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fix HARDCODED HOMEDIRS

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This commit is contained in:
Tanushree Tunstall 2023-02-19 18:01:03 +00:00
parent db7e2912e1
commit 1571f430a5
50 changed files with 78 additions and 78 deletions
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2
scripts/count_vars_ML.R
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@ -96,7 +96,7 @@ cat(paste("\nmerged df3 filename:", outfile_merged_df3
# source("~/git/LSHTM_analysis/config/pnca.R") # source("~/git/LSHTM_analysis/config/pnca.R")
# source("~/git/LSHTM_analysis/config/rpob.R") # source("~/git/LSHTM_analysis/config/rpob.R")
# # # #
df3_filename = paste0("/home/tanu/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv") df3_filename = paste0("~/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
df3 = read.csv(df3_filename) df3 = read.csv(df3_filename)
# # # #
# mutationinformation # mutationinformation

2
scripts/count_vars_ML_v1.R
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@ -222,7 +222,7 @@ source("~/git/LSHTM_analysis/config/katg.R")
source("~/git/LSHTM_analysis/config/pnca.R") source("~/git/LSHTM_analysis/config/pnca.R")
source("~/git/LSHTM_analysis/config/rpob.R") source("~/git/LSHTM_analysis/config/rpob.R")
# #
df3_filename = paste0("/home/tanu/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv") df3_filename = paste0("~/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
df3 = read.csv(df3_filename) df3 = read.csv(df3_filename)
# #
# mutationinformation # mutationinformation

2
scripts/functions/tests/test_aa_prop_bp.R
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@ -11,7 +11,7 @@ getwd()
# that will be used in testing the functions # that will be used in testing the functions
#=========================================== #===========================================
source("plotting_data.R") source("plotting_data.R")
infile = "/home/tanu/git/Data/streptomycin/output/" infile = "~/git/Data/streptomycin/output/"
pd_df = plotting_data(infile) pd_df = plotting_data(infile)
my_df = pd_df[[1]] my_df = pd_df[[1]]
my_df_u = pd_df[[2]] my_df_u = pd_df[[2]]

12
scripts/functions/tests/test_combining_dfs_plotting.R
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@ -38,12 +38,12 @@ source("combining_dfs_plotting.R")
#--------------------- #---------------------
#gene = 'gid' #gene = 'gid'
#drug = 'streptomycin' #drug = 'streptomycin'
#source("/home/tanu/git/LSHTM_analysis/config/gid.R") #source("~/git/LSHTM_analysis/config/gid.R")
#source("/home/tanu/git/LSHTM_analysis/config/alr.R") #source("~/git/LSHTM_analysis/config/alr.R")
#source("/home/tanu/git/LSHTM_analysis/config/katg.R") #source("~/git/LSHTM_analysis/config/katg.R")
source("/home/tanu/git/LSHTM_analysis/config/pnca.R") source("~/git/LSHTM_analysis/config/pnca.R")
#source("/home/tanu/git/LSHTM_analysis/config/rpob.R") #source("~/git/LSHTM_analysis/config/rpob.R")
#source("/home/tanu/git/LSHTM_analysis/config/embb.R") #source("~/git/LSHTM_analysis/config/embb.R")

2
scripts/functions/tests/test_ed_pfm_data.R
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@ -2,7 +2,7 @@ source("~/git/LSHTM_analysis/scripts/Header_TT.R")
source("~/git/LSHTM_analysis/scripts/functions/ed_pfm_data.R") source("~/git/LSHTM_analysis/scripts/functions/ed_pfm_data.R")
# data msa: mut # data msa: mut
my_data = read.csv("/home/tanu/git/Misc/practice_plots/pnca_msa_eg2.csv", header = F) #15 cols only my_data = read.csv("~/git/Misc/practice_plots/pnca_msa_eg2.csv", header = F) #15 cols only
msaSeq_mut = my_data$V1 msaSeq_mut = my_data$V1
msa_seq = msaSeq_mut msa_seq = msaSeq_mut

2
scripts/functions/tests/test_plotting_data.R
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@ -19,7 +19,7 @@ import_dirs(drug_name = drug, gene_name = gene)
#------------------------------- #-------------------------------
source("plotting_data.R") source("plotting_data.R")
infile_params = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv" infile_params = "~/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
mcsm_comb_data = read.csv(infile_params, header = T) mcsm_comb_data = read.csv(infile_params, header = T)
pd_df = plotting_data(df = mcsm_comb_data pd_df = plotting_data(df = mcsm_comb_data

4
scripts/plotting/LINEAGE.R
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@ -5,8 +5,8 @@ library("ggforce")
library(gginference) library(gginference)
library(ggpubr) library(ggpubr)
#%% read data #%% read data
df = read.csv("/home/tanu/git/Data/pyrazinamide/output/pnca_merged_df2.csv") df = read.csv("~/git/Data/pyrazinamide/output/pnca_merged_df2.csv")
#df2 = read.csv("/home/tanu/git/Data/pyrazinamide/output/pnca_merged_df3.csv") #df2 = read.csv("~/git/Data/pyrazinamide/output/pnca_merged_df3.csv")
foo = as.data.frame(colnames(df)) foo = as.data.frame(colnames(df))

2
scripts/plotting/basic_barplots.R
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@ -68,7 +68,7 @@ import_dirs(drug, gene)
# my_df_u_lig # my_df_u_lig
# dup_muts # dup_muts
#*********************************** #***********************************
#infile_params = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv" #infile_params = "~/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
if (!exists("infile_params") && exists("gene")){ if (!exists("infile_params") && exists("gene")){
#if (!is.character(infile_params) && exists("gene")){ #if (!is.character(infile_params) && exists("gene")){

2
scripts/plotting/lineage_plots_multipage.R
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@ -14,7 +14,7 @@ lineage_plot=function(gene,drug){
full_file_path = paste0(lineage_data_path,"/",lineage_filename) full_file_path = paste0(lineage_data_path,"/",lineage_filename)
print(paste0("Loading: ",full_file_path)) print(paste0("Loading: ",full_file_path))
df = read.csv(full_file_path) df = read.csv(full_file_path)
#df2 = read.csv("/home/tanu/git/Data/pyrazinamide/output/pnca_merged_df3.csv") #df2 = read.csv("~/git/Data/pyrazinamide/output/pnca_merged_df3.csv")
foo = as.data.frame(colnames(df)) foo = as.data.frame(colnames(df))

4
scripts/plotting/logo_data_msa.R
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@ -5,12 +5,12 @@ cat("\n=========================================="
, "\nLogo MSA Plots Data: ALL params" , "\nLogo MSA Plots Data: ALL params"
, "\n=========================================") , "\n=========================================")
#msa1 = read.csv("/home/tanu/git/Data/cycloserine/output/gid_msa.csv", header = F) #msa1 = read.csv("~/git/Data/cycloserine/output/gid_msa.csv", header = F)
#head(msa1) #head(msa1)
#msa_seq= msa1$V1 #msa_seq= msa1$V1
#head(msa_seq) #head(msa_seq)
#msa2 = read.csv("/home/tanu/git/Data/cycloserine/input/gid.1fasta", header = F) #msa2 = read.csv("~/git/Data/cycloserine/input/gid.1fasta", header = F)
#head(msa2) #head(msa2)
#wt_seq = msa2$V1 #wt_seq = msa2$V1
#head(wt_seq) #head(wt_seq)

4
scripts/plotting/mcsm_affinity_data_only.R
View file

@ -5,7 +5,7 @@
#source("~/git/LSHTM_analysis/config/katg.R") #source("~/git/LSHTM_analysis/config/katg.R")
source("~/git/LSHTM_analysis/config/rpob.R") source("~/git/LSHTM_analysis/config/rpob.R")
source("/home/tanu/git/LSHTM_analysis/my_header.R") source("~/git/LSHTM_analysis/my_header.R")
######################################################### #########################################################
# TASK: Generate averaged affinity values # TASK: Generate averaged affinity values
# across all affinity tools for a given structure # across all affinity tools for a given structure
@ -32,7 +32,7 @@ print(paste0("Output file:", outfile_mean_aff_priorty))
#============= #=============
# Input # Input
#============= #=============
df3_filename = paste0("/home/tanu/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv") df3_filename = paste0("~/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
df3 = read.csv(df3_filename) df3 = read.csv(df3_filename)
length(df3$mutationinformation) length(df3$mutationinformation)

2
scripts/plotting/plotting_thesis/alr/DONOTUSEdm_om_plots_layout_alr.R
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@ -1,5 +1,5 @@
# # source dm_om_plots.R # # source dm_om_plots.R
# source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R") # source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R")
# #
# ##### plots to combine #### # ##### plots to combine ####
# duetP # duetP

2
scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist_layout.R
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@ -1,5 +1,5 @@
#!/usr/bin/env Rscript #!/usr/bin/env Rscript
source("/home/sethp/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist.R")
########################################### ###########################################
# TASK: generate plots for lineage # TASK: generate plots for lineage

2
scripts/plotting/plotting_thesis/alr/alr_other_plots.R
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@ -1,2 +1,2 @@
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")

4
scripts/plotting/plotting_thesis/alr/basic_barplots_alr_layout.R
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@ -4,8 +4,8 @@
source("~/git/LSHTM_analysis/config/alr.R") source("~/git/LSHTM_analysis/config/alr.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/basic_barplots_alr.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/basic_barplots_alr.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/pe_sens_site_count_alr.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/pe_sens_site_count_alr.R")
if ( tolower(gene)%in%c("alr") ){ if ( tolower(gene)%in%c("alr") ){
cat("\nPlots available for layout are:") cat("\nPlots available for layout are:")

4
scripts/plotting/plotting_thesis/alr/gg_pairs_all_alr.R
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@ -256,7 +256,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
#### Combine plots ##### #### Combine plots #####
# #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300) # #png("~/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
# png(paste0(outdir_images # png(paste0(outdir_images
# ,tolower(gene) # ,tolower(gene)
# ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300) # ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300)
@ -272,7 +272,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
# dev.off() # dev.off()
# #
# # affinity corr # # affinity corr
# #png("/home/tanu/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300) # #png("~/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
# png(paste0(outdir_images # png(paste0(outdir_images
# ,tolower(gene) # ,tolower(gene)
# ,"_CorrC.png"), height =7, width=7, unit="in",res=300) # ,"_CorrC.png"), height =7, width=7, unit="in",res=300)

4
scripts/plotting/plotting_thesis/alr/pe_sens_site_count_alr.R
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@ -1,5 +1,5 @@
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/prominent_effects_alr.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/prominent_effects_alr.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/sensitivity_count_alr.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/sensitivity_count_alr.R")
############################################################## ##############################################################
# PE count # PE count

4
scripts/plotting/plotting_thesis/embb/basic_barplots_embb_layout.R
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@ -4,8 +4,8 @@
source("~/git/LSHTM_analysis/config/embb.R") source("~/git/LSHTM_analysis/config/embb.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/basic_barplots_embb.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/basic_barplots_embb.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/pe_sens_site_count_embb.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/pe_sens_site_count_embb.R")
if ( tolower(gene)%in%c("embb") ){ if ( tolower(gene)%in%c("embb") ){
cat("\nPlots available for layout are:") cat("\nPlots available for layout are:")

2
scripts/plotting/plotting_thesis/embb/dm_om_plots_layout_embb.R
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@ -1,5 +1,5 @@
# source dm_om_plots.R # source dm_om_plots.R
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R")
##### plots to combine #### ##### plots to combine ####
duetP duetP

2
scripts/plotting/plotting_thesis/embb/embb_other_plots.R
View file

@ -1,2 +1,2 @@
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")

4
scripts/plotting/plotting_thesis/embb/gg_pairs_all_embb.R
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@ -148,7 +148,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
) )
#### Combine plots ##### #### Combine plots #####
# #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300) # #png("~/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
# png(paste0(outdir_images # png(paste0(outdir_images
# ,tolower(gene) # ,tolower(gene)
# ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300) # ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300)
@ -164,7 +164,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
# dev.off() # dev.off()
# #
# # affinity corr # # affinity corr
# #png("/home/tanu/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300) # #png("~/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
# png(paste0(outdir_images # png(paste0(outdir_images
# ,tolower(gene) # ,tolower(gene)
# ,"_CorrC.png"), height =7, width=7, unit="in",res=300) # ,"_CorrC.png"), height =7, width=7, unit="in",res=300)

4
scripts/plotting/plotting_thesis/embb/pe_sens_site_count_embb.R
View file

@ -1,5 +1,5 @@
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/prominent_effects_embb.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/prominent_effects_embb.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/sensitivity_count_embb.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/sensitivity_count_embb.R")
############################################################## ##############################################################
# PE count # PE count

4
scripts/plotting/plotting_thesis/gid/basic_barplots_gid_layout.R
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@ -4,8 +4,8 @@
source("~/git/LSHTM_analysis/config/gid.R") source("~/git/LSHTM_analysis/config/gid.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/basic_barplots_gid.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/basic_barplots_gid.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/pe_sens_site_count_gid.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/pe_sens_site_count_gid.R")
#cat("\nSourced plotting cols as well:", length(plotting_cols)) #cat("\nSourced plotting cols as well:", length(plotting_cols))
#======= #=======

2
scripts/plotting/plotting_thesis/gid/dm_om_plots_gid_ayout.R
View file

@ -1,5 +1,5 @@
# source dm_om_plots.R # source dm_om_plots.R
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R")
##### plots to combine #### ##### plots to combine ####
duetP duetP

4
scripts/plotting/plotting_thesis/gid/gg_pairs_all_gid.R
View file

@ -159,7 +159,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
) )
#### Combine plots (OLD, AB + C) ##### #### Combine plots (OLD, AB + C) #####
# #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300) # #png("~/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
# png(paste0(outdir_images # png(paste0(outdir_images
# ,tolower(gene) # ,tolower(gene)
# ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300) # ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300)
@ -175,7 +175,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
# dev.off() # dev.off()
# #
# # affinity corr # # affinity corr
# #png("/home/tanu/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300) # #png("~/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
# png(paste0(outdir_images # png(paste0(outdir_images
# ,tolower(gene) # ,tolower(gene)
# ,"_CorrC.png"), height =7, width=7, unit="in",res=300) # ,"_CorrC.png"), height =7, width=7, unit="in",res=300)

2
scripts/plotting/plotting_thesis/gid/gid_other_plots.R
View file

@ -1,2 +1,2 @@
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")

4
scripts/plotting/plotting_thesis/gid/pe_sens_site_count_gid.R
View file

@ -1,5 +1,5 @@
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/prominent_effects_gid.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/prominent_effects_gid.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/sensitivity_count_gid.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/sensitivity_count_gid.R")
############################################################## ##############################################################
# PE count # PE count

4
scripts/plotting/plotting_thesis/katg/basic_barplots_katg_layout.R
View file

@ -4,8 +4,8 @@
source("~/git/LSHTM_analysis/config/katg.R") source("~/git/LSHTM_analysis/config/katg.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/basic_barplots_katg.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/basic_barplots_katg.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/pe_sens_site_count_katg.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/pe_sens_site_count_katg.R")
if ( tolower(gene)%in%c("katg") ){ if ( tolower(gene)%in%c("katg") ){
cat("\nPlots available for layout are:") cat("\nPlots available for layout are:")

4
scripts/plotting/plotting_thesis/katg/gg_pairs_all_katg.R
View file

@ -156,7 +156,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
) )
#### Combine plots ##### #### Combine plots #####
# #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300) # #png("~/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
# png(paste0(outdir_images # png(paste0(outdir_images
# ,tolower(gene) # ,tolower(gene)
# ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300) # ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300)
@ -172,7 +172,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
# dev.off() # dev.off()
# #
# # affinity corr # # affinity corr
# #png("/home/tanu/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300) # #png("~/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
# png(paste0(outdir_images # png(paste0(outdir_images
# ,tolower(gene) # ,tolower(gene)
# ,"_CorrC.png"), height =7, width=7, unit="in",res=300) # ,"_CorrC.png"), height =7, width=7, unit="in",res=300)

2
scripts/plotting/plotting_thesis/katg/katg_dm_om_plots_layout.R
View file

@ -1,5 +1,5 @@
# source dm_om_plots.R # source dm_om_plots.R
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/katg_dm_om_plots.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/katg_dm_om_plots.R")
##### plots to combine #### ##### plots to combine ####
duetP duetP

2
scripts/plotting/plotting_thesis/katg/katg_other_plots.R
View file

@ -1,2 +1,2 @@
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")

4
scripts/plotting/plotting_thesis/katg/pe_sens_site_count_katg.R
View file

@ -1,5 +1,5 @@
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/prominent_effects_katg.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/prominent_effects_katg.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/sensitivity_count_katg.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/sensitivity_count_katg.R")
############################################################## ##############################################################
# PE count # PE count

2
scripts/plotting/plotting_thesis/lineage_bp_dist_layout.R
View file

@ -1,5 +1,5 @@
#!/usr/bin/env Rscript #!/usr/bin/env Rscript
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/lineage_bp_dist.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/lineage_bp_dist.R")
#======= #=======
# output # output

4
scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca_layout.R
View file

@ -4,8 +4,8 @@
#source("~/git/LSHTM_analysis/config/pnca.R") #source("~/git/LSHTM_analysis/config/pnca.R")
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") #source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/pe_sens_site_count_pnca.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/pe_sens_site_count_pnca.R")
if ( tolower(gene)%in%c("pnca") ){ if ( tolower(gene)%in%c("pnca") ){
cat("\nPlots available for layout are:") cat("\nPlots available for layout are:")

4
scripts/plotting/plotting_thesis/pnca/gg_pairs_all_pnca.R
View file

@ -156,7 +156,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
) )
#### Combine plots ##### #### Combine plots #####
# #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300) # #png("~/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
# png(paste0(outdir_images # png(paste0(outdir_images
# ,tolower(gene) # ,tolower(gene)
# ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300) # ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300)
@ -172,7 +172,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
# dev.off() # dev.off()
# #
# # affinity corr # # affinity corr
# #png("/home/tanu/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300) # #png("~/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
# png(paste0(outdir_images # png(paste0(outdir_images
# ,tolower(gene) # ,tolower(gene)
# ,"_CorrC.png"), height =7, width=7, unit="in",res=300) # ,"_CorrC.png"), height =7, width=7, unit="in",res=300)

2
scripts/plotting/plotting_thesis/pnca/lineage_bp_dist_layout.R
View file

@ -1,5 +1,5 @@
#!/usr/bin/env Rscript #!/usr/bin/env Rscript
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/lineage_bp_dist.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/lineage_bp_dist.R")
#======= #=======
# output # output

4
scripts/plotting/plotting_thesis/pnca/pe_sens_site_count_pnca.R
View file

@ -1,5 +1,5 @@
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/prominent_effects_pnca.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/prominent_effects_pnca.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/sensitivity_count_pnca.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/sensitivity_count_pnca.R")
############################################################## ##############################################################
# PE count # PE count

2
scripts/plotting/plotting_thesis/pnca/pnca_dm_om_plots_layout.R
View file

@ -1,5 +1,5 @@
# source dm_om_plots.R # source dm_om_plots.R
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/pnca_dm_om_plots.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/pnca_dm_om_plots.R")
##### plots to combine #### ##### plots to combine ####
duetP duetP

4
scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob_layout.R
View file

@ -26,8 +26,8 @@ table(df3_ppi2$sensitivity)
outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/") outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
cat("plots will output to:", outdir_images) cat("plots will output to:", outdir_images)
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/pe_sens_site_count_rpob.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/pe_sens_site_count_rpob.R")
if ( tolower(gene)%in%c("rpob") ){ if ( tolower(gene)%in%c("rpob") ){
cat("\nPlots available for layout are:") cat("\nPlots available for layout are:")

4
scripts/plotting/plotting_thesis/rpob/dm_om_plots_layout_rpob.R
View file

@ -1,6 +1,6 @@
# source dm_om_plots.R # source dm_om_plots.R
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/dm_om_plots_rpob.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/dm_om_plots_rpob.R")
# source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R") # source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R")
##### plots to combine #### ##### plots to combine ####
duetP duetP

4
scripts/plotting/plotting_thesis/rpob/gg_pairs_all_rpob.R
View file

@ -160,7 +160,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
) )
#### Combine plots ##### #### Combine plots #####
# #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300) # #png("~/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
# png(paste0(outdir_images # png(paste0(outdir_images
# ,tolower(gene) # ,tolower(gene)
# ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300) # ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300)
@ -176,7 +176,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
# dev.off() # dev.off()
# #
# # affinity corr # # affinity corr
# #png("/home/tanu/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300) # #png("~/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
# png(paste0(outdir_images # png(paste0(outdir_images
# ,tolower(gene) # ,tolower(gene)
# ,"_CorrC.png"), height =7, width=7, unit="in",res=300) # ,"_CorrC.png"), height =7, width=7, unit="in",res=300)

4
scripts/plotting/plotting_thesis/rpob/pe_sens_site_count_rpob.R
View file

@ -1,5 +1,5 @@
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/prominent_effects_rpob.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/prominent_effects_rpob.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/sensitivity_count_rpob.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/sensitivity_count_rpob.R")
############################################################## ##############################################################
# PE count # PE count

2
scripts/plotting/plotting_thesis/rpob/rpob_other_plots.R
View file

@ -1,2 +1,2 @@
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R") source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist_layout.R")

4
scripts/plotting/plotting_thesis/version1/gg_pairs_all.R
View file

@ -148,7 +148,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff, plot_title="Affinity estimates", tt_
# combine # combine
#============= #=============
#png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300) #png("~/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
png(paste0(outdir_images png(paste0(outdir_images
,tolower(gene) ,tolower(gene)
,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300) ,"_CorrAB.png"), height = 6, width=11.75, unit="in",res=300)
@ -164,7 +164,7 @@ cowplot::plot_grid(ggmatrix_gtable(plot_corr_df_ps),
dev.off() dev.off()
# affinity corr # affinity corr
#png("/home/tanu/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300) #png("~/tmp/gg_pairs_affinity.png", height =7, width=7, unit="in",res=300)
png(paste0(outdir_images png(paste0(outdir_images
,tolower(gene) ,tolower(gene)
,"_CorrC.png"), height =7, width=7, unit="in",res=300) ,"_CorrC.png"), height =7, width=7, unit="in",res=300)

2
scripts/plotting/redundant/basic_barplots_LIG.R
View file

@ -76,7 +76,7 @@ import_dirs(drug, gene)
# my_df_u_lig # my_df_u_lig
# dup_muts # dup_muts
#---------------------------------------------- #----------------------------------------------
#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv" #infile = "~/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
#infile = "" #infile = ""
#if (!exists("infile") && exists("gene")){ #if (!exists("infile") && exists("gene")){

2
scripts/plotting/redundant/basic_barplots_PS.R
View file

@ -75,7 +75,7 @@ import_dirs(drug, gene)
# my_df_u_lig # my_df_u_lig
# dup_muts # dup_muts
#---------------------------------------------- #----------------------------------------------
#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv" #infile = "~/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
#infile = "" #infile = ""
#if (!exists("infile") && exists("gene")){ #if (!exists("infile") && exists("gene")){

2
scripts/plotting/redundant/combining_dfs_plotting.R
View file

@ -80,7 +80,7 @@ import_dirs(drug, gene)
# my_df_u_lig # my_df_u_lig
# dup_muts # dup_muts
#*********************************** #***********************************
#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv" #infile = "~/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
if (!exists("infile") && exists("gene")){ if (!exists("infile") && exists("gene")){
#if (!is.character(infile) && exists("gene")){ #if (!is.character(infile) && exists("gene")){

2
scripts/plotting/structure_figures/mut_landscape.R
View file

@ -24,7 +24,7 @@ outfile_meta2 = paste0(outdir_images, "/", tolower(gene), "_mutpos_annot_cu.txt
#============= #=============
# Input # Input
#============= #=============
df3_filename = paste0("/home/tanu/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv") df3_filename = paste0("~/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
df3 = read.csv(df3_filename) df3 = read.csv(df3_filename)
# Determine for each gene # Determine for each gene

2
scripts/plotting/structure_figures/mut_landscape_5uhc_rpob.R
View file

@ -19,7 +19,7 @@ outfile_meta2 = paste0(outdir_images, "/5uhc_", tolower(gene), "_mutpos_annot_c
#============= #=============
# Input # Input
#============= #=============
df3_filename = paste0("/home/tanu/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv") df3_filename = paste0("~/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
df3 = read.csv(df3_filename) df3 = read.csv(df3_filename)
chain_suffix = ".C" chain_suffix = ".C"

2
scripts/plotting/structure_figures/replaceBfactor_pdb_stability.R
View file

@ -39,7 +39,7 @@ outdir = paste0("~/git/Data", "/", drug, "/output")
# input # input
#====== #======
in_filename_pdb = paste0(tolower(gene), "_complex.pdb") in_filename_pdb = paste0(tolower(gene), "_complex.pdb")
#in_filename_pdb = "/home/tanu/git/Writing/thesis/images/results/gid/str_figures/gid_complex_copy_arpeg.pdb" #in_filename_pdb = "~/git/Writing/thesis/images/results/gid/str_figures/gid_complex_copy_arpeg.pdb"
infile_pdb = paste0(indir, "/", in_filename_pdb) infile_pdb = paste0(indir, "/", in_filename_pdb)
cat(paste0("Input file:", infile_pdb) ) cat(paste0("Input file:", infile_pdb) )