added shiny app and turned stability bp to function
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4 changed files with 386 additions and 4 deletions
156
scripts/plotting/myshiny/bp_app.R
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156
scripts/plotting/myshiny/bp_app.R
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## This is a Shiny web application. You can run the application by clicking
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# the 'Run App' button above.
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#
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# Find out more about building applications with Shiny here:
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#
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# http://shiny.rstudio.com/
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##
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###################################
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# load libraries and function
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#source("Header_TT.R")
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library(shiny)
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library(ggplot2)
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library(data.table)
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library(dplyr)
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#require("getopt", quietly = TRUE) # cmd parse arguments
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# load functions
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source("../plotting_globals.R")
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source("../plotting_data.R")
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###################################
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# command line args :
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# INSERT HERE
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# hardcoded vars
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infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
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drug = "streptomycin"
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gene = "gid"
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###################################
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# call functions with relevant args
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#------------------------------------------
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# import_dirs()
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# should return the follwoing variables:
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# datadir
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# indir
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# outdir
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# plotdir
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# dr_muts_col
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# other_muts_col
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# resistance_col
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#--------------------------------------------
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import_dirs(drug, gene)
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#---------------------------------------------
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# plotting_data()
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# should return the following dfs:
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# my_df
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# my_df_u
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# my_df_u_lig
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# dup_muts
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#----------------------------------------------
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#if (!exists("infile") && exists("gene")){
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if (!is.character(infile) && exists("gene")){
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#in_filename_params = paste0(tolower(gene), "_all_params.csv")
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in_filename_params = paste0(tolower(gene), "_comb_stab_struc_params.csv") # part combined for gid
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infile = paste0(outdir, "/", in_filename_params)
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cat("\nInput file not specified, assuming filename: ", infile, "\n")
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}
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# Get the DFs out of plotting_data()
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pd_df = plotting_data(infile)
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my_df = pd_df[[1]]
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my_df_u = pd_df[[2]]
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my_df_u_lig = pd_df[[3]]
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dup_muts = pd_df[[4]]
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#########################################################
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cat(paste0("Directories imported:"
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, "\ndatadir:", datadir
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, "\nindir:", indir
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, "\noutdir:", outdir
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, "\nplotdir:", plotdir))
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cat(paste0("Variables imported:"
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, "\ndrug:", drug
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, "\ngene:", gene))
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#==========================================================
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#================
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# Data for plots
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#================
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# REASSIGNMENT as necessary
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df = my_df_u
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# sanity checks
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str(df)
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#===========================================================
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# Define UI for application that draws a histogram
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ui <- fluidPage(
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# Application title
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titlePanel("Mtb target: gid"),
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# Sidebar with a slider input for number of bins
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sidebarLayout(
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sidebarPanel(radioButtons("rb", "biophysical effect"
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, choiceNames = list(
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"mCSM"
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, "FoldX")
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, choiceValues = list(
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"mCSM"
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, "FoldX")
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))
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# Show a plot of the generated distribution
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, mainPanel(plotOutput("distPlot")
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, textOutput("txt"))))
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# Define server logic required to draw a histogram
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my_ats = 25 # axis text size
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my_als = 22 # axis label size
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theme_set(theme_grey())
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server <- function(input, output) {output$distPlot <- renderPlot({
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axisType = input$rb
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my_title = paste0("Barplots for biophyiscal effects ", axisType)
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if (axisType == "mCSM") {
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y_value = "duet_outcome"
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leg_name = "DUET outcome"}
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if (axisType == "FoldX") {
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y_value = "foldx_outcome"
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leg_name = "FoldX outcome"}
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ggplot(df, aes(x = eval(parse(text = y_value)))) +
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geom_bar(aes(fill = eval(parse(text = y_value))), show.legend = TRUE) +
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geom_label(stat = "count"
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, aes(label = ..count..)
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, color = "black"
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, show.legend = FALSE
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, size = 10) +
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theme(axis.text.x = element_blank()
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, axis.title.x = element_blank()
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, axis.title.y = element_text(size=my_als)
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, axis.text.y = element_text(size = my_ats)
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, legend.position = c(0.73,0.8)
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, legend.text = element_text(size=my_als-2)
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, legend.title = element_text(size=my_als)
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, plot.title = element_blank()) +
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labs(title = ""
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, y = "Number of nsSNPs"
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#, fill="DUET Outcome"
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) +
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scale_fill_discrete(name = leg_name
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, labels = c("Destabilising", "Stabilising"))
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})
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#output$txt <- renderText({
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# paste("You chose", input$rb)})
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}
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stabiliyPlot <- function(input, output) {
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}
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# Run the application
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shinyApp(ui = ui, server = server)
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150
scripts/plotting/myshiny/bp_app_test.R
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150
scripts/plotting/myshiny/bp_app_test.R
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## This is a Shiny web application. You can run the application by clicking
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# the 'Run App' button above.
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#
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# Find out more about building applications with Shiny here:
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#
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# http://shiny.rstudio.com/
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##
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###################################
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# load libraries and function
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#source("Header_TT.R")
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library(shiny)
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library(ggplot2)
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library(data.table)
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library(dplyr)
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#require("getopt", quietly = TRUE) # cmd parse arguments
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# load functions
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source("../plotting_globals.R")
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source("../plotting_data.R")
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source("my_stability_bp.R")
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###################################
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# command line args :
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# INSERT HERE
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# hardcoded vars
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infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
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drug = "streptomycin"
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gene = "gid"
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###################################
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# call functions with relevant args
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#------------------------------------------
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# import_dirs()
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# should return the follwoing variables:
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# datadir
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# indir
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# outdir
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# plotdir
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# dr_muts_col
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# other_muts_col
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# resistance_col
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#--------------------------------------------
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import_dirs(drug, gene)
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#---------------------------------------------
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# plotting_data()
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# should return the following dfs:
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# my_df
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# my_df_u
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# my_df_u_lig
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# dup_muts
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#----------------------------------------------
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#if (!exists("infile") && exists("gene")){
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if (!is.character(infile) && exists("gene")){
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#in_filename_params = paste0(tolower(gene), "_all_params.csv")
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in_filename_params = paste0(tolower(gene), "_comb_stab_struc_params.csv") # part combined for gid
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infile = paste0(outdir, "/", in_filename_params)
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cat("\nInput file not specified, assuming filename: ", infile, "\n")
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}
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# Get the DFs out of plotting_data()
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pd_df = plotting_data(infile)
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my_df = pd_df[[1]]
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my_df_u = pd_df[[2]]
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my_df_u_lig = pd_df[[3]]
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dup_muts = pd_df[[4]]
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#########################################################
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cat(paste0("Directories imported:"
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, "\ndatadir:", datadir
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, "\nindir:", indir
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, "\noutdir:", outdir
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, "\nplotdir:", plotdir))
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cat(paste0("Variables imported:"
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, "\ndrug:", drug
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, "\ngene:", gene))
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#==========================================================
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#================
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# Data for plots
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#================
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# REASSIGNMENT as necessary
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#df = my_df_u
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# sanity checks
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str(df)
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#===========================================================
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# Define UI for application that draws a histogram
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ui <- fluidPage(
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# Application title
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titlePanel("Mtb target: gid"),
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# Sidebar with a slider input for number of bins
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sidebarLayout(
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sidebarPanel(radioButtons("rb", "Biophysical effect"
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, choiceNames = list(
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"mCSM"
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, "FoldX"
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, "mCSM-lig")
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, choiceValues = list(
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"mCSM"
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, "FoldX"
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, "mCSM-lig")
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))
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# Show a plot of the generated distribution
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, mainPanel(plotOutput("distPlot")
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, textOutput("txt"))))
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# Define server logic required to draw a histogram
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server <- function(input, output) {output$distPlot <- renderPlot({
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axisType = input$rb
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my_title = paste0("Barplots for biophyiscal effects ", axisType)
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if (axisType == "mCSM") {
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data_plot = my_df_u
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stability_colname = "duet_outcome"
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leg_name = "DUET outcome"
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p_title = ""}
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if (axisType == "FoldX") {
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data_plot = my_df_u
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stability_colname = "foldx_outcome"
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leg_name = "FoldX outcome"
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p_title = ""}
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if (axisType == "mCSM-lig") {
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data_plot = my_df_u_lig
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stability_colname = "ligand_outcome"
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leg_name = "Ligand affinity outcome"
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p_title = "Sites < 10 Ang of ligand"}
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# plot the basic barplots
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my_stability_count(plotdf = data_plot
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, df_colname = stability_colname,
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, leg_title = leg_name
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, bp_plot_title = p_title)
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})
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#output$txt <- renderText({
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# paste("You chose", input$rb)})
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}
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stabiliyPlot <- function(input, output) {
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}
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# Run the application
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shinyApp(ui = ui, server = server)
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77
scripts/plotting/myshiny/my_stability_bp.R
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77
scripts/plotting/myshiny/my_stability_bp.R
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#!/usr/bin/env Rscript
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# load libraries
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#########################################################
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# TASK: function for basic barplot returning stability counts
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#########################################################
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# load libraries and functions
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library(ggplot2)
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theme_set(theme_grey())
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#==========================================================
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# my_stability_count(): basic barplots for stability counts
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# input args
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## df containing data to plot
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## df column name containing stability outcome
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## legend title
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## ...opt args
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#==========================================================
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my_stability_count <- function(plotdf
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, df_colname
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, leg_title
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, axis_text_size = 25
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, axis_label_size = 22
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, leg_text_size = 20
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, yaxis_title = "Number of nsSNPs"
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, bp_plot_title = ""){
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OutPlot_count = ggplot(plotdf, aes(x = eval(parse(text = df_colname)))) +
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geom_bar(aes(fill = eval(parse(text = df_colname))), show.legend = TRUE) +
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geom_label(stat = "count"
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, aes(label = ..count..)
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, color = "black"
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, show.legend = FALSE
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, size = 10) +
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theme(axis.text.x = element_blank()
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, axis.title.x = element_blank()
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, axis.title.y = element_text(size = axis_label_size)
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, axis.text.y = element_text(size = axis_text_size)
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, legend.position = c(0.73,0.8)
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, legend.text = element_text(size = leg_text_size)
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, legend.title = element_text(size = axis_label_size)
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, plot.title = element_text(size = axis_label_size)) +
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labs(title = bp_plot_title
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, y = yaxis_title) +
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scale_fill_discrete(name = leg_title
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, labels = c("Destabilising", "Stabilising"))
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return(OutPlot_count)
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}
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#############################################################
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# end of function
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#############################################################
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#=================
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# Test function
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#==================
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source("../plotting_data.R")
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infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
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pd_df = plotting_data(infile)
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#my_df = pd_df[[1]]
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my_df_u = pd_df[[2]]
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#my_df_u_lig = pd_df[[3]]
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#dup_muts = pd_df[[4]]
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#------------------------------
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# barplot for mscm stability
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#------------------------------
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#my_stability_count(plotdf = my_df,
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# , df_colname = "duet_outcome",
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# , leg_title = "DUET outcome")
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#------------------------------
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# barplot for ligand affinity
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#------------------------------
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my_stability_count(plotdf = my_df_u,
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, df_colname = "ligand_outcome",
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, leg_title = "Ligand outcome"
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, bp_plot_title = "Sites < 10 Ang of ligand"
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)
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@ -5,8 +5,7 @@
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# load libraries and functions
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library(data.table)
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library(dplyr)
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#########################################################
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#========================================================
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# plotting_data(): formatting data for plots
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# input args:
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## input csv file
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@ -16,7 +15,7 @@ library(dplyr)
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## my_df_u
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## my_df_u_lig
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## dup_muts
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#========================================================
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plotting_data <- function(infile_params, mcsm_lig_cutoff = 10) {
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my_df = data.frame()
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my_df_u = data.frame()
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