0000000
--- a/scripts/plotting/plotting_thesis/linage_dist_ens_stability.R
+++ /dev/null
@@ -1,186 +0,0 @@
-#!/usr/bin/env Rscript  
-
-#########################################################
-# TASK: Lineage dist plots for stability:
-# average the four tools
-
-# func from : lineage_dist.R
-# plotdf
-# , x_axis = "duet_scaled"
-# , y_axis = "lineage_labels"
-# , x_lab = "DUET"
-# , all_lineages = F
-# , use_lineages = c("L1", "L2", "L3", "L4")
-# , with_facet = F
-# , facet_wrap_var = "" # FIXME: document what this is for
-# , fill_categ = "mutation_info_labels"
-# , fill_categ_cols = c("#E69F00", "#999999")
-# , my_ats = 15 # axis text size
-# , my_als = 20 # axis label size
-# , my_leg_ts = 16
-# , my_leg_title = 16
-# , my_strip_ts = 20
-# , leg_pos = c(0.8, 0.9)
-# , leg_pos_wf = c("top", "left", "bottom", "right")
-# , leg_dir_wf = c("horizontal", "vertical")
-# , leg_label = ""
-#########################################################
-
-#=======
-# output
-#=======
-outdir_images = paste0("~/git/Writing/thesis/images/results/"
-                       , tolower(gene), "/")
-cat("plots will output to:", outdir_images)
-#########################################################
-#=======
-# Data
-#=======
-df2 = merged_df2
-
-#==================================
-# PREFORMATTING: for consistency
-# IMPORTANT for calculating effects
-#==================================
-head(df2$ddg_foldx)
-df2['ddg_foldxC'] = abs(df2$ddg_foldx)
-head(df2['ddg_foldxC'])
-
-# reverse signs for foldx scaled values for consistency with other tools
-df2['foldx_scaled_signC'] = abs(df2$foldx_scaled)
-
-# remove the old ones from 
-rm_foldx_cols = c("ddg_foldx","foldx_scaled")
-raw_cols_stab_revised    = raw_cols_stability[!raw_cols_stability%in%rm_foldx_cols]
-raw_cols_stab_revised    = c(raw_cols_stab_revised,"ddg_foldxC")
-
-scaled_cols_stab_revised = scaled_cols_stability[!scaled_cols_stability%in%rm_foldx_cols]
-scaled_cols_stab_revised = c(scaled_cols_stab_revised, "foldx_scaled_signC")
-
-
-#=================
-# PREFORMATTING: for consistency
-#=================
-cols_to_extract  = colnames(df2)[colnames(df2)%in%c(common_cols
-                                                    , outcome_cols_stability
-                                                    , raw_cols_stability
-                                                    , scaled_cols_stability
-                                                    , raw_cols_stab_revised
-                                                    , scaled_cols_stab_revised
-                                                    , "lineage","lineage_labels")]
-
-df2_plot = df2[, cols_to_extract]
-
-all(table(df2_plot$lineage) == table(df2_plot$lineage_labels))
-
-# find which stability cols to average: should contain revised foldx
-if ("foldx_scaled_signC"%in%colnames(df2_plot)){
-  cat("\nPASS: finding stability cols to average")
-  cols2avg_new = which(colnames(df2_plot)%in%scaled_cols_stab_revised)
-}else{
-  stop("\nAbort: Foldx column has opposing sign. Can't proceed to avergae.")
-}
-
-# ensemble average across predictors
-df2_plot['ens_stab_new'] = rowMeans(df2_plot[, cols2avg_new])
-
-head(df2_plot$position); head(df2_plot$mutationinformation)
-table(df2_plot['ens_stab_new'])
-
-# scaling average values
-df2_plot["ens_stab_new_scaled"] = lapply(df2_plot["ens_stab_new"]
-                                         , function(x) {
-                                           scales::rescale_mid(x
-                                                           , to  = c(-1,1)
-                                                           , from = c( min(df2_plot["ens_stab_new"])
-                                                                       , max(df2_plot["ens_stab_new"]))
-                                                           , mid = 0
-                                                           #, from = c(0,1))
-                                           )})
-
-min(df2_plot['ens_stab_new']); max(df2_plot['ens_stab_new'])
-foo = df2_plot[c("cols2avg_new", "ens_stab_new_scaled"),]
-min(df2_plot['ens_stab_new_scaled']); max(df2_plot['ens_stab_new_scaled'])
-
-###########################################################
-nrow(df2_plot)
-table(df2_plot$lineage)
-table(df2_plot$lineage_labels)
-
-
-#===============
-#Quick numbers checks
-#===============
-nsample_lin = df2_plot[df2_plot$lineage%in%c("L1", "L2", "L3", "L4"),]
-
-if ( all(table(nsample_lin$sensitivity)== table(nsample_lin$mutation_info_labels)) ){
-  cat("\nTotal no. of samples belonging to L1-l4 for", gene,":", nrow(nsample_lin)
-      , "\nCounting R and S samples")
-  if( sum(table(nsample_lin$sensitivity)) ==  nrow(nsample_lin) ){
-    cat("\nPASSNumbers cross checked:")
-    print(table(nsample_lin$sensitivity))
-  }
-}else{
-  stop("Abort: Numbers mismatch. Please check")
-}
-
-
-#====================
-# Output Lineage plot
-#====================
-
-my_xlabel = paste0("Average stability ", "(", stability_suffix, ")"); my_xlabel
-
-# linD_ens_stabP = paste0(outdir_images
-#                           , tolower(gene)
-#                           ,"_linD_ens_stabP.svg")
-# 
-# cat("\nOutput plot:", linD_ens_stabP)
-# svg(linD_ens_stabP, width = 10, height = 10)
-
-linP_dm_om = lineage_distP(df2_plot
-                           , with_facet = F
-                           , x_axis = "ens_stab_new_scaled"
-                           , y_axis = "lineage_labels"
-                           , x_lab = my_xlabel
-                           , use_lineages = c("L1", "L2", "L3", "L4")
-                           #, fill_categ = "mutation_info_orig", fill_categ_cols = c("#E69F00", "#999999")
-                           , fill_categ = "sensitivity"
-                           , fill_categ_cols = c("red", "blue")
-                           , label_categories = c("Resistant", "Sensitive")
-                           , leg_label = "Mutation group"
-                           , my_ats = 22 # axis text size
-                           , my_als = 22 # axis label size
-                           , my_leg_ts = 22
-                           , my_leg_title = 22
-                           , my_strip_ts = 22
-                           , alpha = 0.56
-)
-
-linP_dm_om
-#dev.off()
-
-###########################################
-my_label_size = 25
-
-linPlots_combined = paste0(outdir_images
-                        , tolower(gene)
-                        ,"_linP_combined.svg")
-
-cat("\nOutput plot:", linPlots_combined)
-svg(linPlots_combined, width = 18, height = 12)
-
-cowplot::plot_grid(
-  cowplot::plot_grid(lin_countP, lin_diversityP
-                     , nrow = 2
-                     # , ncols = 2
-                     , labels = "AUTO"
-                     , label_size = my_label_size),
-  NULL,
-  linP_dm_om,
-  nrow = 1,
-  labels = c("", "", "C"),
-  label_size = my_label_size,
-  rel_widths = c(35, 3, 52)
-)
-dev.off()
\ No newline at end of file
diff --git a/scripts/plotting/plotting_thesis/lineage_bp_both.R b/scripts/plotting/plotting_thesis/lineage_bp_both.R
deleted file mode 100644
index a723bfd..0000000
--- a/scripts/plotting/plotting_thesis/lineage_bp_both.R
+++ /dev/null
@@ -1,75 +0,0 @@
-# get plotting_dfs()
-# using dfs [lf and wf] from lineage_dfL
-# FIXME: add SNP diversity as the title
-#===============================
-# lineage sample and SNP count
-#===============================
-lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']]
-             , all_lineages = F
-             , x_categ = "sel_lineages"
-             , y_count = "p_count"
-             , use_lineages = c("L1", "L2", "L3", "L4")
-             , bar_fill_categ = "count_categ"
-             , display_label_col = "p_count"
-             , bar_stat_stype = "identity"
-             , d_lab_size = 8
-             , d_lab_col = "black"
-             , my_xats = 25 # x axis text size
-             , my_yats = 25 # y axis text sized_lab_size
-             , my_xals = 25 # x axis label size
-             , my_yals = 25 # y axis label size
-             , my_lls  = 25 # legend label size
-             , bar_col_labels =  c("SNPs", "Total Samples")
-             , bar_col_values = c("grey50", "gray75")
-             , bar_leg_name = ""
-             , leg_location = "top"
-             , y_log10 = F
-             , y_scale_percent = FALSE
-             , y_label = c("Count")
-             )
-
-#===============================
-# lineage SNP diversity count
-#===============================
-lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']]
-                              , x_categ = "sel_lineages"
-                              , y_count = "snp_diversity"
-                              #, all_lineages = F
-                              , use_lineages = c("L1", "L2", "L3", "L4")
-                              , display_label_col = "snp_diversity_f"
-                              , bar_stat_stype = "identity"
-                              , x_lab_angle = 90
-                              , d_lab_size =9
-                              , my_xats = 25 # x axis text size
-                              , my_yats = 25 # y axis text size
-                              , my_xals = 25 # x axis label size
-                              , my_yals = 25 # y axis label size
-                              , my_lls  = 25 # legend label size
-                              , y_log10 = F
-                              , y_scale_percent = F
-                              , leg_location = "top"
-                              , y_label = "Percent" #"SNP diversity"
-                              , bp_plot_title = "nsSNP diversity"
-                              , title_colour = "black" #"chocolate4"
-                              , subtitle_text = NULL
-                              , sts = 20
-                              , subtitle_colour = "#350E20FF")
-
-#=============================================
-# Output plots: Lineage count and Diversity
-#=============================================
-# lineage_bp_CL =  paste0(outdir_images
-#                         ,tolower(gene)
-#                         ,"_lineage_bp_CL_Tall.svg")
-# 
-# cat("Lineage barplots:", lineage_bp_CL)
-# svg(lineage_bp_CL, width = 8, height = 15)
-# 
-# cowplot::plot_grid(lin_countP, lin_diversityP
-#                      #, labels = c("(a)", "(b)", "(c)", "(d)")
-#                       , nrow = 2
-#                      # , ncols = 2
-#                       , labels = "AUTO"
-#                       , label_size = 25)
-# 
-# dev.off()
\ No newline at end of file