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This commit is contained in:
Tanushree Tunstall 2022-09-03 09:53:52 +00:00
parent 59caed060b
commit 18d03594d2
2 changed files with 19 additions and 17 deletions
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34
drug-target/global.R
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@ -4,32 +4,32 @@ library(NGLVieweR)
library(hash) library(hash)
# FIXME This is slow and should happen *once only* # 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 # FIXME: these are needed but slow to load every time
# source("~/git/LSHTM_analysis/config/alr.R") # source("/srv/shiny-server/git/LSHTM_analysis/config/alr.R")
# source("~/git/LSHTM_analysis/config/gid.R") # source("/srv/shiny-server/git/LSHTM_analysis/config/gid.R")
# source("~/git/LSHTM_analysis/config/pnca.R") # source("/srv/shiny-server/git/LSHTM_analysis/config/pnca.R")
# source("~/git/LSHTM_analysis/config/rpob.R") # source("/srv/shiny-server/git/LSHTM_analysis/config/rpob.R")
# source("~/git/LSHTM_analysis/config/katg.R") # source("/srv/shiny-server/git/LSHTM_analysis/config/katg.R")
# TODO: this is TEMPORARY and will shortly get replaced with a target picker # 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 # that'll reload everything when changing targets. the lapply() is *much* quicker
# than previous approaches # than previous approaches
# system.time({ # 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){ load_target_globals=function(target){
cat(paste0("Reloading Target: ", 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_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("~/git/Misc/shiny_dashboard/data/",target,"-merged_df2.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("~/git/Misc/shiny_dashboard/data/",target,"-corr_df_m3_f.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("~/git/Misc/shiny_dashboard/data/",target,"-lin_lf.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("~/git/Misc/shiny_dashboard/data/",target,"-lin_wf.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( lapply(
c( c(
"duet", "duet",
@ -44,12 +44,12 @@ load_target_globals=function(target){
"mcsm_ppi2"#, "mcsm_ppi2"#,
#"mcsm_na" #"mcsm_na"
), function(x){ ), 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) wf_var=paste0("wf_",x)
if (file.exists(wf_filename)){ if (file.exists(wf_filename)){
invisible(assign(wf_var,read.csv(wf_filename), envir = .GlobalEnv)) # FILTH 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) lf_var=paste0(target, "_lf_",x)
if (file.exists(lf_filename)){ if (file.exists(lf_filename)){
invisible(assign(lf_var,read.csv(lf_filename), envir = .GlobalEnv)) # FILTH 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){ load_msa_global=function(gene){
drug=target_map[[gene]] drug=target_map[[gene]]
in_filename_msa = paste0(tolower(gene), "_msa.csv") 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) print(infile_msa)
msa1 = read.csv(infile_msa, header = F) msa1 = read.csv(infile_msa, header = F)
msa_seq = msa1$V1 msa_seq = msa1$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) print(infile_fasta)
msa2 = read.csv(infile_fasta, header = F) msa2 = read.csv(infile_fasta, header = F)
wt_seq = msa2$V1 wt_seq = msa2$V1

2
drug-target/ui.R
View file

@ -1,6 +1,7 @@
#### Shiny UI ##### #### Shiny UI #####
#dashboardHeader(title = paste0(gene, "/", drug)), #dashboardHeader(title = paste0(gene, "/", drug)),
dashboardPage(skin="purple",
dashboardHeader(title = "Drug/Target Explorer"), dashboardHeader(title = "Drug/Target Explorer"),
dashboardSidebar( dashboardSidebar(
@ -254,3 +255,4 @@ body <- dashboardBody(
) )
) )
) )
)