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use feather instead of CSV

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This commit is contained in:
Tanushree Tunstall 2022-09-09 16:28:36 +01:00
parent 8e29bacd15
commit dd2752050b
1 changed files with 8 additions and 13 deletions
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21
drug-target/global.R
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@ -2,7 +2,7 @@ library(shinycssloaders)
library(DT)
library(NGLVieweR)
library(hash)
library(feather)
# FIXME This is slow and should happen *once only*
#source(load_dir, "git/LSHTM_analysis/scripts/Header_TT.R")
@ -33,11 +33,11 @@ load_target_globals=function(target){
invisible(assign(paste0(target, "_aa_pos_lig1"), aa_pos_lig1, envir = .GlobalEnv))
invisible(assign(paste0(target, "_aa_pos_lig2"), aa_pos_lig2, envir = .GlobalEnv))
invisible(assign(paste0(target, "_aa_pos_lig3"), aa_pos_lig3, envir = .GlobalEnv))
invisible(assign(paste0(target, "_merged_df3"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-merged_df3.csv")), envir = .GlobalEnv))
invisible(assign(paste0(target, "_merged_df2"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-merged_df2.csv")), envir = .GlobalEnv))
invisible(assign(paste0(target, "_corr_df_m3_f"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-corr_df_m3_f.csv")), envir = .GlobalEnv))
invisible(assign(paste0(target, "_lin_lf"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-lin_lf.csv")), envir = .GlobalEnv))
invisible(assign(paste0(target, "_lin_wf"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-lin_wf.csv")), envir = .GlobalEnv))
invisible(assign(paste0(target, "_merged_df3"), read_feather(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-merged_df3.feather")), envir = .GlobalEnv))
invisible(assign(paste0(target, "_merged_df2"), read_feather(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-merged_df2.feather")), envir = .GlobalEnv))
invisible(assign(paste0(target, "_corr_df_m3_f"), read_feather(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-corr_df_m3_f.feather")), envir = .GlobalEnv))
invisible(assign(paste0(target, "_lin_lf"), read_feather(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-lin_lf.feather")), envir = .GlobalEnv))
invisible(assign(paste0(target, "_lin_wf"), read_feather(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-lin_wf.feather")), envir = .GlobalEnv))
lapply(
c(
"duet",
@ -55,15 +55,10 @@ load_target_globals=function(target){
#,
#"mcsm_na"
), function(x){
wf_filename=paste0(load_dir, "Misc/shiny_dashboard/data/", tolower(gene), "-wf_", x ,".csv")
wf_var=paste0(target, "wf_",x)
if (file.exists(wf_filename)){
invisible(assign(wf_var,read.csv(wf_filename), envir = .GlobalEnv)) # FILTH
}
lf_filename=paste0(load_dir, "Misc/shiny_dashboard/data/", tolower(gene), "-lf_", x ,".csv")
lf_filename=paste0(load_dir, "Misc/shiny_dashboard/data/", tolower(gene), "-lf_", x ,".feather")
lf_var=paste0(target, "_lf_",x)
if (file.exists(lf_filename)){
invisible(assign(lf_var,read.csv(lf_filename), envir = .GlobalEnv)) # FILTH
invisible(assign(lf_var,read_feather(lf_filename), envir = .GlobalEnv)) # FILTH
}
}
)