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

added scripts

Browse source
This commit is contained in:
Tanushree Tunstall 2022-08-23 16:30:42 +01:00
parent dd69da01f6
commit 23b4f06017
10 changed files with 147 additions and 1014 deletions
Download patch file Download diff file Expand all files Collapse all files

8
scripts/plotting/plotting_thesis/gid/basic_barplots_gid_layout.R
View file

@ -2,12 +2,18 @@
# Data: Input
#==============
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")
#cat("\nSourced plotting cols as well:", length(plotting_cols))
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")
#=======
# output
#=======
outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
cat("plots will output to:", outdir_images)
#########################################################
if ( tolower(gene)%in%c("gid") ){
cat("\nPlots available for layout are:")

7
scripts/plotting/plotting_thesis/gid/sensitivity_count_gid.R
View file

@ -12,11 +12,12 @@ sensP_df = merged_df3[,c("mutationinformation",
head(sensP_df)
table(sensP_df$sensitivity)
#---------------
#--------------------------
# Total unique positions
#----------------
#--------------------------
tot_mut_pos = length(unique(sensP_df[[pos_colname_c]]))
cat("\nNo of Tot muts sites:", tot_mut_pos)
cat("\nThese are:", unique(sensP_df[[pos_colname_c]]))
# resistant mut pos
sens_site_allR = sensP_df[[pos_colname_c]][sensP_df$sensitivity=="R"]
@ -34,7 +35,7 @@ length(sens_site_UR)
common_pos = intersect(sens_site_UR,sens_site_US)
site_Cc = length(common_pos)
cat("\nNo of Common sites:", site_Cc
, "\nThese are:", common_pos)
, "\nThese are:", sort(unique(common_pos)))
#---------------
# Resistant muts