initial run
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2 changed files with 19 additions and 17 deletions
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@ -4,32 +4,32 @@ library(NGLVieweR)
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library(hash)
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# FIXME This is slow and should happen *once only*
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#source("~/git/LSHTM_analysis/scripts/Header_TT.R")
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#source("/srv/shiny-server/git/LSHTM_analysis/scripts/Header_TT.R")
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# FIXME: these are needed but slow to load every time
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# source("~/git/LSHTM_analysis/config/alr.R")
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# source("~/git/LSHTM_analysis/config/gid.R")
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# source("/srv/shiny-server/git/LSHTM_analysis/config/alr.R")
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# source("/srv/shiny-server/git/LSHTM_analysis/config/gid.R")
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# source("~/git/LSHTM_analysis/config/pnca.R")
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# source("~/git/LSHTM_analysis/config/rpob.R")
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# source("~/git/LSHTM_analysis/config/katg.R")
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# source("/srv/shiny-server/git/LSHTM_analysis/config/pnca.R")
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# source("/srv/shiny-server/git/LSHTM_analysis/config/rpob.R")
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# source("/srv/shiny-server/git/LSHTM_analysis/config/katg.R")
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# TODO: this is TEMPORARY and will shortly get replaced with a target picker
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# that'll reload everything when changing targets. the lapply() is *much* quicker
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# than previous approaches
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# system.time({
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source("~/git/LSHTM_analysis/scripts/Header_TT.R")
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source("/srv/shiny-server/git/LSHTM_analysis/scripts/Header_TT.R")
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load_target_globals=function(target){
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cat(paste0("Reloading Target: ", target))
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source(paste0("~/git/LSHTM_analysis/config/", target, ".R")) # load per-target config file
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source(paste0("/srv/shiny-server/git/LSHTM_analysis/config/", target, ".R")) # load per-target config file
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invisible(assign(paste0(target, "_merged_df3"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-merged_df3.csv")), envir = .GlobalEnv))
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invisible(assign(paste0(target, "_merged_df2"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-merged_df2.csv")), envir = .GlobalEnv))
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invisible(assign(paste0(target, "_corr_df_m3_f"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-corr_df_m3_f.csv")), envir = .GlobalEnv))
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invisible(assign(paste0(target, "_lin_lf"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-lin_lf.csv")), envir = .GlobalEnv))
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invisible(assign(paste0(target, "_lin_wf"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-lin_wf.csv")), envir = .GlobalEnv))
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invisible(assign(paste0(target, "_merged_df3"), read.csv(paste0("/srv/shiny-server/git/Misc/shiny_dashboard/data/",target,"-merged_df3.csv")), envir = .GlobalEnv))
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invisible(assign(paste0(target, "_merged_df2"), read.csv(paste0("/srv/shiny-server/git/Misc/shiny_dashboard/data/",target,"-merged_df2.csv")), envir = .GlobalEnv))
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invisible(assign(paste0(target, "_corr_df_m3_f"), read.csv(paste0("/srv/shiny-server/git/Misc/shiny_dashboard/data/",target,"-corr_df_m3_f.csv")), envir = .GlobalEnv))
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invisible(assign(paste0(target, "_lin_lf"), read.csv(paste0("/srv/shiny-server/git/Misc/shiny_dashboard/data/",target,"-lin_lf.csv")), envir = .GlobalEnv))
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invisible(assign(paste0(target, "_lin_wf"), read.csv(paste0("/srv/shiny-server/git/Misc/shiny_dashboard/data/",target,"-lin_wf.csv")), envir = .GlobalEnv))
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lapply(
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c(
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"duet",
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@ -44,12 +44,12 @@ load_target_globals=function(target){
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"mcsm_ppi2"#,
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#"mcsm_na"
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), function(x){
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wf_filename=paste0("~/git/Misc/shiny_dashboard/data/", tolower(gene), "-wf_", x ,".csv")
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wf_filename=paste0("/srv/shiny-server/git/Misc/shiny_dashboard/data/", tolower(gene), "-wf_", x ,".csv")
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wf_var=paste0("wf_",x)
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if (file.exists(wf_filename)){
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invisible(assign(wf_var,read.csv(wf_filename), envir = .GlobalEnv)) # FILTH
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}
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lf_filename=paste0("~/git/Misc/shiny_dashboard/data/", tolower(gene), "-lf_", x ,".csv")
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lf_filename=paste0("/srv/shiny-server/git/Misc/shiny_dashboard/data/", tolower(gene), "-lf_", x ,".csv")
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lf_var=paste0(target, "_lf_",x)
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if (file.exists(lf_filename)){
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invisible(assign(lf_var,read.csv(lf_filename), envir = .GlobalEnv)) # FILTH
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@ -61,12 +61,12 @@ load_target_globals=function(target){
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load_msa_global=function(gene){
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drug=target_map[[gene]]
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in_filename_msa = paste0(tolower(gene), "_msa.csv")
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infile_msa = paste0("~/git/Data/", drug, "/output/", in_filename_msa)
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infile_msa = paste0("/srv/shiny-server/git/Data/", drug, "/output/", in_filename_msa)
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print(infile_msa)
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msa1 = read.csv(infile_msa, header = F)
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msa_seq = msa1$V1
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infile_fasta = paste0("~/git/Data/", drug, "/input/", tolower(gene), "2_f2.fasta")
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infile_fasta = paste0("/srv/shiny-server/git/Data/", drug, "/input/", tolower(gene), "2_f2.fasta")
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print(infile_fasta)
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msa2 = read.csv(infile_fasta, header = F)
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wt_seq = msa2$V1
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@ -1,6 +1,7 @@
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#### Shiny UI #####
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#dashboardHeader(title = paste0(gene, "/", drug)),
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dashboardPage(skin="purple",
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dashboardHeader(title = "Drug/Target Explorer"),
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dashboardSidebar(
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@ -254,3 +255,4 @@ body <- dashboardBody(
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)
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)
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)
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)
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