diff --git a/dynamut/run_format_results_dynamut.py b/dynamut/run_format_results_dynamut.py
index cb6fe70..67dc2f1 100755
--- a/dynamut/run_format_results_dynamut.py
+++ b/dynamut/run_format_results_dynamut.py
@@ -17,61 +17,52 @@ os.chdir (homedir + '/git/LSHTM_analysis/dynamut')
 from format_results_dynamut import *
 from format_results_dynamut2 import *
 ########################################################################
-# variables
-# TODO: add cmd line args
-
-#gene = 
-#drug = 
-
 #%% command line args
 arg_parser = argparse.ArgumentParser()
-arg_parser.add_argument('-d', '--drug', help='drug name (case sensitive)', default = None)
-arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = None)
-arg_parser.add_argument('--datadir', help = 'Data Directory. By default, it assmumes homedir + git/Data')
-arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb files. By default, it assmumes homedir + <drug> + input')
+arg_parser.add_argument('-d', '--drug'      , help = 'drug name (case sensitive)', default = None)
+arg_parser.add_argument('-g', '--gene'      , help = 'gene name (case sensitive)', default = None)
+arg_parser.add_argument('--datadir'         , help = 'Data Directory. By default, it assmumes homedir + git/Data')
+arg_parser.add_argument('-i', '--input_dir' , help = 'Input dir containing pdb files. By default, it assmumes homedir + <drug> + input')
 arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + <drug> + output')
-#arg_parser.add_argument('-m', '--make_dirs', help = 'Make dir for input and output', action='store_true') # should be handled elsewhere!
-
-arg_parser.add_argument('--debug', action ='store_true', help = 'Debug Mode')
+#arg_parser.add_argument('--mkdir_name'      , help = 'Output dir for processed results. This will be created if it does not exist') 
+arg_parser.add_argument('-m', '--make_dirs' , help = 'Make dir for input and output', action='store_true')
+arg_parser.add_argument('--debug'           , action = 'store_true' , help = 'Debug Mode')
 
 args = arg_parser.parse_args()
-#=======================================================================
-#%% variable assignment: input and output paths & filenames
-drug = args.drug
-gene = args.gene
-datadir = args.datadir
-indir   = args.input_dir
-outdir  = args.output_dir
-#make_dirs  = args.make_dirs
+#%%============================================================================ 
+# variable assignment: input and output paths & filenames
+drug         = args.drug
+gene         = args.gene
+datadir      = args.datadir
+indir        = args.input_dir
+outdir       = args.output_dir
+#outdir_dynamut2  = args.mkdir_name
+make_dirs    = args.make_dirs
 
-#%% input and output dirs and files
 #=======
 # dirs
 #=======
 if not datadir:
-    datadir = homedir + '/' + 'git/Data'
+    datadir = homedir + '/git/Data/'
     
 if not indir:
-    indir = datadir + '/' + drug + '/input'
+    indir = datadir + drug + '/input/'
     
 if not outdir:
-    outdir = datadir + '/' + drug + '/output'
-
-#%%=====================================================================
-
-datadir = homedir + '/git/Data'
-indir = datadir + '/' + drug + '/input'
-outdir = datadir + '/' + drug + '/output'
-outdir_dynamut = outdir + '/dynamut_results/'
-outdir_dynamut2 = outdir + '/dynamut_results/dynamut2/'
+    outdir = datadir + drug + '/output/'
+    
+#if not mkdir_name:
+outdir_dynamut = outdir + 'dynamut_results/'
+outdir_dynamut2 = outdir + 'dynamut_results/dynamut2/'
 
 # Input file
 #infile_dynamut =  outdir_dynamut + gene.lower() + '_dynamut_all_output_clean.csv'
 infile_dynamut2 =  outdir_dynamut2 + gene.lower() + '_dynamut2_output_combined_clean.csv'
 
 # Formatted output filename
-#outfile_dynamut_f = outdir_dynamut2 + gene + '_dynamut_norm.csv'
-outfile_dynamut2_f = outdir_dynamut2 + gene.lower() + '_dynamut2_norm.csv'
+outfile_dynamut_f = outdir_dynamut2 + gene + '_dynamut_norm.csv'
+outfile_dynamut2_f = outdir_dynamut2 + gene + '_dynamut2_norm.csv'
+#%%========================================================================
 
 #===============================
 # CALL: format_results_dynamut
diff --git a/dynamut/run_get_results_dynamut.py b/dynamut/run_get_results_dynamut.py
index 029e934..b8e6662 100755
--- a/dynamut/run_get_results_dynamut.py
+++ b/dynamut/run_get_results_dynamut.py
@@ -17,8 +17,8 @@ my_host = 'http://biosig.unimelb.edu.au'
 #headers = {"User-Agent":"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/83.0.4103.97 Safari/537.36"}
 
 # TODO: add cmd line args
-# gene = 
-# drug = 
+#gene = ''
+#drug = ''
 datadir = homedir + '/git/Data/'
 indir = datadir + drug + '/input/'
 outdir = datadir + drug + '/output/'
diff --git a/mcsm/run_mcsm.py b/mcsm/run_mcsm.py
index da621f5..9bfd140 100755
--- a/mcsm/run_mcsm.py
+++ b/mcsm/run_mcsm.py
@@ -16,7 +16,7 @@ arg_parser.add_argument('-H', '--host',    help='mCSM Server', default = 'http:/
 arg_parser.add_argument('-U', '--url',     help='mCSM Server URL', default = 'http://biosig.unimelb.edu.au/mcsm_lig/prediction')
 arg_parser.add_argument('-c', '--chain',   help='Chain ID as per PDB, Case sensitive', default = 'A')
 arg_parser.add_argument('-l','--ligand',   help='Ligand ID as per PDB, Case sensitive. REQUIRED only in "submit" stage', default = None)
-arg_parser.add_argument('-a','--affinity', help='Affinity in nM. REQUIRED only in "submit" stage', default = 0.99) 
+arg_parser.add_argument('-a','--affinity', help='Affinity in nM. REQUIRED only in "submit" stage', default = 10) #0.99 for pnca, gid, embb. For SP targets (alr,katg, rpob), use 10.
 
 arg_parser.add_argument('-pdb','--pdb_file', help = 'PDB File') 
 arg_parser.add_argument('-m','--mutation_file', help = 'Mutation File, mcsm style') 
@@ -42,8 +42,8 @@ args = arg_parser.parse_args()
 #%% variables
 #host = "http://biosig.unimelb.edu.au"
 #prediction_url = f"{host}/mcsm_lig/prediction"
-#drug = 'isoniazid'
-#gene = 'KatG'
+#drug = ''
+#gene = ''
 #%%=====================================================================
 # Command line options
 gene         = args.gene
diff --git a/mcsm_ppi2/format_results_mcsm_ppi2.py b/mcsm_ppi2/format_results_mcsm_ppi2.py
index 69d4835..49c05b2 100755
--- a/mcsm_ppi2/format_results_mcsm_ppi2.py
+++ b/mcsm_ppi2/format_results_mcsm_ppi2.py
@@ -22,12 +22,11 @@ from pandas.api.types import is_numeric_dtype
 sys.path.append(homedir + '/git/LSHTM_analysis/scripts')
 from reference_dict import up_3letter_aa_dict
 from reference_dict import oneletter_aa_dict
-
-#%%#####################################################################
+#%%============================================================================    
 
 def format_mcsm_ppi2_output(mcsm_ppi2_output_csv):
     """
-    @param mcsm_ppi2_output_csv: file containing mcsm_ppi2_results for all muts 
+    @param mcsm_ppi2_output_csv: file containing mcsm_ppi2_results for all mcsm snps 
      which is the result of combining all mcsm_ppi2 batch results, and using
      bash scripts to combine all the batch results into one file. 
      Formatting df to a pandas df and output as csv.
diff --git a/mcsm_ppi2/run_format_results_mcsm_ppi2.py b/mcsm_ppi2/run_format_results_mcsm_ppi2.py
index 25912da..ab036f9 100755
--- a/mcsm_ppi2/run_format_results_mcsm_ppi2.py
+++ b/mcsm_ppi2/run_format_results_mcsm_ppi2.py
@@ -19,19 +19,22 @@ arg_parser.add_argument('-g', '--gene'      , help = 'gene name (case sensitive)
 arg_parser.add_argument('--datadir'         , help = 'Data Directory. By default, it assmumes homedir + git/Data')
 arg_parser.add_argument('-i', '--input_dir' , help = 'Input dir containing pdb files. By default, it assmumes homedir + <drug> + input')
 arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + <drug> + output')
+arg_parser.add_argument('--input_file'      , help = 'Output dir for results. By default, it assmes homedir + <drug> + output')
+
 #arg_parser.add_argument('--mkdir_name'      , help = 'Output dir for processed results. This will be created if it does not exist') 
 arg_parser.add_argument('-m', '--make_dirs' , help = 'Make dir for input and output', action='store_true')
-
 arg_parser.add_argument('--debug'           , action = 'store_true' , help = 'Debug Mode')
 
 args = arg_parser.parse_args()
 #%%============================================================================ 
 # variable assignment: input and output paths & filenames
-drug         = args.drug
-gene         = args.gene
-datadir      = args.datadir
-indir        = args.input_dir
-outdir       = args.output_dir
+drug               = args.drug
+gene               = args.gene
+datadir            = args.datadir
+indir              = args.input_dir
+outdir             = args.output_dir
+infile_mcsm_ppi2   = args.input_file
+
 #outdir_ppi2  = args.mkdir_name
 make_dirs    = args.make_dirs
 
@@ -53,7 +56,8 @@ if not outdir:
 outdir_ppi2 = outdir + 'mcsm_ppi2/'
 
 # Input file
-infile_mcsm_ppi2 =  outdir_ppi2 +  gene.lower() + '_output_combined_clean.csv'
+if not infile_mcsm_ppi2:
+    infile_mcsm_ppi2 =  outdir_ppi2 +  gene.lower() + '_output_combined_clean.csv'
 
 # Formatted output file
 outfile_mcsm_ppi2_f = outdir_ppi2 + gene.lower() + '_complex_mcsm_ppi2_norm.csv'
@@ -75,4 +79,4 @@ print('Finished writing file:'
        , '\nExpected no. of cols:', len(mcsm_ppi2_df_f.columns)
        , '\n=============================================================')
 
-#%%#####################################################################
\ No newline at end of file
+#%%#####################################################################
diff --git a/scripts/combining_dfs.py b/scripts/combining_dfs.py
index 53361c7..cb47d50 100755
--- a/scripts/combining_dfs.py
+++ b/scripts/combining_dfs.py
@@ -116,9 +116,10 @@ if not outdir:
 #=======
 gene_list_normal = ["pnca", "katg", "rpob", "alr"]
 
+#FIXME: for gid, this should be SRY as this is the drug...please check!!!!
 if gene.lower() == "gid":
     print("\nReading mCSM file for gene:", gene)
-    in_filename_mcsm = gene.lower() + '_complex_mcsm_norm_SAM.csv'
+    in_filename_mcsm = gene.lower() + '_complex_mcsm_norm_SRY.csv' # was incorrectly SAM previously
 if gene.lower() == "embb":
     print("\nReading mCSM file for gene:", gene)
     in_filename_mcsm = gene.lower() + '_complex_mcsm_norm1.csv'
@@ -139,7 +140,7 @@ deepddg_df            = pd.read_csv(infile_deepddg, sep = ',')
 
 in_filename_dssp      = gene.lower() + '_dssp.csv'
 infile_dssp           = outdir + in_filename_dssp
-dssp_df               = pd.read_csv(infile_dssp, sep = ',')
+dssp_df_raw           = pd.read_csv(infile_dssp, sep = ',')
 
 in_filename_kd        = gene.lower() + '_kd.csv'
 infile_kd             = outdir + in_filename_kd
@@ -163,10 +164,13 @@ infilename_dynamut2    = gene.lower() + '_dynamut2_norm.csv'
 infile_dynamut2        = outdir + 'dynamut_results/dynamut2/' + infilename_dynamut2
 dynamut2_df            = pd.read_csv(infile_dynamut2, sep = ',')
 
-#------------------------------------------------------------
+infilename_mcsm_f_snps = gene.lower() + '_mcsm_formatted_snps.csv'
+infile_mcsm_f_snps     = outdir + infilename_mcsm_f_snps
+mcsm_f_snps            = pd.read_csv(infile_mcsm_f_snps, sep = ',', names = ['mutationinformation'], header = None)
+
+#------------------------------------------------------------------------------
 # ONLY:for gene pnca and gid: End logic should pick this up!
-geneL_dy_na = ["pnca", "gid"]
-#if gene.lower() == "pnca" or "gid" :
+geneL_dy_na = ['gid']
 if gene.lower() in geneL_dy_na :
     print("\nGene:", gene.lower()
           , "\nReading Dynamut and mCSM_na files")
@@ -179,24 +183,27 @@ if gene.lower() in geneL_dy_na :
     mcsm_na_df            = pd.read_csv(infile_mcsm_na, sep = ',')
 
 # ONLY:for gene embb and alr: End logic should pick this up!
-geneL_ppi2 = ["embb", "alr"]
+geneL_ppi2 = ['embb', 'alr']
 #if gene.lower() == "embb" or "alr":
-if gene.lower() in "embb" or "alr":
+if gene.lower() in geneL_ppi2:
     infilename_mcsm_ppi2   = gene.lower() + '_complex_mcsm_ppi2_norm.csv'
     infile_mcsm_ppi2       = outdir + 'mcsm_ppi2/' + infilename_mcsm_ppi2
     mcsm_ppi2_df           = pd.read_csv(infile_mcsm_ppi2, sep = ',')
-#--------------------------------------------------------------
-infilename_mcsm_f_snps = gene.lower() + '_mcsm_formatted_snps.csv'
-infile_mcsm_f_snps     = outdir + infilename_mcsm_f_snps
-mcsm_f_snps            = pd.read_csv(infile_mcsm_f_snps, sep = ',', names = ['mutationinformation'], header = None)
-
+    
+    
+if gene.lower() == "embb":
+    sel_chain = "B"
+else:
+    sel_chain = "A"
+#------------------------------------------------------------------------------
 #=======
 # output 
 #=======
 out_filename_comb = gene.lower() + '_all_params.csv'
 outfile_comb =  outdir + out_filename_comb
-print('Output filename:', outfile_comb
+print('\nOutput filename:', outfile_comb
       , '\n===================================================================')
+
 # end of variable assignment for input and output files
 #%%############################################################################  
 #=====================
@@ -230,7 +237,7 @@ len(foldx_df.loc[foldx_df['ddg_foldx'] < 0])
 foldx_scale = lambda x : x/abs(foldx_min) if x < 0 else (x/foldx_max if x >= 0 else 'failed')
 
 foldx_df['foldx_scaled'] = foldx_df['ddg_foldx'].apply(foldx_scale)
-print('Raw foldx scores:\n', foldx_df['ddg_foldx']
+print('\nRaw foldx scores:\n', foldx_df['ddg_foldx']
     , '\n---------------------------------------------------------------'
     , '\nScaled foldx scores:\n', foldx_df['foldx_scaled'])
 
@@ -273,9 +280,42 @@ else:
 
 #=======================
 # Deepddg
+# TODO: RERUN 'gid'
 #=======================
 deepddg_df.shape
 
+#--------------------------
+# check if >1 chain
+#--------------------------
+deepddg_df.loc[:,'chain_id'].value_counts()
+
+if len(deepddg_df.loc[:,'chain_id'].value_counts()) > 1:
+    print("\nChains detected: >1"
+          , "\nGene:", gene
+          , "\nChains:", deepddg_df.loc[:,'chain_id'].value_counts().index)
+    
+print('\nSelecting chain:', sel_chain, 'for gene:', gene)
+
+deepddg_df = deepddg_df[deepddg_df['chain_id'] == sel_chain]
+    
+#--------------------------
+# Check for duplicates
+#--------------------------
+if len(deepddg_df['mutationinformation'].duplicated().value_counts())> 1:
+    print("\nFAIL: Duplicates detected in DeepDDG infile"
+          , "\nNo. of duplicates:"
+          , deepddg_df['mutationinformation'].duplicated().value_counts()[1]
+          , "\nformat deepDDG infile before proceeding")
+    sys.exit()
+else:
+    print("\nPASS: No duplicates detected in DeepDDG infile")
+
+#--------------------------
+# Drop chain id col as other targets don't have it.Check for duplicates
+#--------------------------
+col_to_drop = ['chain_id']
+deepddg_df = deepddg_df.drop(col_to_drop, axis = 1)
+
 #-------------------------
 # scale Deepddg values
 #-------------------------
@@ -287,7 +327,7 @@ deepddg_max = deepddg_df['deepddg'].max()
 deepddg_scale = lambda x : x/abs(deepddg_min) if x < 0 else (x/deepddg_max if x >= 0 else 'failed')
 
 deepddg_df['deepddg_scaled'] = deepddg_df['deepddg'].apply(deepddg_scale)
-print('Raw deepddg scores:\n', deepddg_df['deepddg']
+print('\nRaw deepddg scores:\n', deepddg_df['deepddg']
     , '\n---------------------------------------------------------------'
     , '\nScaled deepddg scores:\n', deepddg_df['deepddg_scaled'])
     
@@ -307,8 +347,8 @@ else:
     print('\nFAIL: deepddg values scaled numbers MISmatch'
           , '\nExpected number:', deepddg_pos
           , '\nGot:', deepddg_pos2
-          , '\n======================================================')
-    
+          , '\n======================================================')    
+
 #--------------------------
 # Deepddg outcome category
 #--------------------------
@@ -324,48 +364,15 @@ else:
           , '\nGot:', doc[0]
           , '\n======================================================')
     sys.exit()
-
-#--------------------------
-# check if >1 chain
-#--------------------------
-deepddg_df.loc[:,'chain_id'].value_counts()
-
-if len(deepddg_df.loc[:,'chain_id'].value_counts()) > 1:
-    print("\nChains detected: >1"
-          , "\nGene:", gene
-          , "\nChains:", deepddg_df.loc[:,'chain_id'].value_counts().index)
     
-#--------------------------
-# subset chain
-#--------------------------
-if gene.lower() == "embb":
-    sel_chain = "B"
-else:
-    sel_chain = "A"
     
-deepddg_df = deepddg_df[deepddg_df['chain_id'] == sel_chain]
+if deepddg_df['deepddg_scaled'].min() == -1 and deepddg_df['deepddg_scaled'].max() == 1:
+    print('\nPASS: Deepddg data is scaled between -1 and 1',
+           '\nproceeding with merge')
     
-#--------------------------
-# Check for duplicates
-#--------------------------
-if len(deepddg_df['mutationinformation'].duplicated().value_counts())> 1:
-    print("\nFAIL: Duplicates detected in DeepDDG infile"
-          , "\nNo. of duplicates:"
-          , deepddg_df['mutationinformation'].duplicated().value_counts()[1]
-          , "\nformat deepDDG infile before proceeding")
-    sys.exit()
-else:
-    print("\nPASS: No duplicates detected in DeepDDG infile")
-
-#--------------------------
-# Drop chain id col as other targets don't have itCheck for duplicates
-#--------------------------
-col_to_drop = ['chain_id']
-deepddg_df = deepddg_df.drop(col_to_drop, axis = 1)
-
-#%%=============================================================================
+#%%============================================================================
 # Now merges begin
-#%%=============================================================================
+
 print('==================================='
       , '\nFirst merge: mcsm + foldx'
       , '\n===================================')
@@ -395,10 +402,11 @@ print('\n\nResult of first merge:', mcsm_foldx_dfs.shape
 mcsm_foldx_dfs[merging_cols_m1].apply(len)
 mcsm_foldx_dfs[merging_cols_m1].apply(len) == len(mcsm_foldx_dfs)
 
-#%% for embB and any other targets where mCSM-lig hasn't run for 
-# get the empty cells to be full of meaningful info
+#%% for embB and any other targets where mCSM-lig hasn't run for ALL nsSNPs.
+# Get the empty cells to be full of meaningful info
 if mcsm_foldx_dfs.loc[:,'wild_type': 'mut_aa_3lower'].isnull().values.any():  
-    print ("NAs detected in mcsm cols after merge")
+    print ('\nNAs detected in mcsm cols after merge.'
+           , '\nCleaning data before merging deepddg_df')
     
     ##############################
     # Extract relevant col values 
@@ -442,6 +450,8 @@ if mcsm_foldx_dfs.loc[:,'wild_type': 'mut_aa_3lower'].isnull().values.any():
         mcsm_foldx_dfs['wt_aa_3lower'] = wt.map(lookup_dict)   
         mut = mcsm_foldx_dfs['mutant_type'].squeeze()
         mcsm_foldx_dfs['mut_aa_3lower'] = mut.map(lookup_dict)
+else:
+    print('\nNo NAs detected in mcsm_fold_dfs. Proceeding to merge deepddg_df')
     
 #%%
 print('==================================='
@@ -460,14 +470,18 @@ ncols_deepddg_merge = len(mcsm_foldx_deepddg_dfs.columns)
 mcsm_foldx_deepddg_dfs['position'] = mcsm_foldx_deepddg_dfs['position'].astype('int64')
 
 #%%============================================================================
+#FIXME: select df with 'chain' to allow corret dim merging!
 print('==================================='
-      , '\Third merge: dssp + kd'
+      , '\nThird merge: dssp + kd'
       , '\n===================================')
 
-dssp_df.shape
+dssp_df_raw.shape
 kd_df.shape
 rd_df.shape
 
+dssp_df = dssp_df_raw[dssp_df_raw['chain_id'] == sel_chain]
+dssp_df['chain_id'].value_counts()
+
 #dssp_kd_dfs = combine_dfs_with_checks(dssp_df, kd_df, my_join = "outer")
 merging_cols_m2 = detect_common_cols(dssp_df, kd_df)
 dssp_kd_dfs = pd.merge(dssp_df
@@ -553,17 +567,19 @@ combined_df['wild_type'].equals(combined_df['wild_type_dssp'])
 foo = combined_df[['wild_type', 'wild_type_kd', 'wt_3letter_caps', 'wt_aa_3lower', 'mut_aa_3lower']] 
 
 # Drop cols
-cols_to_drop = ['chain_id', 'wild_type_kd', 'wild_type_dssp', 'wt_3letter_caps' ]
+cols_to_drop = ['chain_id', 'wild_type_kd', 'wild_type_dssp', 'wt_3letter_caps']
 combined_df_clean = combined_df.drop(cols_to_drop, axis = 1)
 
 del(foo)
 #%%============================================================================
 # Output columns
 out_filename_stab_struc = gene.lower() + '_comb_stab_struc_params.csv'
-outfile_stab_struc =  outdir + '/' + out_filename_stab_struc
+outfile_stab_struc =  outdir + out_filename_stab_struc
 print('Output filename:', outfile_stab_struc
       , '\n===================================================================')
 
+combined_df_clean
+
 # write csv
 print('\nWriting file: combined stability and structural parameters')
 combined_df_clean.to_csv(outfile_stab_struc, index = False)
@@ -642,7 +658,7 @@ else:
 #%%============================================================================
 # Output columns: when dynamut, dynamut2 and others weren't being combined
 out_filename_comb_afor = gene.lower() + '_comb_afor.csv'
-outfile_comb_afor =  outdir + '/' + out_filename_comb_afor
+outfile_comb_afor =  outdir + out_filename_comb_afor
 print('Output filename:', outfile_comb_afor
       , '\n===================================================================')
 
@@ -657,7 +673,7 @@ print('\nFinished writing file:'
 #dfs_list = [dynamut_df, dynamut2_df, mcsm_na_df] # gid
 
 if gene.lower() == "pnca":
-    dfs_list = [dynamut_df, dynamut2_df]
+    dfs_list = [dynamut2_df]
 if gene.lower() == "gid":
     dfs_list = [dynamut_df, dynamut2_df, mcsm_na_df]
 if gene.lower() == "embb":
@@ -709,4 +725,4 @@ combined_all_params.to_csv(outfile_comb, index = False)
 print('\nFinished writing file:'
       , '\nNo. of rows:', combined_all_params.shape[0]
       , '\nNo. of cols:', combined_all_params.shape[1])
-#%% end of script
\ No newline at end of file
+#%% end of script
diff --git a/scripts/plotting/TESTING_PLOTS.R b/scripts/plotting/TESTING_PLOTS.R
new file mode 100755
index 0000000..b761415
--- /dev/null
+++ b/scripts/plotting/TESTING_PLOTS.R
@@ -0,0 +1,112 @@
+#!/usr/bin/env Rscript
+getwd()
+setwd("~/git/LSHTM_analysis/scripts/plotting")
+getwd()
+source("Header_TT.R")
+
+drug = 'streptomycin'
+gene = 'gid'
+
+spec = matrix(c(
+  "drug"       , "d",  1, "character",
+  "gene"       , "g",  1, "character",
+  "data_file1" , "fa", 2, "character",
+  "data_file2" , "fb", 2, "character" 
+), byrow = TRUE, ncol = 4)
+
+opt = getopt(spec)
+
+drug            = opt$drug
+gene            = opt$gene
+infile_params   = opt$data_file1
+infile_metadata = opt$data_file2
+
+if(is.null(drug)|is.null(gene)) {
+  stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
+}
+
+#===========
+# Input
+#===========
+source("get_plotting_dfs.R")
+
+#===========
+# output
+#===========
+# PS
+bp_subcols_duet = "barplot_coloured_PS.svg"
+plot_bp_subcols_duet = paste0(plotdir, "/", bp_subcols_duet)
+
+##############################################################################
+# add frequency of positions (from lib data.table)
+
+setDT(subcols_df_ps)[, pos_count := .N, by = .(position)]
+
+
+foo = data.frame(subcols_df_ps$mutationinformation
+                 , subcols_df_ps$position
+                 , subcols_df_ps$pos_count)
+
+#snpsBYpos_df <- subcols_df_ps %>%
+#  group_by(position) %>%
+#  summarize(snpsBYpos = mean(pos_count))
+
+
+#********************
+# generate plot: PS
+# NO axis colours
+#********************
+g = ggplot(subcols_df_ps
+           , aes(x = factor(position, ordered = T)))
+g2 = g + geom_bar()
+
+g2
+
+foo = g2 + geom_text(stat='count', aes(label = ..count..))
+foo
+
+######
+bp_subcols_duet = "TEST_PS.svg"
+plot_bp_subcols_duet = paste0(plotdir, "/", bp_subcols_duet)
+print(paste0("plot name:", plot_bp_subcols_duet))
+svg(plot_bp_subcols_duet, width = 26, height = 4)
+
+g1 = ggplot(subcols_df_ps, aes(x = factor(position, ordered = T)
+                               , y = pos_count)) + 
+  geom_bar(stat = "summary"
+           , aes(fill = group), colour = "grey") +
+
+
+
+
+
+###################################
+
+g = ggplot(subcols_df_ps
+           , aes(x = factor(position, ordered = T)))
+outPlot_bp_ps = g + 
+  geom_bar(aes(fill = group), colour = "grey") +
+  scale_fill_manual( values = subcols_ps
+                     , guide = "none") +
+  theme( axis.text.x = element_text(size = my_xaxls
+                                    , angle = 90
+                                    , hjust = 1
+                                    , vjust = 0.4)
+         , axis.text.y = element_text(size = my_yaxls 
+                                      , angle = 0
+                                      , hjust = 1
+                                      , vjust = 0)
+         , axis.title.x = element_text(size = my_xaxts)
+         , axis.title.y = element_text(size = my_yaxts ) ) +
+  labs(title = ""
+       #title = my_title
+       , x = "Position"
+       , y = "Frequency")
+
+print(outPlot_bp_ps)
+#dev.off()
+
+######################################################################=
+#                             End of script
+######################################################################=
+