diff --git a/scripts/plotting/myshiny/bp_app.R b/scripts/plotting/myshiny/bp_app.R
new file mode 100644
index 0000000..81f0423
--- /dev/null
+++ b/scripts/plotting/myshiny/bp_app.R
@@ -0,0 +1,156 @@
+## This is a Shiny web application. You can run the application by clicking
+# the 'Run App' button above.
+#
+# Find out more about building applications with Shiny here:
+#
+#    http://shiny.rstudio.com/
+##
+###################################
+# load libraries and function
+#source("Header_TT.R")
+library(shiny)
+library(ggplot2)
+library(data.table)
+library(dplyr)
+#require("getopt", quietly = TRUE) # cmd parse arguments
+
+# load functions
+source("../plotting_globals.R")
+source("../plotting_data.R")
+###################################
+# command line args : 
+
+
+# INSERT HERE
+
+# hardcoded vars
+infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
+drug = "streptomycin"
+gene = "gid"
+
+###################################
+# call functions with relevant args
+#------------------------------------------
+# import_dirs()
+# should return the follwoing variables:
+# datadir
+# indir
+# outdir
+# plotdir
+# dr_muts_col
+# other_muts_col
+# resistance_col
+#--------------------------------------------
+import_dirs(drug, gene)
+#---------------------------------------------
+# plotting_data()
+# should return the following dfs:
+# my_df
+# my_df_u
+# my_df_u_lig
+# dup_muts
+#----------------------------------------------
+
+#if (!exists("infile") && exists("gene")){
+if (!is.character(infile) && exists("gene")){
+    #in_filename_params = paste0(tolower(gene), "_all_params.csv") 
+    in_filename_params = paste0(tolower(gene), "_comb_stab_struc_params.csv") # part combined for gid
+    infile = paste0(outdir, "/", in_filename_params)
+    cat("\nInput file not specified, assuming filename: ", infile, "\n")
+}
+
+# Get the DFs out of plotting_data()
+pd_df = plotting_data(infile)
+my_df       = pd_df[[1]]
+my_df_u     = pd_df[[2]]
+my_df_u_lig = pd_df[[3]]
+dup_muts    = pd_df[[4]]
+
+#########################################################
+cat(paste0("Directories imported:"
+           , "\ndatadir:", datadir
+           , "\nindir:", indir
+           , "\noutdir:", outdir
+           , "\nplotdir:", plotdir))
+
+cat(paste0("Variables imported:"
+           , "\ndrug:", drug
+           , "\ngene:", gene))
+#==========================================================
+#================
+# Data for plots
+#================
+# REASSIGNMENT as necessary
+df  = my_df_u
+
+# sanity checks
+str(df)
+#===========================================================
+# Define UI for application that draws a histogram
+ui <- fluidPage(
+
+    # Application title
+    titlePanel("Mtb target: gid"),
+
+    # Sidebar with a slider input for number of bins 
+    sidebarLayout(
+        sidebarPanel(radioButtons("rb", "biophysical effect"
+                         , choiceNames = list(
+                             "mCSM"
+                            , "FoldX")
+                         , choiceValues = list(
+                             "mCSM"
+                             , "FoldX")
+                         ))
+        # Show a plot of the generated distribution
+        , mainPanel(plotOutput("distPlot")
+                  , textOutput("txt"))))
+
+# Define server logic required to draw a histogram
+my_ats = 25 # axis text size
+my_als = 22 # axis label size
+
+theme_set(theme_grey())
+
+server <- function(input, output) {output$distPlot <- renderPlot({
+        axisType = input$rb
+        my_title = paste0("Barplots for biophyiscal effects ", axisType)
+        if (axisType == "mCSM") {
+            y_value = "duet_outcome"
+            leg_name = "DUET outcome"}
+        
+        if (axisType == "FoldX") {
+            y_value = "foldx_outcome"
+            leg_name = "FoldX outcome"}
+        
+        ggplot(df, aes(x = eval(parse(text = y_value)))) + 
+                       geom_bar(aes(fill = eval(parse(text = y_value))), show.legend = TRUE) +
+            geom_label(stat = "count"
+                       , aes(label = ..count..)
+                       , color = "black"
+                       , show.legend = FALSE
+                       , size = 10) + 
+            theme(axis.text.x = element_blank()
+                  , axis.title.x = element_blank()
+                  , axis.title.y = element_text(size=my_als)
+                  , axis.text.y = element_text(size = my_ats)
+                  , legend.position = c(0.73,0.8)
+                  , legend.text = element_text(size=my_als-2)
+                  , legend.title = element_text(size=my_als)
+                  , plot.title = element_blank()) + 
+            labs(title = ""
+                 , y = "Number of nsSNPs"
+                 #, fill="DUET Outcome"
+            ) + 
+            scale_fill_discrete(name = leg_name
+                                , labels = c("Destabilising", "Stabilising"))
+    })
+    #output$txt <- renderText({
+    #    paste("You chose", input$rb)})
+    
+}
+
+stabiliyPlot <- function(input, output) {
+}
+# Run the application 
+shinyApp(ui = ui, server = server)
diff --git a/scripts/plotting/myshiny/bp_app_test.R b/scripts/plotting/myshiny/bp_app_test.R
new file mode 100644
index 0000000..e60b792
--- /dev/null
+++ b/scripts/plotting/myshiny/bp_app_test.R
@@ -0,0 +1,150 @@
+## This is a Shiny web application. You can run the application by clicking
+# the 'Run App' button above.
+#
+# Find out more about building applications with Shiny here:
+#
+#    http://shiny.rstudio.com/
+##
+###################################
+# load libraries and function
+#source("Header_TT.R")
+library(shiny)
+library(ggplot2)
+library(data.table)
+library(dplyr)
+#require("getopt", quietly = TRUE) # cmd parse arguments
+
+# load functions
+source("../plotting_globals.R")
+source("../plotting_data.R")
+source("my_stability_bp.R")
+###################################
+# command line args : 
+
+
+# INSERT HERE
+
+# hardcoded vars
+infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
+drug = "streptomycin"
+gene = "gid"
+
+###################################
+# call functions with relevant args
+#------------------------------------------
+# import_dirs()
+# should return the follwoing variables:
+# datadir
+# indir
+# outdir
+# plotdir
+# dr_muts_col
+# other_muts_col
+# resistance_col
+#--------------------------------------------
+import_dirs(drug, gene)
+#---------------------------------------------
+# plotting_data()
+# should return the following dfs:
+# my_df
+# my_df_u
+# my_df_u_lig
+# dup_muts
+#----------------------------------------------
+
+#if (!exists("infile") && exists("gene")){
+if (!is.character(infile) && exists("gene")){
+    #in_filename_params = paste0(tolower(gene), "_all_params.csv") 
+    in_filename_params = paste0(tolower(gene), "_comb_stab_struc_params.csv") # part combined for gid
+    infile = paste0(outdir, "/", in_filename_params)
+    cat("\nInput file not specified, assuming filename: ", infile, "\n")
+}
+
+# Get the DFs out of plotting_data()
+pd_df = plotting_data(infile)
+my_df       = pd_df[[1]]
+my_df_u     = pd_df[[2]]
+my_df_u_lig = pd_df[[3]]
+dup_muts    = pd_df[[4]]
+
+#########################################################
+cat(paste0("Directories imported:"
+           , "\ndatadir:", datadir
+           , "\nindir:", indir
+           , "\noutdir:", outdir
+           , "\nplotdir:", plotdir))
+
+cat(paste0("Variables imported:"
+           , "\ndrug:", drug
+           , "\ngene:", gene))
+#==========================================================
+#================
+# Data for plots
+#================
+# REASSIGNMENT as necessary
+#df  = my_df_u
+
+# sanity checks
+str(df)
+#===========================================================
+# Define UI for application that draws a histogram
+ui <- fluidPage(
+
+    # Application title
+    titlePanel("Mtb target: gid"),
+
+    # Sidebar with a slider input for number of bins 
+    sidebarLayout(
+        sidebarPanel(radioButtons("rb", "Biophysical effect"
+                         , choiceNames = list(
+                             "mCSM"
+                            , "FoldX"
+                            , "mCSM-lig")
+                         , choiceValues = list(
+                             "mCSM"
+                             , "FoldX"
+                             , "mCSM-lig")
+                         ))
+        # Show a plot of the generated distribution
+        , mainPanel(plotOutput("distPlot")
+                  , textOutput("txt"))))
+
+# Define server logic required to draw a histogram
+server <- function(input, output) {output$distPlot <- renderPlot({
+        axisType = input$rb
+        my_title = paste0("Barplots for biophyiscal effects ", axisType)
+        
+        if (axisType == "mCSM") {
+            data_plot = my_df_u
+            stability_colname = "duet_outcome"
+            leg_name = "DUET outcome"
+            p_title = ""}
+        
+        if (axisType == "FoldX") {
+            data_plot = my_df_u
+            stability_colname = "foldx_outcome"
+            leg_name = "FoldX outcome"
+            p_title = ""}
+        
+        if (axisType == "mCSM-lig") {
+            data_plot = my_df_u_lig
+            stability_colname = "ligand_outcome"
+            leg_name = "Ligand affinity outcome"
+            p_title = "Sites < 10 Ang of ligand"}
+    
+        # plot the  basic barplots
+        my_stability_count(plotdf = data_plot
+                           , df_colname = stability_colname, 
+                           , leg_title = leg_name
+                           , bp_plot_title = p_title) 
+       
+    })
+    #output$txt <- renderText({
+    #    paste("You chose", input$rb)})
+    
+}
+
+stabiliyPlot <- function(input, output) {
+}
+# Run the application 
+shinyApp(ui = ui, server = server)
diff --git a/scripts/plotting/myshiny/my_stability_bp.R b/scripts/plotting/myshiny/my_stability_bp.R
new file mode 100644
index 0000000..e9b6463
--- /dev/null
+++ b/scripts/plotting/myshiny/my_stability_bp.R
@@ -0,0 +1,77 @@
+#!/usr/bin/env Rscript 
+# load libraries
+#########################################################
+# TASK: function for basic barplot returning stability counts
+#########################################################
+# load libraries and functions
+library(ggplot2)
+theme_set(theme_grey())
+#==========================================================
+# my_stability_count(): basic barplots for stability counts
+# input args
+  ## df containing data to plot
+  ## df column name containing stability outcome
+  ## legend title
+  ## ...opt args
+#==========================================================
+my_stability_count <- function(plotdf
+         , df_colname
+         , leg_title
+         , axis_text_size = 25
+         , axis_label_size = 22
+         , leg_text_size = 20
+         , yaxis_title = "Number of nsSNPs"
+         , bp_plot_title = ""){
+ 
+  OutPlot_count = ggplot(plotdf, aes(x = eval(parse(text = df_colname)))) + 
+    geom_bar(aes(fill = eval(parse(text = df_colname))), show.legend = TRUE) +
+    geom_label(stat = "count"
+               , aes(label = ..count..)
+               , color = "black"
+               , show.legend = FALSE
+               , size = 10) +
+    theme(axis.text.x = element_blank()
+          , axis.title.x = element_blank()
+          , axis.title.y = element_text(size =  axis_label_size)
+          , axis.text.y = element_text(size = axis_text_size)
+          , legend.position = c(0.73,0.8)
+          , legend.text = element_text(size = leg_text_size)
+          , legend.title = element_text(size =  axis_label_size)
+          , plot.title = element_text(size =  axis_label_size)) + 
+    labs(title = bp_plot_title
+         , y = yaxis_title) + 
+    scale_fill_discrete(name = leg_title
+                        , labels = c("Destabilising", "Stabilising"))
+  
+  return(OutPlot_count)
+}
+#############################################################
+# end of function
+#############################################################
+#=================
+# Test function
+#==================
+source("../plotting_data.R")
+infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
+pd_df = plotting_data(infile)
+#my_df       = pd_df[[1]]
+my_df_u     = pd_df[[2]]
+#my_df_u_lig = pd_df[[3]]
+#dup_muts    = pd_df[[4]]
+
+#------------------------------
+# barplot for mscm stability
+#------------------------------
+#my_stability_count(plotdf = my_df, 
+#                , df_colname = "duet_outcome", 
+#                , leg_title = "DUET outcome")
+
+#------------------------------
+# barplot for ligand affinity
+#------------------------------
+my_stability_count(plotdf = my_df_u, 
+                , df_colname = "ligand_outcome", 
+                , leg_title = "Ligand outcome"
+                , bp_plot_title = "Sites < 10 Ang of ligand"
+)
+
diff --git a/scripts/plotting/plotting_data.R b/scripts/plotting/plotting_data.R
index e5c0849..b955723 100755
--- a/scripts/plotting/plotting_data.R
+++ b/scripts/plotting/plotting_data.R
@@ -5,8 +5,7 @@
 # load libraries and functions
 library(data.table)
 library(dplyr)
-#########################################################
-
+#========================================================
 # plotting_data(): formatting data for plots
 # input args: 
  ## input csv file
@@ -16,7 +15,7 @@ library(dplyr)
   ## my_df_u
   ## my_df_u_lig
   ## dup_muts
-
+#========================================================
 plotting_data <- function(infile_params, mcsm_lig_cutoff = 10) {
 my_df       = data.frame()
 my_df_u     = data.frame()
@@ -124,4 +123,4 @@ return(all_df)
 
 ########################################################################
 #               end of data extraction and cleaning for plots          #
-########################################################################
\ No newline at end of file
+########################################################################