tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

fix HARDCODED HOMEDIRS

Browse source
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
Download patch file Download diff file Expand all files Collapse all files

2
scripts/plotting/plotting_thesis/alr/DONOTUSEdm_om_plots_layout_alr.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

2
scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist_layout.R
View file

@ -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
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/alr/basic_barplots_alr_layout.R
View file

@ -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