diff --git a/scripts/count_vars_ML.R b/scripts/count_vars_ML.R
index 464fd6d..b0a6d6f 100644
--- a/scripts/count_vars_ML.R
+++ b/scripts/count_vars_ML.R
@@ -96,7 +96,7 @@ cat(paste("\nmerged df3 filename:", outfile_merged_df3
 # source("~/git/LSHTM_analysis/config/pnca.R")
 # source("~/git/LSHTM_analysis/config/rpob.R")
 # # 
-df3_filename = paste0("/home/tanu/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
+df3_filename = paste0("~/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
 df3 = read.csv(df3_filename)
 # # 
 # mutationinformation
diff --git a/scripts/count_vars_ML_v1.R b/scripts/count_vars_ML_v1.R
index a0675cd..d6c3355 100644
--- a/scripts/count_vars_ML_v1.R
+++ b/scripts/count_vars_ML_v1.R
@@ -222,7 +222,7 @@ source("~/git/LSHTM_analysis/config/katg.R")
 source("~/git/LSHTM_analysis/config/pnca.R")
 source("~/git/LSHTM_analysis/config/rpob.R")
 # 
-df3_filename = paste0("/home/tanu/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
+df3_filename = paste0("~/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
 df3 = read.csv(df3_filename)
 # 
 # mutationinformation
diff --git a/scripts/functions/tests/test_aa_prop_bp.R b/scripts/functions/tests/test_aa_prop_bp.R
index fa1a218..529017f 100644
--- a/scripts/functions/tests/test_aa_prop_bp.R
+++ b/scripts/functions/tests/test_aa_prop_bp.R
@@ -11,7 +11,7 @@ getwd()
 # that will be used in testing the functions
 #===========================================
 source("plotting_data.R")
-infile = "/home/tanu/git/Data/streptomycin/output/"
+infile = "~/git/Data/streptomycin/output/"
 pd_df = plotting_data(infile)
 my_df       = pd_df[[1]]
 my_df_u     = pd_df[[2]]
diff --git a/scripts/functions/tests/test_combining_dfs_plotting.R b/scripts/functions/tests/test_combining_dfs_plotting.R
index 501bca6..99812dc 100644
--- a/scripts/functions/tests/test_combining_dfs_plotting.R
+++ b/scripts/functions/tests/test_combining_dfs_plotting.R
@@ -38,12 +38,12 @@ source("combining_dfs_plotting.R")
 #---------------------
 #gene = 'gid'
 #drug = 'streptomycin'
-#source("/home/tanu/git/LSHTM_analysis/config/gid.R")
-#source("/home/tanu/git/LSHTM_analysis/config/alr.R")
-#source("/home/tanu/git/LSHTM_analysis/config/katg.R")
-source("/home/tanu/git/LSHTM_analysis/config/pnca.R")
-#source("/home/tanu/git/LSHTM_analysis/config/rpob.R")
-#source("/home/tanu/git/LSHTM_analysis/config/embb.R")
+#source("~/git/LSHTM_analysis/config/gid.R")
+#source("~/git/LSHTM_analysis/config/alr.R")
+#source("~/git/LSHTM_analysis/config/katg.R")
+source("~/git/LSHTM_analysis/config/pnca.R")
+#source("~/git/LSHTM_analysis/config/rpob.R")
+#source("~/git/LSHTM_analysis/config/embb.R")
 
 
 
diff --git a/scripts/functions/tests/test_ed_pfm_data.R b/scripts/functions/tests/test_ed_pfm_data.R
index 0744ef9..af91318 100644
--- a/scripts/functions/tests/test_ed_pfm_data.R
+++ b/scripts/functions/tests/test_ed_pfm_data.R
@@ -2,7 +2,7 @@ source("~/git/LSHTM_analysis/scripts/Header_TT.R")
 source("~/git/LSHTM_analysis/scripts/functions/ed_pfm_data.R")
 
 # data msa: mut
-my_data = read.csv("/home/tanu/git/Misc/practice_plots/pnca_msa_eg2.csv", header = F) #15 cols only
+my_data = read.csv("~/git/Misc/practice_plots/pnca_msa_eg2.csv", header = F) #15 cols only
 msaSeq_mut = my_data$V1
 msa_seq = msaSeq_mut
 
diff --git a/scripts/functions/tests/test_plotting_data.R b/scripts/functions/tests/test_plotting_data.R
index bb5ea3c..1f7cb23 100644
--- a/scripts/functions/tests/test_plotting_data.R
+++ b/scripts/functions/tests/test_plotting_data.R
@@ -19,7 +19,7 @@ import_dirs(drug_name = drug, gene_name = gene)
 #-------------------------------
 source("plotting_data.R")
 
-infile_params = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
+infile_params = "~/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
 mcsm_comb_data = read.csv(infile_params, header = T)
 
 pd_df = plotting_data(df = mcsm_comb_data
diff --git a/scripts/plotting/LINEAGE.R b/scripts/plotting/LINEAGE.R
index d49e28d..e2de5fc 100644
--- a/scripts/plotting/LINEAGE.R
+++ b/scripts/plotting/LINEAGE.R
@@ -5,8 +5,8 @@ library("ggforce")
 library(gginference)
 library(ggpubr)
 #%% read data
-df = read.csv("/home/tanu/git/Data/pyrazinamide/output/pnca_merged_df2.csv")
-#df2 = read.csv("/home/tanu/git/Data/pyrazinamide/output/pnca_merged_df3.csv")
+df = read.csv("~/git/Data/pyrazinamide/output/pnca_merged_df2.csv")
+#df2 = read.csv("~/git/Data/pyrazinamide/output/pnca_merged_df3.csv")
 
 foo = as.data.frame(colnames(df))
 
diff --git a/scripts/plotting/basic_barplots.R b/scripts/plotting/basic_barplots.R
index 4ea3fea..318a463 100755
--- a/scripts/plotting/basic_barplots.R
+++ b/scripts/plotting/basic_barplots.R
@@ -68,7 +68,7 @@ import_dirs(drug, gene)
   # my_df_u_lig
   # dup_muts
 #***********************************
-#infile_params = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
+#infile_params = "~/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
 
 if (!exists("infile_params") && exists("gene")){
 #if (!is.character(infile_params) && exists("gene")){
diff --git a/scripts/plotting/lineage_plots_multipage.R b/scripts/plotting/lineage_plots_multipage.R
index f09d195..97129d4 100644
--- a/scripts/plotting/lineage_plots_multipage.R
+++ b/scripts/plotting/lineage_plots_multipage.R
@@ -14,7 +14,7 @@ lineage_plot=function(gene,drug){
   full_file_path = paste0(lineage_data_path,"/",lineage_filename)
   print(paste0("Loading: ",full_file_path))
   df = read.csv(full_file_path)
-  #df2 = read.csv("/home/tanu/git/Data/pyrazinamide/output/pnca_merged_df3.csv")
+  #df2 = read.csv("~/git/Data/pyrazinamide/output/pnca_merged_df3.csv")
   
   foo = as.data.frame(colnames(df))
   
diff --git a/scripts/plotting/logo_data_msa.R b/scripts/plotting/logo_data_msa.R
index 79aea06..8bd1a09 100644
--- a/scripts/plotting/logo_data_msa.R
+++ b/scripts/plotting/logo_data_msa.R
@@ -5,12 +5,12 @@ cat("\n=========================================="
     , "\nLogo MSA Plots Data: ALL params"
     , "\n=========================================")
 
-#msa1 = read.csv("/home/tanu/git/Data/cycloserine/output/gid_msa.csv", header = F)
+#msa1 = read.csv("~/git/Data/cycloserine/output/gid_msa.csv", header = F)
 #head(msa1)
 #msa_seq= msa1$V1
 #head(msa_seq)
 
-#msa2 = read.csv("/home/tanu/git/Data/cycloserine/input/gid.1fasta", header = F)
+#msa2 = read.csv("~/git/Data/cycloserine/input/gid.1fasta", header = F)
 #head(msa2)
 #wt_seq = msa2$V1
 #head(wt_seq)
diff --git a/scripts/plotting/mcsm_affinity_data_only.R b/scripts/plotting/mcsm_affinity_data_only.R
index 597e44d..712ef69 100644
--- a/scripts/plotting/mcsm_affinity_data_only.R
+++ b/scripts/plotting/mcsm_affinity_data_only.R
@@ -5,7 +5,7 @@
 #source("~/git/LSHTM_analysis/config/katg.R")
 source("~/git/LSHTM_analysis/config/rpob.R")
 
-source("/home/tanu/git/LSHTM_analysis/my_header.R")
+source("~/git/LSHTM_analysis/my_header.R")
 #########################################################
 # TASK: Generate averaged affinity values 
 # across all affinity tools for a given structure
@@ -32,7 +32,7 @@ print(paste0("Output file:", outfile_mean_aff_priorty))
 #=============
 # Input
 #=============
-df3_filename = paste0("/home/tanu/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
+df3_filename = paste0("~/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
 df3 = read.csv(df3_filename)
 length(df3$mutationinformation)
 
diff --git a/scripts/plotting/plotting_thesis/alr/DONOTUSEdm_om_plots_layout_alr.R b/scripts/plotting/plotting_thesis/alr/DONOTUSEdm_om_plots_layout_alr.R
index cab13ae..96b3df0 100644
--- a/scripts/plotting/plotting_thesis/alr/DONOTUSEdm_om_plots_layout_alr.R
+++ b/scripts/plotting/plotting_thesis/alr/DONOTUSEdm_om_plots_layout_alr.R
@@ -1,5 +1,5 @@
 # # source dm_om_plots.R
-# source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R")
+# source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R")
 # 
 # ##### plots to combine ####
 # duetP
diff --git a/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist_layout.R b/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist_layout.R
index d093aeb..34e48e7 100644
--- a/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist_layout.R
+++ b/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist_layout.R
@@ -1,5 +1,5 @@
 #!/usr/bin/env Rscript  
-source("/home/sethp/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist.R")
 
 ###########################################
 # TASK: generate plots for lineage
diff --git a/scripts/plotting/plotting_thesis/alr/alr_other_plots.R b/scripts/plotting/plotting_thesis/alr/alr_other_plots.R
index 989f8ee..2d7ba51 100644
--- a/scripts/plotting/plotting_thesis/alr/alr_other_plots.R
+++ b/scripts/plotting/plotting_thesis/alr/alr_other_plots.R
@@ -1,2 +1,2 @@
 
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")
\ No newline at end of file
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")
diff --git a/scripts/plotting/plotting_thesis/alr/basic_barplots_alr_layout.R b/scripts/plotting/plotting_thesis/alr/basic_barplots_alr_layout.R
index f9f3269..b6a32da 100644
--- a/scripts/plotting/plotting_thesis/alr/basic_barplots_alr_layout.R
+++ b/scripts/plotting/plotting_thesis/alr/basic_barplots_alr_layout.R
@@ -4,8 +4,8 @@
 source("~/git/LSHTM_analysis/config/alr.R")
 source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
 
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/basic_barplots_alr.R")
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/pe_sens_site_count_alr.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/basic_barplots_alr.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/pe_sens_site_count_alr.R")
 
 if ( tolower(gene)%in%c("alr") ){
   cat("\nPlots available for layout are:")
diff --git a/scripts/plotting/plotting_thesis/alr/gg_pairs_all_alr.R b/scripts/plotting/plotting_thesis/alr/gg_pairs_all_alr.R
index f311967..fd911dc 100644
--- a/scripts/plotting/plotting_thesis/alr/gg_pairs_all_alr.R
+++ b/scripts/plotting/plotting_thesis/alr/gg_pairs_all_alr.R
@@ -256,7 +256,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
 
 
 #### Combine plots #####
-# #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
+# #png("~/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
 # png(paste0(outdir_images
 #            ,tolower(gene)
 #            ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300)
@@ -272,7 +272,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
 # dev.off()
 #
 # # affinity corr
-# #png("/home/tanu/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
+# #png("~/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
 # png(paste0(outdir_images
 #            ,tolower(gene)
 #            ,"_CorrC.png"), height =7, width=7, unit="in",res=300)
diff --git a/scripts/plotting/plotting_thesis/alr/pe_sens_site_count_alr.R b/scripts/plotting/plotting_thesis/alr/pe_sens_site_count_alr.R
index 6cf8c6b..acb3ff4 100644
--- a/scripts/plotting/plotting_thesis/alr/pe_sens_site_count_alr.R
+++ b/scripts/plotting/plotting_thesis/alr/pe_sens_site_count_alr.R
@@ -1,5 +1,5 @@
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/prominent_effects_alr.R")
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/sensitivity_count_alr.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/prominent_effects_alr.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/sensitivity_count_alr.R")
 
 ##############################################################
 #                         PE count
diff --git a/scripts/plotting/plotting_thesis/embb/basic_barplots_embb_layout.R b/scripts/plotting/plotting_thesis/embb/basic_barplots_embb_layout.R
index 7e70c03..7b8b564 100644
--- a/scripts/plotting/plotting_thesis/embb/basic_barplots_embb_layout.R
+++ b/scripts/plotting/plotting_thesis/embb/basic_barplots_embb_layout.R
@@ -4,8 +4,8 @@
 source("~/git/LSHTM_analysis/config/embb.R")
 source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
 
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/basic_barplots_embb.R")
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/pe_sens_site_count_embb.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/basic_barplots_embb.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/pe_sens_site_count_embb.R")
 
 if ( tolower(gene)%in%c("embb") ){
   cat("\nPlots available for layout are:")
diff --git a/scripts/plotting/plotting_thesis/embb/dm_om_plots_layout_embb.R b/scripts/plotting/plotting_thesis/embb/dm_om_plots_layout_embb.R
index b8994bd..a463c29 100644
--- a/scripts/plotting/plotting_thesis/embb/dm_om_plots_layout_embb.R
+++ b/scripts/plotting/plotting_thesis/embb/dm_om_plots_layout_embb.R
@@ -1,5 +1,5 @@
 # source dm_om_plots.R
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R")
 
 ##### plots to combine ####
 duetP
diff --git a/scripts/plotting/plotting_thesis/embb/embb_other_plots.R b/scripts/plotting/plotting_thesis/embb/embb_other_plots.R
index 989f8ee..c758072 100644
--- a/scripts/plotting/plotting_thesis/embb/embb_other_plots.R
+++ b/scripts/plotting/plotting_thesis/embb/embb_other_plots.R
@@ -1,2 +1,2 @@
 
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")
\ No newline at end of file
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")
\ No newline at end of file
diff --git a/scripts/plotting/plotting_thesis/embb/gg_pairs_all_embb.R b/scripts/plotting/plotting_thesis/embb/gg_pairs_all_embb.R
index 2970bb1..1ab6e44 100644
--- a/scripts/plotting/plotting_thesis/embb/gg_pairs_all_embb.R
+++ b/scripts/plotting/plotting_thesis/embb/gg_pairs_all_embb.R
@@ -148,7 +148,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
                                )
 
 #### Combine plots #####
-# #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
+# #png("~/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
 # png(paste0(outdir_images
 #            ,tolower(gene)
 #            ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300)
@@ -164,7 +164,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
 # dev.off()
 # 
 # # affinity corr
-# #png("/home/tanu/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
+# #png("~/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
 # png(paste0(outdir_images
 #            ,tolower(gene)
 #            ,"_CorrC.png"), height =7, width=7, unit="in",res=300)
diff --git a/scripts/plotting/plotting_thesis/embb/pe_sens_site_count_embb.R b/scripts/plotting/plotting_thesis/embb/pe_sens_site_count_embb.R
index 365dad0..c8f6a31 100644
--- a/scripts/plotting/plotting_thesis/embb/pe_sens_site_count_embb.R
+++ b/scripts/plotting/plotting_thesis/embb/pe_sens_site_count_embb.R
@@ -1,5 +1,5 @@
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/prominent_effects_embb.R")
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/sensitivity_count_embb.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/prominent_effects_embb.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/sensitivity_count_embb.R")
 
 ##############################################################
 #                         PE count
diff --git a/scripts/plotting/plotting_thesis/gid/basic_barplots_gid_layout.R b/scripts/plotting/plotting_thesis/gid/basic_barplots_gid_layout.R
index d93518b..366b28d 100644
--- a/scripts/plotting/plotting_thesis/gid/basic_barplots_gid_layout.R
+++ b/scripts/plotting/plotting_thesis/gid/basic_barplots_gid_layout.R
@@ -4,8 +4,8 @@
 source("~/git/LSHTM_analysis/config/gid.R")
 source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
 
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/basic_barplots_gid.R")
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/pe_sens_site_count_gid.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/basic_barplots_gid.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/pe_sens_site_count_gid.R")
 #cat("\nSourced plotting cols as well:", length(plotting_cols))
 
 #=======
diff --git a/scripts/plotting/plotting_thesis/gid/dm_om_plots_gid_ayout.R b/scripts/plotting/plotting_thesis/gid/dm_om_plots_gid_ayout.R
index ec4854d..48779c9 100644
--- a/scripts/plotting/plotting_thesis/gid/dm_om_plots_gid_ayout.R
+++ b/scripts/plotting/plotting_thesis/gid/dm_om_plots_gid_ayout.R
@@ -1,5 +1,5 @@
 # source dm_om_plots.R
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R")
 
 ##### plots to combine ####
 duetP
diff --git a/scripts/plotting/plotting_thesis/gid/gg_pairs_all_gid.R b/scripts/plotting/plotting_thesis/gid/gg_pairs_all_gid.R
index f60ed48..3f3a92d 100644
--- a/scripts/plotting/plotting_thesis/gid/gg_pairs_all_gid.R
+++ b/scripts/plotting/plotting_thesis/gid/gg_pairs_all_gid.R
@@ -159,7 +159,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
                                )
 
 #### Combine plots (OLD, AB + C) #####
-# #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
+# #png("~/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
 # png(paste0(outdir_images
 #            ,tolower(gene)
 #            ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300)
@@ -175,7 +175,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
 # dev.off()
 # 
 # # affinity corr
-# #png("/home/tanu/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
+# #png("~/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
 # png(paste0(outdir_images
 #            ,tolower(gene)
 #            ,"_CorrC.png"), height =7, width=7, unit="in",res=300)
diff --git a/scripts/plotting/plotting_thesis/gid/gid_other_plots.R b/scripts/plotting/plotting_thesis/gid/gid_other_plots.R
index 80d95e5..2d7ba51 100644
--- a/scripts/plotting/plotting_thesis/gid/gid_other_plots.R
+++ b/scripts/plotting/plotting_thesis/gid/gid_other_plots.R
@@ -1,2 +1,2 @@
 
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")
diff --git a/scripts/plotting/plotting_thesis/gid/pe_sens_site_count_gid.R b/scripts/plotting/plotting_thesis/gid/pe_sens_site_count_gid.R
index 28e97f7..e551fd5 100644
--- a/scripts/plotting/plotting_thesis/gid/pe_sens_site_count_gid.R
+++ b/scripts/plotting/plotting_thesis/gid/pe_sens_site_count_gid.R
@@ -1,5 +1,5 @@
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/prominent_effects_gid.R")
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/sensitivity_count_gid.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/prominent_effects_gid.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/sensitivity_count_gid.R")
 
 ##############################################################
 #                         PE count
diff --git a/scripts/plotting/plotting_thesis/katg/basic_barplots_katg_layout.R b/scripts/plotting/plotting_thesis/katg/basic_barplots_katg_layout.R
index 4001908..9cd757f 100644
--- a/scripts/plotting/plotting_thesis/katg/basic_barplots_katg_layout.R
+++ b/scripts/plotting/plotting_thesis/katg/basic_barplots_katg_layout.R
@@ -4,8 +4,8 @@
 source("~/git/LSHTM_analysis/config/katg.R")
 source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
 
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/basic_barplots_katg.R")
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/pe_sens_site_count_katg.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/basic_barplots_katg.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/pe_sens_site_count_katg.R")
 
 if ( tolower(gene)%in%c("katg") ){
   cat("\nPlots available for layout are:")
diff --git a/scripts/plotting/plotting_thesis/katg/gg_pairs_all_katg.R b/scripts/plotting/plotting_thesis/katg/gg_pairs_all_katg.R
index 91be116..758eeb2 100644
--- a/scripts/plotting/plotting_thesis/katg/gg_pairs_all_katg.R
+++ b/scripts/plotting/plotting_thesis/katg/gg_pairs_all_katg.R
@@ -156,7 +156,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
                                )
 
 #### Combine plots #####
-# #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
+# #png("~/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
 # png(paste0(outdir_images
 #            ,tolower(gene)
 #            ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300)
@@ -172,7 +172,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
 # dev.off()
 # 
 # # affinity corr
-# #png("/home/tanu/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
+# #png("~/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
 # png(paste0(outdir_images
 #            ,tolower(gene)
 #            ,"_CorrC.png"), height =7, width=7, unit="in",res=300)
diff --git a/scripts/plotting/plotting_thesis/katg/katg_dm_om_plots_layout.R b/scripts/plotting/plotting_thesis/katg/katg_dm_om_plots_layout.R
index 5dd5625..e9bc1ae 100644
--- a/scripts/plotting/plotting_thesis/katg/katg_dm_om_plots_layout.R
+++ b/scripts/plotting/plotting_thesis/katg/katg_dm_om_plots_layout.R
@@ -1,5 +1,5 @@
 # source dm_om_plots.R
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/katg_dm_om_plots.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/katg_dm_om_plots.R")
 
 ##### plots to combine ####
 duetP
diff --git a/scripts/plotting/plotting_thesis/katg/katg_other_plots.R b/scripts/plotting/plotting_thesis/katg/katg_other_plots.R
index 989f8ee..c758072 100644
--- a/scripts/plotting/plotting_thesis/katg/katg_other_plots.R
+++ b/scripts/plotting/plotting_thesis/katg/katg_other_plots.R
@@ -1,2 +1,2 @@
 
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")
\ No newline at end of file
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")
\ No newline at end of file
diff --git a/scripts/plotting/plotting_thesis/katg/pe_sens_site_count_katg.R b/scripts/plotting/plotting_thesis/katg/pe_sens_site_count_katg.R
index 235b8b6..db60628 100644
--- a/scripts/plotting/plotting_thesis/katg/pe_sens_site_count_katg.R
+++ b/scripts/plotting/plotting_thesis/katg/pe_sens_site_count_katg.R
@@ -1,5 +1,5 @@
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/prominent_effects_katg.R")
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/sensitivity_count_katg.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/prominent_effects_katg.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/sensitivity_count_katg.R")
 
 ##############################################################
 #                         PE count
diff --git a/scripts/plotting/plotting_thesis/lineage_bp_dist_layout.R b/scripts/plotting/plotting_thesis/lineage_bp_dist_layout.R
index 464ec43..6183743 100644
--- a/scripts/plotting/plotting_thesis/lineage_bp_dist_layout.R
+++ b/scripts/plotting/plotting_thesis/lineage_bp_dist_layout.R
@@ -1,5 +1,5 @@
 #!/usr/bin/env Rscript  
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/lineage_bp_dist.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/lineage_bp_dist.R")
 
 #=======
 # output
diff --git a/scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca_layout.R b/scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca_layout.R
index 5e45805..ceeeb8b 100644
--- a/scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca_layout.R
+++ b/scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca_layout.R
@@ -4,8 +4,8 @@
 #source("~/git/LSHTM_analysis/config/pnca.R")
 #source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
 
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca.R")
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/pe_sens_site_count_pnca.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/pe_sens_site_count_pnca.R")
 
 if ( tolower(gene)%in%c("pnca") ){
   cat("\nPlots available for layout are:")
diff --git a/scripts/plotting/plotting_thesis/pnca/gg_pairs_all_pnca.R b/scripts/plotting/plotting_thesis/pnca/gg_pairs_all_pnca.R
index 4a5c0d7..dc1095e 100644
--- a/scripts/plotting/plotting_thesis/pnca/gg_pairs_all_pnca.R
+++ b/scripts/plotting/plotting_thesis/pnca/gg_pairs_all_pnca.R
@@ -156,7 +156,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
                                )
 
 #### Combine plots #####
-# #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
+# #png("~/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
 # png(paste0(outdir_images
 #            ,tolower(gene)
 #            ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300)
@@ -172,7 +172,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
 # dev.off()
 # 
 # # affinity corr
-# #png("/home/tanu/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
+# #png("~/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
 # png(paste0(outdir_images
 #            ,tolower(gene)
 #            ,"_CorrC.png"), height =7, width=7, unit="in",res=300)
diff --git a/scripts/plotting/plotting_thesis/pnca/lineage_bp_dist_layout.R b/scripts/plotting/plotting_thesis/pnca/lineage_bp_dist_layout.R
index d574273..40003d9 100644
--- a/scripts/plotting/plotting_thesis/pnca/lineage_bp_dist_layout.R
+++ b/scripts/plotting/plotting_thesis/pnca/lineage_bp_dist_layout.R
@@ -1,5 +1,5 @@
 #!/usr/bin/env Rscript  
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/lineage_bp_dist.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/lineage_bp_dist.R")
 
 #=======
 # output
diff --git a/scripts/plotting/plotting_thesis/pnca/pe_sens_site_count_pnca.R b/scripts/plotting/plotting_thesis/pnca/pe_sens_site_count_pnca.R
index 8713a29..df1c23b 100644
--- a/scripts/plotting/plotting_thesis/pnca/pe_sens_site_count_pnca.R
+++ b/scripts/plotting/plotting_thesis/pnca/pe_sens_site_count_pnca.R
@@ -1,5 +1,5 @@
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/prominent_effects_pnca.R")
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/sensitivity_count_pnca.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/prominent_effects_pnca.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/sensitivity_count_pnca.R")
 
 ##############################################################
 #                         PE count
diff --git a/scripts/plotting/plotting_thesis/pnca/pnca_dm_om_plots_layout.R b/scripts/plotting/plotting_thesis/pnca/pnca_dm_om_plots_layout.R
index d0ca67e..71c56b3 100644
--- a/scripts/plotting/plotting_thesis/pnca/pnca_dm_om_plots_layout.R
+++ b/scripts/plotting/plotting_thesis/pnca/pnca_dm_om_plots_layout.R
@@ -1,5 +1,5 @@
 # source dm_om_plots.R
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/pnca_dm_om_plots.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/pnca_dm_om_plots.R")
 
 ##### plots to combine ####
 duetP
diff --git a/scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob_layout.R b/scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob_layout.R
index 554221b..86fe2ab 100644
--- a/scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob_layout.R
+++ b/scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob_layout.R
@@ -26,8 +26,8 @@ table(df3_ppi2$sensitivity)
 outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
 cat("plots will output to:", outdir_images)
 
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob.R")
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/pe_sens_site_count_rpob.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/pe_sens_site_count_rpob.R")
 
 if ( tolower(gene)%in%c("rpob") ){
   cat("\nPlots available for layout are:")
diff --git a/scripts/plotting/plotting_thesis/rpob/dm_om_plots_layout_rpob.R b/scripts/plotting/plotting_thesis/rpob/dm_om_plots_layout_rpob.R
index 1c46246..ccea591 100644
--- a/scripts/plotting/plotting_thesis/rpob/dm_om_plots_layout_rpob.R
+++ b/scripts/plotting/plotting_thesis/rpob/dm_om_plots_layout_rpob.R
@@ -1,6 +1,6 @@
 # source dm_om_plots.R
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/dm_om_plots_rpob.R")
-# source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/dm_om_plots_rpob.R")
+# source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R")
 
 ##### plots to combine ####
 duetP
diff --git a/scripts/plotting/plotting_thesis/rpob/gg_pairs_all_rpob.R b/scripts/plotting/plotting_thesis/rpob/gg_pairs_all_rpob.R
index ae4e26a..f11f6ae 100644
--- a/scripts/plotting/plotting_thesis/rpob/gg_pairs_all_rpob.R
+++ b/scripts/plotting/plotting_thesis/rpob/gg_pairs_all_rpob.R
@@ -160,7 +160,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
                                )
 
 #### Combine plots #####
-# #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
+# #png("~/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
 # png(paste0(outdir_images
 #            ,tolower(gene)
 #            ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300)
@@ -176,7 +176,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
 # dev.off()
 # 
 # # affinity corr
-# #png("/home/tanu/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
+# #png("~/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
 # png(paste0(outdir_images
 #            ,tolower(gene)
 #            ,"_CorrC.png"), height =7, width=7, unit="in",res=300)
diff --git a/scripts/plotting/plotting_thesis/rpob/pe_sens_site_count_rpob.R b/scripts/plotting/plotting_thesis/rpob/pe_sens_site_count_rpob.R
index 6dbe2b4..d417294 100644
--- a/scripts/plotting/plotting_thesis/rpob/pe_sens_site_count_rpob.R
+++ b/scripts/plotting/plotting_thesis/rpob/pe_sens_site_count_rpob.R
@@ -1,5 +1,5 @@
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/prominent_effects_rpob.R")
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/sensitivity_count_rpob.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/prominent_effects_rpob.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/sensitivity_count_rpob.R")
 
 ##############################################################
 #                         PE count
diff --git a/scripts/plotting/plotting_thesis/rpob/rpob_other_plots.R b/scripts/plotting/plotting_thesis/rpob/rpob_other_plots.R
index 989f8ee..c758072 100644
--- a/scripts/plotting/plotting_thesis/rpob/rpob_other_plots.R
+++ b/scripts/plotting/plotting_thesis/rpob/rpob_other_plots.R
@@ -1,2 +1,2 @@
 
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")
\ No newline at end of file
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")
\ No newline at end of file
diff --git a/scripts/plotting/plotting_thesis/version1/gg_pairs_all.R b/scripts/plotting/plotting_thesis/version1/gg_pairs_all.R
index c103304..9042ed7 100644
--- a/scripts/plotting/plotting_thesis/version1/gg_pairs_all.R
+++ b/scripts/plotting/plotting_thesis/version1/gg_pairs_all.R
@@ -148,7 +148,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff, plot_title="Affinity estimates", tt_
 # combine
 #=============
 
-#png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
+#png("~/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
 png(paste0(outdir_images
            ,tolower(gene)
            ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300)
@@ -164,7 +164,7 @@ cowplot::plot_grid(ggmatrix_gtable(plot_corr_df_ps),
 dev.off()
 
 # affinity corr
-#png("/home/tanu/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
+#png("~/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
 png(paste0(outdir_images
            ,tolower(gene)
            ,"_CorrC.png"), height =7, width=7, unit="in",res=300)
diff --git a/scripts/plotting/redundant/basic_barplots_LIG.R b/scripts/plotting/redundant/basic_barplots_LIG.R
index 748f2ad..03545a0 100755
--- a/scripts/plotting/redundant/basic_barplots_LIG.R
+++ b/scripts/plotting/redundant/basic_barplots_LIG.R
@@ -76,7 +76,7 @@ import_dirs(drug, gene)
 # my_df_u_lig
 # dup_muts
 #----------------------------------------------
-#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
+#infile = "~/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
 #infile = ""
 
 #if (!exists("infile") && exists("gene")){
diff --git a/scripts/plotting/redundant/basic_barplots_PS.R b/scripts/plotting/redundant/basic_barplots_PS.R
index 9ae2f7d..deff8b8 100755
--- a/scripts/plotting/redundant/basic_barplots_PS.R
+++ b/scripts/plotting/redundant/basic_barplots_PS.R
@@ -75,7 +75,7 @@ import_dirs(drug, gene)
   # my_df_u_lig
   # dup_muts
 #----------------------------------------------
-#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
+#infile = "~/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
 #infile = ""
 
 #if (!exists("infile") && exists("gene")){
diff --git a/scripts/plotting/redundant/combining_dfs_plotting.R b/scripts/plotting/redundant/combining_dfs_plotting.R
index db35adc..7c606bb 100644
--- a/scripts/plotting/redundant/combining_dfs_plotting.R
+++ b/scripts/plotting/redundant/combining_dfs_plotting.R
@@ -80,7 +80,7 @@ import_dirs(drug, gene)
   # my_df_u_lig
   # dup_muts
 #***********************************
-#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
+#infile = "~/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
 
 if (!exists("infile") && exists("gene")){
 #if (!is.character(infile) && exists("gene")){
diff --git a/scripts/plotting/structure_figures/mut_landscape.R b/scripts/plotting/structure_figures/mut_landscape.R
index aeeb5c2..89e47c1 100644
--- a/scripts/plotting/structure_figures/mut_landscape.R
+++ b/scripts/plotting/structure_figures/mut_landscape.R
@@ -24,7 +24,7 @@ outfile_meta2 =  paste0(outdir_images, "/", tolower(gene), "_mutpos_annot_cu.txt
 #=============
 # Input
 #=============
-df3_filename = paste0("/home/tanu/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
+df3_filename = paste0("~/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
 df3 = read.csv(df3_filename)
 
 # Determine for each gene
diff --git a/scripts/plotting/structure_figures/mut_landscape_5uhc_rpob.R b/scripts/plotting/structure_figures/mut_landscape_5uhc_rpob.R
index 53f95d0..2501c44 100644
--- a/scripts/plotting/structure_figures/mut_landscape_5uhc_rpob.R
+++ b/scripts/plotting/structure_figures/mut_landscape_5uhc_rpob.R
@@ -19,7 +19,7 @@ outfile_meta2 =  paste0(outdir_images, "/5uhc_", tolower(gene), "_mutpos_annot_c
 #=============
 # Input
 #=============
-df3_filename = paste0("/home/tanu/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
+df3_filename = paste0("~/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
 df3 = read.csv(df3_filename)
 
 chain_suffix = ".C"
diff --git a/scripts/plotting/structure_figures/replaceBfactor_pdb_stability.R b/scripts/plotting/structure_figures/replaceBfactor_pdb_stability.R
index ba6999b..4537d4c 100644
--- a/scripts/plotting/structure_figures/replaceBfactor_pdb_stability.R
+++ b/scripts/plotting/structure_figures/replaceBfactor_pdb_stability.R
@@ -39,7 +39,7 @@ outdir = paste0("~/git/Data", "/", drug, "/output")
 # input
 #======
 in_filename_pdb = paste0(tolower(gene), "_complex.pdb") 
-#in_filename_pdb = "/home/tanu/git/Writing/thesis/images/results/gid/str_figures/gid_complex_copy_arpeg.pdb"
+#in_filename_pdb = "~/git/Writing/thesis/images/results/gid/str_figures/gid_complex_copy_arpeg.pdb"
 infile_pdb = paste0(indir, "/", in_filename_pdb)
 cat(paste0("Input file:", infile_pdb) )