From 586927ca562c2994ac47e860edba18e5793ad3e7 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Wed, 26 Jan 2022 11:39:03 +0000 Subject: [PATCH] wholesale change for Header_TT.R location --- scripts/af_or_calcs.R | 2 +- scripts/functions/combining_dfs_plotting.R | 2 +- scripts/functions/tests/test_af_or_calcs.R | 2 +- scripts/functions/tests/test_lf_bp.R | 2 +- scripts/functions/tests/test_lineage_dist.R | 2 +- scripts/plotting/TESTING_PLOTS.R | 2 +- scripts/plotting/barplots_subcolours.R | 2 +- scripts/plotting/barplots_subcolours_aa_LIG.R | 2 +- scripts/plotting/barplots_subcolours_aa_PS.R | 2 +- scripts/plotting/basic_barplots.R | 2 +- scripts/plotting/corr_adjusted_PS_LIG.R | 2 +- scripts/plotting/corr_plots.R | 2 +- scripts/plotting/dist_plots_check.R | 2 +- scripts/plotting/extreme_muts.R | 2 +- scripts/plotting/get_plotting_dfs_with_lig.R | 2 +- scripts/plotting/ggcorr_all_PS_LIG.R | 2 +- scripts/plotting/hist_af_or_base.R | 2 +- scripts/plotting/hist_af_or_combined.R | 2 +- scripts/plotting/lineage_basic_barplot.R | 2 +- scripts/plotting/lineage_basic_barplots_combined.R | 2 +- scripts/plotting/lineage_dist_combined_PS.R | 2 +- scripts/plotting/lineage_dist_dm_om_combined_PS.R | 2 +- scripts/plotting/lineage_dist_plots.R | 2 +- scripts/plotting/logo_plots.R | 2 +- scripts/plotting/mcsm_mean_stability.R | 2 +- scripts/plotting/myshiny/subcols_bp.R | 2 +- scripts/plotting/or_plots_combined.R | 2 +- scripts/plotting/other_plots_combined.R | 2 +- scripts/plotting/other_plots_data.R | 2 +- scripts/plotting/output_tables.R | 2 +- scripts/plotting/ps_plots_combined.R | 2 +- scripts/plotting/redundant/barplots_subcolours_PS.R | 2 +- scripts/plotting/redundant/basic_barplots_LIG.R | 2 +- scripts/plotting/redundant/basic_barplots_PS.R | 2 +- scripts/plotting/redundant/combining_dfs_plotting.R | 2 +- scripts/plotting/redundant/combining_two_df_FIXME.R | 2 +- scripts/plotting/redundant/corr_PS_LIG.R | 2 +- scripts/plotting/redundant/corr_data.R | 2 +- scripts/plotting/redundant/lineage_basic_barplot.R | 2 +- scripts/plotting/redundant/lineage_dist_combined_PS.R | 2 +- scripts/plotting/redundant/lineage_dist_dm_om_combined_PS.R | 2 +- scripts/plotting/redundant/logo_multiple_muts.R | 2 +- scripts/plotting/redundant/logo_plot.R | 2 +- scripts/plotting/redundant/other_plots_data_SAFEGUARD.R | 2 +- scripts/plotting/replaceBfactor_pdb.R | 2 +- scripts/plotting/scratch_plots/lineage_dist_dm_om_PS.R | 2 +- 46 files changed, 46 insertions(+), 46 deletions(-) diff --git a/scripts/af_or_calcs.R b/scripts/af_or_calcs.R index 08b614b..2503624 100755 --- a/scripts/af_or_calcs.R +++ b/scripts/af_or_calcs.R @@ -8,7 +8,7 @@ setwd("~/git/LSHTM_analysis/scripts") getwd() # load libraries -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") require("getopt", quietly = TRUE) # cmd parse arguments # load functions diff --git a/scripts/functions/combining_dfs_plotting.R b/scripts/functions/combining_dfs_plotting.R index e7faaa2..6016aea 100644 --- a/scripts/functions/combining_dfs_plotting.R +++ b/scripts/functions/combining_dfs_plotting.R @@ -6,7 +6,7 @@ ########################################################### # load libraries and functions -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") #========================================================== # combining_dfs_plotting(): diff --git a/scripts/functions/tests/test_af_or_calcs.R b/scripts/functions/tests/test_af_or_calcs.R index 0532f83..6f41aba 100644 --- a/scripts/functions/tests/test_af_or_calcs.R +++ b/scripts/functions/tests/test_af_or_calcs.R @@ -4,7 +4,7 @@ # Odds Ratio from master data ######################################################### # load libraries -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") require("getopt", quietly = TRUE) # cmd parse arguments # working dir and loading libraries diff --git a/scripts/functions/tests/test_lf_bp.R b/scripts/functions/tests/test_lf_bp.R index f3d2327..2102585 100644 --- a/scripts/functions/tests/test_lf_bp.R +++ b/scripts/functions/tests/test_lf_bp.R @@ -1,5 +1,5 @@ setwd("~/git/LSHTM_analysis/scripts/plotting/") -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") source("../functions/lf_bp.R") # ================================================ # Data: run get_plotting_data.R diff --git a/scripts/functions/tests/test_lineage_dist.R b/scripts/functions/tests/test_lineage_dist.R index eeeebe5..d9a0e52 100644 --- a/scripts/functions/tests/test_lineage_dist.R +++ b/scripts/functions/tests/test_lineage_dist.R @@ -7,7 +7,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting/") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") source("get_plotting_dfs.R") diff --git a/scripts/plotting/TESTING_PLOTS.R b/scripts/plotting/TESTING_PLOTS.R index b761415..d676a31 100755 --- a/scripts/plotting/TESTING_PLOTS.R +++ b/scripts/plotting/TESTING_PLOTS.R @@ -2,7 +2,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") drug = 'streptomycin' gene = 'gid' diff --git a/scripts/plotting/barplots_subcolours.R b/scripts/plotting/barplots_subcolours.R index 1f98bec..dc724b4 100755 --- a/scripts/plotting/barplots_subcolours.R +++ b/scripts/plotting/barplots_subcolours.R @@ -2,7 +2,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") drug = 'streptomycin' gene = 'gid' diff --git a/scripts/plotting/barplots_subcolours_aa_LIG.R b/scripts/plotting/barplots_subcolours_aa_LIG.R index 1924664..5c30385 100755 --- a/scripts/plotting/barplots_subcolours_aa_LIG.R +++ b/scripts/plotting/barplots_subcolours_aa_LIG.R @@ -15,7 +15,7 @@ getwd() # 1: Installing and loading required packages and functions ############################################################ -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggplot2) library(data.table) source("../functions/bp_subcolours.R") diff --git a/scripts/plotting/barplots_subcolours_aa_PS.R b/scripts/plotting/barplots_subcolours_aa_PS.R index 14c5bdd..546f4ff 100755 --- a/scripts/plotting/barplots_subcolours_aa_PS.R +++ b/scripts/plotting/barplots_subcolours_aa_PS.R @@ -14,7 +14,7 @@ getwd() # 1: Installing and loading required packages and functions ############################################################ -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggplot2) library(data.table) source("../functions/bp_subcolours.R") diff --git a/scripts/plotting/basic_barplots.R b/scripts/plotting/basic_barplots.R index ef5a4dd..4ea3fea 100755 --- a/scripts/plotting/basic_barplots.R +++ b/scripts/plotting/basic_barplots.R @@ -9,7 +9,7 @@ setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() # load libraries -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggplot2) library(data.table) library(dplyr) diff --git a/scripts/plotting/corr_adjusted_PS_LIG.R b/scripts/plotting/corr_adjusted_PS_LIG.R index ed96b4b..4355a23 100644 --- a/scripts/plotting/corr_adjusted_PS_LIG.R +++ b/scripts/plotting/corr_adjusted_PS_LIG.R @@ -11,7 +11,7 @@ setwd("~/git/LSHTM_analysis/scripts/plotting/") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") require(cowplot) source("combining_dfs_plotting.R") source("my_pairs_panel.R") diff --git a/scripts/plotting/corr_plots.R b/scripts/plotting/corr_plots.R index 8ab78ef..ed5979d 100755 --- a/scripts/plotting/corr_plots.R +++ b/scripts/plotting/corr_plots.R @@ -2,7 +2,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") spec = matrix(c( "drug" , "d", 1, "character", diff --git a/scripts/plotting/dist_plots_check.R b/scripts/plotting/dist_plots_check.R index f8ce2b0..341df92 100644 --- a/scripts/plotting/dist_plots_check.R +++ b/scripts/plotting/dist_plots_check.R @@ -9,7 +9,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(tidyverse) library(ggplot2) library(data.table) diff --git a/scripts/plotting/extreme_muts.R b/scripts/plotting/extreme_muts.R index 73cae0f..bca1ac6 100644 --- a/scripts/plotting/extreme_muts.R +++ b/scripts/plotting/extreme_muts.R @@ -10,7 +10,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(tidyverse) library(ggplot2) library(data.table) diff --git a/scripts/plotting/get_plotting_dfs_with_lig.R b/scripts/plotting/get_plotting_dfs_with_lig.R index f17e997..e0f1f3b 100755 --- a/scripts/plotting/get_plotting_dfs_with_lig.R +++ b/scripts/plotting/get_plotting_dfs_with_lig.R @@ -7,7 +7,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") source("../functions/my_pairs_panel.R") # with lower panel turned off source("../functions/plotting_globals.R") source("../functions/plotting_data.R") diff --git a/scripts/plotting/ggcorr_all_PS_LIG.R b/scripts/plotting/ggcorr_all_PS_LIG.R index ed68401..b603e7c 100644 --- a/scripts/plotting/ggcorr_all_PS_LIG.R +++ b/scripts/plotting/ggcorr_all_PS_LIG.R @@ -10,7 +10,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting/") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") require(cowplot) source("combining_dfs_plotting.R") #source("my_pairs_panel.R") diff --git a/scripts/plotting/hist_af_or_base.R b/scripts/plotting/hist_af_or_base.R index b5ecb37..0962a0c 100644 --- a/scripts/plotting/hist_af_or_base.R +++ b/scripts/plotting/hist_af_or_base.R @@ -16,7 +16,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggplot2) library(data.table) library(dplyr) diff --git a/scripts/plotting/hist_af_or_combined.R b/scripts/plotting/hist_af_or_combined.R index aa828be..f162f8c 100644 --- a/scripts/plotting/hist_af_or_combined.R +++ b/scripts/plotting/hist_af_or_combined.R @@ -16,7 +16,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggplot2) library(data.table) library(dplyr) diff --git a/scripts/plotting/lineage_basic_barplot.R b/scripts/plotting/lineage_basic_barplot.R index e4503d1..e65af2e 100644 --- a/scripts/plotting/lineage_basic_barplot.R +++ b/scripts/plotting/lineage_basic_barplot.R @@ -10,7 +10,7 @@ getwd() ########################################################## # Installing and loading required packages ########################################################## -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") require(data.table) source("combining_dfs_plotting.R") # should return the following dfs, directories and variables diff --git a/scripts/plotting/lineage_basic_barplots_combined.R b/scripts/plotting/lineage_basic_barplots_combined.R index 837e57b..659c129 100755 --- a/scripts/plotting/lineage_basic_barplots_combined.R +++ b/scripts/plotting/lineage_basic_barplots_combined.R @@ -11,7 +11,7 @@ getwd() ########################################################## # Installing and loading required packages ########################################################## -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") #=========== # input diff --git a/scripts/plotting/lineage_dist_combined_PS.R b/scripts/plotting/lineage_dist_combined_PS.R index bf1c75b..e6e1092 100644 --- a/scripts/plotting/lineage_dist_combined_PS.R +++ b/scripts/plotting/lineage_dist_combined_PS.R @@ -14,7 +14,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting/") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggridges) source("combining_dfs_plotting.R") # PS combined: diff --git a/scripts/plotting/lineage_dist_dm_om_combined_PS.R b/scripts/plotting/lineage_dist_dm_om_combined_PS.R index 07912ac..86ba608 100644 --- a/scripts/plotting/lineage_dist_dm_om_combined_PS.R +++ b/scripts/plotting/lineage_dist_dm_om_combined_PS.R @@ -14,7 +14,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting/") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggridges) library(plyr) source("combining_dfs_plotting.R") diff --git a/scripts/plotting/lineage_dist_plots.R b/scripts/plotting/lineage_dist_plots.R index cd1563d..1e4a66e 100644 --- a/scripts/plotting/lineage_dist_plots.R +++ b/scripts/plotting/lineage_dist_plots.R @@ -11,7 +11,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting/") getwd() -source("Header_TT.R") # also loads all my functions +source("~/git/LSHTM_analysis/scripts/Header_TT.R") # also loads all my functions #=========== # input diff --git a/scripts/plotting/logo_plots.R b/scripts/plotting/logo_plots.R index c3301b7..448a553 100755 --- a/scripts/plotting/logo_plots.R +++ b/scripts/plotting/logo_plots.R @@ -15,7 +15,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") spec = matrix(c( "drug" , "d", 1, "character", diff --git a/scripts/plotting/mcsm_mean_stability.R b/scripts/plotting/mcsm_mean_stability.R index 217b183..7e35e79 100755 --- a/scripts/plotting/mcsm_mean_stability.R +++ b/scripts/plotting/mcsm_mean_stability.R @@ -6,7 +6,7 @@ getwd() # TASK: ######################################################### -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") #require(data.table) #require(dplyr) diff --git a/scripts/plotting/myshiny/subcols_bp.R b/scripts/plotting/myshiny/subcols_bp.R index 9346577..1d29a9f 100644 --- a/scripts/plotting/myshiny/subcols_bp.R +++ b/scripts/plotting/myshiny/subcols_bp.R @@ -6,7 +6,7 @@ library(shinyBS) getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") drug = 'streptomycin' gene = 'gid' diff --git a/scripts/plotting/or_plots_combined.R b/scripts/plotting/or_plots_combined.R index c3f1cc6..bbac9e1 100644 --- a/scripts/plotting/or_plots_combined.R +++ b/scripts/plotting/or_plots_combined.R @@ -11,7 +11,7 @@ setwd("~/git/LSHTM_analysis/scripts/plotting/") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") require(cowplot) source("combining_dfs_plotting.R") # should return the following dfs, directories and variables diff --git a/scripts/plotting/other_plots_combined.R b/scripts/plotting/other_plots_combined.R index 3047f38..48b2fac 100644 --- a/scripts/plotting/other_plots_combined.R +++ b/scripts/plotting/other_plots_combined.R @@ -9,7 +9,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") #library(ggplot2) #library(data.table) #library(dplyr) diff --git a/scripts/plotting/other_plots_data.R b/scripts/plotting/other_plots_data.R index df5c1e3..a3e052f 100644 --- a/scripts/plotting/other_plots_data.R +++ b/scripts/plotting/other_plots_data.R @@ -9,7 +9,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggplot2) library(data.table) library(dplyr) diff --git a/scripts/plotting/output_tables.R b/scripts/plotting/output_tables.R index 0a15176..4ac7dd1 100644 --- a/scripts/plotting/output_tables.R +++ b/scripts/plotting/output_tables.R @@ -9,7 +9,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggplot2) library(data.table) library(dplyr) diff --git a/scripts/plotting/ps_plots_combined.R b/scripts/plotting/ps_plots_combined.R index f9a658b..87f0ff3 100644 --- a/scripts/plotting/ps_plots_combined.R +++ b/scripts/plotting/ps_plots_combined.R @@ -10,7 +10,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggplot2) library(data.table) #source("combining_dfs_plotting.R") diff --git a/scripts/plotting/redundant/barplots_subcolours_PS.R b/scripts/plotting/redundant/barplots_subcolours_PS.R index 5e80eec..ef58ca8 100755 --- a/scripts/plotting/redundant/barplots_subcolours_PS.R +++ b/scripts/plotting/redundant/barplots_subcolours_PS.R @@ -12,7 +12,7 @@ getwd() # 1: Installing and loading required packages and functions ############################################################# -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggplot2) library(data.table) source("barplot_colour_function.R") diff --git a/scripts/plotting/redundant/basic_barplots_LIG.R b/scripts/plotting/redundant/basic_barplots_LIG.R index 8789086..748f2ad 100755 --- a/scripts/plotting/redundant/basic_barplots_LIG.R +++ b/scripts/plotting/redundant/basic_barplots_LIG.R @@ -14,7 +14,7 @@ setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() # load libraries -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggplot2) library(data.table) library(dplyr) diff --git a/scripts/plotting/redundant/basic_barplots_PS.R b/scripts/plotting/redundant/basic_barplots_PS.R index d6b4530..9ae2f7d 100755 --- a/scripts/plotting/redundant/basic_barplots_PS.R +++ b/scripts/plotting/redundant/basic_barplots_PS.R @@ -14,7 +14,7 @@ setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() # load libraries -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggplot2) library(data.table) library(dplyr) diff --git a/scripts/plotting/redundant/combining_dfs_plotting.R b/scripts/plotting/redundant/combining_dfs_plotting.R index c45ef43..db35adc 100644 --- a/scripts/plotting/redundant/combining_dfs_plotting.R +++ b/scripts/plotting/redundant/combining_dfs_plotting.R @@ -27,7 +27,7 @@ getwd() require("getopt", quietly = TRUE) # cmd parse arguments # load functions -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") source("../functions/plotting_globals.R") source("../functions/plotting_data.R") diff --git a/scripts/plotting/redundant/combining_two_df_FIXME.R b/scripts/plotting/redundant/combining_two_df_FIXME.R index 0d34e06..d9fe003 100644 --- a/scripts/plotting/redundant/combining_two_df_FIXME.R +++ b/scripts/plotting/redundant/combining_two_df_FIXME.R @@ -24,7 +24,7 @@ getwd() ########################################################## # Installing and loading required packages ########################################################## -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") #require(data.table) #require(arsenal) #require(compare) diff --git a/scripts/plotting/redundant/corr_PS_LIG.R b/scripts/plotting/redundant/corr_PS_LIG.R index 54db489..6aab16f 100644 --- a/scripts/plotting/redundant/corr_PS_LIG.R +++ b/scripts/plotting/redundant/corr_PS_LIG.R @@ -11,7 +11,7 @@ setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") require(cowplot) source("../functions/combining_dfs_plotting.R") diff --git a/scripts/plotting/redundant/corr_data.R b/scripts/plotting/redundant/corr_data.R index aabc62e..8bdb929 100644 --- a/scripts/plotting/redundant/corr_data.R +++ b/scripts/plotting/redundant/corr_data.R @@ -8,7 +8,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") source("../functions/my_pairs_panel.R") # with lower panel turned off source("../functions/plotting_globals.R") source("../functions/plotting_data.R") diff --git a/scripts/plotting/redundant/lineage_basic_barplot.R b/scripts/plotting/redundant/lineage_basic_barplot.R index e4503d1..e65af2e 100644 --- a/scripts/plotting/redundant/lineage_basic_barplot.R +++ b/scripts/plotting/redundant/lineage_basic_barplot.R @@ -10,7 +10,7 @@ getwd() ########################################################## # Installing and loading required packages ########################################################## -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") require(data.table) source("combining_dfs_plotting.R") # should return the following dfs, directories and variables diff --git a/scripts/plotting/redundant/lineage_dist_combined_PS.R b/scripts/plotting/redundant/lineage_dist_combined_PS.R index bf1c75b..e6e1092 100755 --- a/scripts/plotting/redundant/lineage_dist_combined_PS.R +++ b/scripts/plotting/redundant/lineage_dist_combined_PS.R @@ -14,7 +14,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting/") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggridges) source("combining_dfs_plotting.R") # PS combined: diff --git a/scripts/plotting/redundant/lineage_dist_dm_om_combined_PS.R b/scripts/plotting/redundant/lineage_dist_dm_om_combined_PS.R index 3875382..a6f669f 100755 --- a/scripts/plotting/redundant/lineage_dist_dm_om_combined_PS.R +++ b/scripts/plotting/redundant/lineage_dist_dm_om_combined_PS.R @@ -14,7 +14,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting/") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") source("get_plotting_dfs.R") diff --git a/scripts/plotting/redundant/logo_multiple_muts.R b/scripts/plotting/redundant/logo_multiple_muts.R index 4902c1c..78c1a00 100755 --- a/scripts/plotting/redundant/logo_multiple_muts.R +++ b/scripts/plotting/redundant/logo_multiple_muts.R @@ -2,7 +2,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") spec = matrix(c( "drug" , "d", 1, "character", diff --git a/scripts/plotting/redundant/logo_plot.R b/scripts/plotting/redundant/logo_plot.R index f9a39fe..949abd5 100755 --- a/scripts/plotting/redundant/logo_plot.R +++ b/scripts/plotting/redundant/logo_plot.R @@ -2,7 +2,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") spec = matrix(c( "drug" , "d", 1, "character", diff --git a/scripts/plotting/redundant/other_plots_data_SAFEGUARD.R b/scripts/plotting/redundant/other_plots_data_SAFEGUARD.R index df5c1e3..a3e052f 100644 --- a/scripts/plotting/redundant/other_plots_data_SAFEGUARD.R +++ b/scripts/plotting/redundant/other_plots_data_SAFEGUARD.R @@ -9,7 +9,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggplot2) library(data.table) library(dplyr) diff --git a/scripts/plotting/replaceBfactor_pdb.R b/scripts/plotting/replaceBfactor_pdb.R index 2bf05e1..0d5cd1a 100755 --- a/scripts/plotting/replaceBfactor_pdb.R +++ b/scripts/plotting/replaceBfactor_pdb.R @@ -21,7 +21,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting") cat(c(getwd(),"\n")) -#source("Header_TT.R") +#source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(bio3d) require("getopt", quietly = TRUE) # cmd parse arguments #======================================================== diff --git a/scripts/plotting/scratch_plots/lineage_dist_dm_om_PS.R b/scripts/plotting/scratch_plots/lineage_dist_dm_om_PS.R index 37e8cbe..eaef8c0 100644 --- a/scripts/plotting/scratch_plots/lineage_dist_dm_om_PS.R +++ b/scripts/plotting/scratch_plots/lineage_dist_dm_om_PS.R @@ -14,7 +14,7 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting/") getwd() -source("Header_TT.R") +source("~/git/LSHTM_analysis/scripts/Header_TT.R") library(ggridges) source("combining_dfs_plotting.R") # PS combined: