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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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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
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@ -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
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@ -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
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@ -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
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@ -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