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fixed source to contain plotting cols and pos_count correctly

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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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28
scripts/functions/combining_dfs_plotting.R
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@ -41,7 +41,7 @@ geneL_ppi2 = c("alr", "embb", "katg", "rpob")
combining_dfs_plotting <- function( my_df_u
, gene_metadata
, gene # ADDED
#, gene # ADDED
, lig_dist_colname = ''
, lig_dist_cutoff = ''){
@ -686,8 +686,11 @@ combining_dfs_plotting <- function( my_df_u
min( merged_df3['avg_lig_affinity_scaled']); max( merged_df3['avg_lig_affinity_scaled'])
###################################################################
# Rectify pos_count column in merged_df3
# The one in merged_df2 is correct
#--------------------------------------------
# merged_df3: Rectify pos_count column
# Rename existing pos_count colum to reflect
# that it is correct according to merged_df2
#--------------------------------------------
nc_pc_CHANGE = which(colnames(merged_df3)== "pos_count"); nc_pc_CHANGE
colnames(merged_df3)[nc_pc_CHANGE] = "df2_pos_count_all"
@ -707,16 +710,25 @@ combining_dfs_plotting <- function( my_df_u
nc_change = which(colnames(merged_df3) == "n")
colnames(merged_df3)[nc_change] <- "pos_count"
class(merged_df3)
####################################################################
#-------------------------------------------------
# merged_df2: Rename existing pos_count
# column to df2_pos_count_all like in above df
#-------------------------------------------------
nc_pc_CHANGE_df2 = which(colnames(merged_df2)== "pos_count"); nc_pc_CHANGE_df2
colnames(merged_df2)[nc_pc_CHANGE_df2] = "df2_pos_count_all"
head(merged_df2$pos_count)
head(merged_df2$df2_pos_count_all)
####################################################################
# ADD: distance to Nucleic acid column for na genes
# already done in plotting_data
####################################################################
#TODO
# Choose few columns to return as plot_df
merged_df3 = merged_df3[, colnames(merged_df3)%in%c(plotting_cols, "pos_count", "df2_pos_count_all")]
merged_df2 = merged_df2[, colnames(merged_df2)%in%c(plotting_cols, "df2_pos_count_all")]
####################################################################
return(list( merged_df2

5
scripts/functions/dm_om_data.R
View file

@ -121,7 +121,7 @@ dm_om_wf_lf_data <- function(df
mmcsm_lig_dn2 = paste0("mmCSM-lig"); mmcsm_lig_dn2
na_dist_dn = paste0("NA Dist(", angstroms_symbol, ")"); na_dist_dn
na_dist_dn = paste0("Dist to NA (", angstroms_symbol, ")"); na_dist_dn
mcsm_na_dn = paste0("mCSM-NA ", stability_suffix); mcsm_na_dn
ppi2_dist_dn = paste0("PPI Dist(", angstroms_symbol, ")"); ppi2_dist_dn
@ -174,7 +174,8 @@ dm_om_wf_lf_data <- function(df
)
display_common_colnames = c(snp_colname
, mut_colname , "dst_mode" , mut_info_label_colname
, mut_colname
, "dst_mode" , mut_info_label_colname
, aa_pos_colname
, "duet_stability_change" , duet_dn , "duet_outcome"

23
scripts/functions/plotting_data.R
View file

@ -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