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a bunch of small changes

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This commit is contained in:
Tanushree Tunstall 2023-02-19 17:22:15 +00:00
parent 4640f9024a
commit 777d3765cf
4 changed files with 14 additions and 8 deletions
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14
scripts/plotting/plotting_thesis/ORandSNP_results.R
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@ -2,15 +2,14 @@
#source("~/git/LSHTM_analysis/config/pnca.R")
#source("~/git/LSHTM_analysis/config/embb.R")
source("~/git/LSHTM_analysis/config/gid.R")
#source("~/git/LSHTM_analysis/config/alr.R")
#source("~/git/LSHTM_analysis/config/gid.R")
source("~/git/LSHTM_analysis/config/alr.R")
#source("~/git/LSHTM_analysis/config/katg.R")
#source("~/git/LSHTM_analysis/config/rpob.R")
# get plottting dfs
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
#=======
# output
#=======
@ -210,8 +209,13 @@ if (nrow(bar_or) == nrow(sen1) + nrow(res1) ){
# percent for OR muts
pc_orR = nrow(res1)/(nrow(sen1) + nrow(res1)); pc_orR
cat("\nPercentage of muts with OR>1 i.e resistant:"
, pc_orR *100 )
cat("\nNo.of DST muts:", nrow(bar_or)
, "\nNo of DST (R):", table(bar_or$sensitivity)[[1]]
, "\nNo of DST (S):", table(bar_or$sensitivity)[[2]]
, "\nNumber of R muts with OR >1 (n = ", nrow(res1),")"
, "\nPercentage of muts with OR>1 i.e resistant:" , pc_orR *100 )
# muts with highest OR
head(bar_or$mutationinformation, 10)