added shiny app and turned stability bp to function

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)