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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/plotting/plotting_thesis/alr/DONOTUSEdm_om_plots_layout_alr.R
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@ -1,5 +1,5 @@
# # 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 ####
# 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
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

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

4
scripts/plotting/plotting_thesis/alr/gg_pairs_all_alr.R
View file

@ -256,7 +256,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
#### 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
# ,tolower(gene)
# ,"_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()
#
# # 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
# ,tolower(gene)
# ,"_CorrC.png"), height =7, width=7, unit="in",res=300)

4
scripts/plotting/plotting_thesis/alr/pe_sens_site_count_alr.R
View file

@ -1,5 +1,5 @@
source("/home/tanu/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/prominent_effects_alr.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/sensitivity_count_alr.R")
##############################################################
# 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/scripts/plotting/get_plotting_dfs.R")
source("/home/tanu/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/basic_barplots_embb.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/pe_sens_site_count_embb.R")
if ( tolower(gene)%in%c("embb") ){
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("/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 ####
duetP

2
scripts/plotting/plotting_thesis/embb/embb_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/embb/gg_pairs_all_embb.R
View file

@ -148,7 +148,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
)
#### 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
# ,tolower(gene)
# ,"_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()
#
# # 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
# ,tolower(gene)
# ,"_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("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/sensitivity_count_embb.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/prominent_effects_embb.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/sensitivity_count_embb.R")
##############################################################
# 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/scripts/plotting/get_plotting_dfs.R")
source("/home/tanu/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/basic_barplots_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))
#=======

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

@ -1,5 +1,5 @@
# 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 ####
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) #####
# #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
# ,tolower(gene)
# ,"_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()
#
# # 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
# ,tolower(gene)
# ,"_CorrC.png"), height =7, width=7, unit="in",res=300)

2
scripts/plotting/plotting_thesis/gid/gid_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/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("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/sensitivity_count_gid.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/prominent_effects_gid.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/sensitivity_count_gid.R")
##############################################################
# PE count

4
scripts/plotting/plotting_thesis/katg/basic_barplots_katg_layout.R
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@ -4,8 +4,8 @@
source("~/git/LSHTM_analysis/config/katg.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("/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/basic_barplots_katg.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/pe_sens_site_count_katg.R")
if ( tolower(gene)%in%c("katg") ){
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 #####
# #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
# ,tolower(gene)
# ,"_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()
#
# # 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
# ,tolower(gene)
# ,"_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("/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 ####
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("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/sensitivity_count_katg.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/prominent_effects_katg.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/sensitivity_count_katg.R")
##############################################################
# PE count

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

@ -1,5 +1,5 @@
#!/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

4
scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca_layout.R
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@ -4,8 +4,8 @@
#source("~/git/LSHTM_analysis/config/pnca.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("/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/basic_barplots_pnca.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/pe_sens_site_count_pnca.R")
if ( tolower(gene)%in%c("pnca") ){
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 #####
# #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
# ,tolower(gene)
# ,"_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()
#
# # 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
# ,tolower(gene)
# ,"_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
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

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("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/sensitivity_count_pnca.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/prominent_effects_pnca.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/sensitivity_count_pnca.R")
##############################################################
# 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("/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 ####
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), "/")
cat("plots will output to:", outdir_images)
source("/home/tanu/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/basic_barplots_rpob.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/pe_sens_site_count_rpob.R")
if ( tolower(gene)%in%c("rpob") ){
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("/home/tanu/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/rpob/dm_om_plots_rpob.R")
# source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R")
##### plots to combine ####
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 #####
# #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
# ,tolower(gene)
# ,"_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()
#
# # 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
# ,tolower(gene)
# ,"_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("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/sensitivity_count_rpob.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/prominent_effects_rpob.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/sensitivity_count_rpob.R")
##############################################################
# 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
#=============
#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
,tolower(gene)
,"_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()
# 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
,tolower(gene)
,"_CorrC.png"), height =7, width=7, unit="in",res=300)