From dd2752050b65b642977cd7f681eccdba4097a6f2 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Fri, 9 Sep 2022 16:28:36 +0100 Subject: [PATCH] use feather instead of CSV --- drug-target/global.R | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/drug-target/global.R b/drug-target/global.R index 9ee519e..2ffcbdf 100644 --- a/drug-target/global.R +++ b/drug-target/global.R @@ -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 } } )