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fixed source to contain plotting cols and pos_count correctly

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This commit is contained in:
Tanushree Tunstall 2022-08-22 14:33:06 +01:00
parent 4147a6b90f
commit 13999a477d
6 changed files with 66 additions and 39 deletions
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23
scripts/functions/plotting_data.R
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@ -7,14 +7,10 @@ library(data.table)
library(dplyr)
# ADDED: New
geneL_normal = c("pnca")
geneL_na = c("gid", "rpob")
geneL_ppi2 = c("alr", "embb", "katg", "rpob")
# geneL_normal = c("pnca")
# geneL_na = c("gid", "rpob")
# geneL_ppi2 = c("alr", "embb", "katg", "rpob")
if (tolower(gene)%in%geneL_na){
infilename_nca = paste0("/home/tanu/git/Misc/mcsm_na_dist/"
, tolower(gene), "_nca_distances.csv")
}
#========================================================
# plotting_data(): formatting data for plots
# input args:
@ -31,8 +27,9 @@ if (tolower(gene)%in%geneL_na){
plotting_data <- function(df
, gene # ADDED
, lig_dist_colname
, lig_dist_cutoff) {
, lig_dist_colname = 'ligand_distance'
, lig_dist_cutoff = 10
) {
my_df = data.frame()
my_df_u = data.frame()
my_df_u_lig = data.frame()
@ -89,11 +86,15 @@ plotting_data <- function(df
# all = T)
#
# }
geneL_na=c("gid","rpob")
if (tolower(gene)%in%geneL_na){
infilename_nca = paste0("/home/tanu/git/Misc/mcsm_na_dist/"
, tolower(gene), "_nca_distances.csv")
distcol_nca_name = read.csv(infilename_nca, header = F)
if (tolower(gene)=='rpob'){
print('WARNING: running special-case handler for rpoB')
# create 5uhc equivalent column for mutationinformation