diff --git a/drug-target/global.R b/drug-target/global.R index f9c190e..a58c782 100644 --- a/drug-target/global.R +++ b/drug-target/global.R @@ -4,32 +4,32 @@ library(NGLVieweR) library(hash) # FIXME This is slow and should happen *once only* -#source("~/git/LSHTM_analysis/scripts/Header_TT.R") +#source("/srv/shiny-server/git/LSHTM_analysis/scripts/Header_TT.R") # FIXME: these are needed but slow to load every time -# source("~/git/LSHTM_analysis/config/alr.R") -# source("~/git/LSHTM_analysis/config/gid.R") +# source("/srv/shiny-server/git/LSHTM_analysis/config/alr.R") +# source("/srv/shiny-server/git/LSHTM_analysis/config/gid.R") -# source("~/git/LSHTM_analysis/config/pnca.R") -# source("~/git/LSHTM_analysis/config/rpob.R") -# source("~/git/LSHTM_analysis/config/katg.R") +# source("/srv/shiny-server/git/LSHTM_analysis/config/pnca.R") +# source("/srv/shiny-server/git/LSHTM_analysis/config/rpob.R") +# source("/srv/shiny-server/git/LSHTM_analysis/config/katg.R") # TODO: this is TEMPORARY and will shortly get replaced with a target picker # that'll reload everything when changing targets. the lapply() is *much* quicker # than previous approaches # system.time({ -source("~/git/LSHTM_analysis/scripts/Header_TT.R") +source("/srv/shiny-server/git/LSHTM_analysis/scripts/Header_TT.R") load_target_globals=function(target){ cat(paste0("Reloading Target: ", target)) - source(paste0("~/git/LSHTM_analysis/config/", target, ".R")) # load per-target config file + source(paste0("/srv/shiny-server/git/LSHTM_analysis/config/", target, ".R")) # load per-target config file - invisible(assign(paste0(target, "_merged_df3"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-merged_df3.csv")), envir = .GlobalEnv)) - invisible(assign(paste0(target, "_merged_df2"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-merged_df2.csv")), envir = .GlobalEnv)) - invisible(assign(paste0(target, "_corr_df_m3_f"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-corr_df_m3_f.csv")), envir = .GlobalEnv)) - invisible(assign(paste0(target, "_lin_lf"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-lin_lf.csv")), envir = .GlobalEnv)) - invisible(assign(paste0(target, "_lin_wf"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-lin_wf.csv")), envir = .GlobalEnv)) + invisible(assign(paste0(target, "_merged_df3"), read.csv(paste0("/srv/shiny-server/git/Misc/shiny_dashboard/data/",target,"-merged_df3.csv")), envir = .GlobalEnv)) + invisible(assign(paste0(target, "_merged_df2"), read.csv(paste0("/srv/shiny-server/git/Misc/shiny_dashboard/data/",target,"-merged_df2.csv")), envir = .GlobalEnv)) + 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)) + invisible(assign(paste0(target, "_lin_lf"), read.csv(paste0("/srv/shiny-server/git/Misc/shiny_dashboard/data/",target,"-lin_lf.csv")), envir = .GlobalEnv)) + invisible(assign(paste0(target, "_lin_wf"), read.csv(paste0("/srv/shiny-server/git/Misc/shiny_dashboard/data/",target,"-lin_wf.csv")), envir = .GlobalEnv)) lapply( c( "duet", @@ -44,12 +44,12 @@ load_target_globals=function(target){ "mcsm_ppi2"#, #"mcsm_na" ), function(x){ - wf_filename=paste0("~/git/Misc/shiny_dashboard/data/", tolower(gene), "-wf_", x ,".csv") + wf_filename=paste0("/srv/shiny-server/git/Misc/shiny_dashboard/data/", tolower(gene), "-wf_", x ,".csv") wf_var=paste0("wf_",x) if (file.exists(wf_filename)){ invisible(assign(wf_var,read.csv(wf_filename), envir = .GlobalEnv)) # FILTH } - lf_filename=paste0("~/git/Misc/shiny_dashboard/data/", tolower(gene), "-lf_", x ,".csv") + lf_filename=paste0("/srv/shiny-server/git/Misc/shiny_dashboard/data/", tolower(gene), "-lf_", x ,".csv") lf_var=paste0(target, "_lf_",x) if (file.exists(lf_filename)){ invisible(assign(lf_var,read.csv(lf_filename), envir = .GlobalEnv)) # FILTH @@ -61,12 +61,12 @@ load_target_globals=function(target){ load_msa_global=function(gene){ drug=target_map[[gene]] in_filename_msa = paste0(tolower(gene), "_msa.csv") - infile_msa = paste0("~/git/Data/", drug, "/output/", in_filename_msa) + infile_msa = paste0("/srv/shiny-server/git/Data/", drug, "/output/", in_filename_msa) print(infile_msa) msa1 = read.csv(infile_msa, header = F) msa_seq = msa1$V1 - infile_fasta = paste0("~/git/Data/", drug, "/input/", tolower(gene), "2_f2.fasta") + infile_fasta = paste0("/srv/shiny-server/git/Data/", drug, "/input/", tolower(gene), "2_f2.fasta") print(infile_fasta) msa2 = read.csv(infile_fasta, header = F) wt_seq = msa2$V1 diff --git a/drug-target/ui.R b/drug-target/ui.R index f159f64..5c314b2 100644 --- a/drug-target/ui.R +++ b/drug-target/ui.R @@ -1,6 +1,7 @@ #### Shiny UI ##### #dashboardHeader(title = paste0(gene, "/", drug)), +dashboardPage(skin="purple", dashboardHeader(title = "Drug/Target Explorer"), dashboardSidebar( @@ -254,3 +255,4 @@ body <- dashboardBody( ) ) ) +)