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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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2
scripts/plotting/get_plotting_dfs.R
View file

@ -88,7 +88,7 @@ cat("\nDim of meta data file: ", dim(gene_metadata))
all_plot_dfs = combining_dfs_plotting(my_df_u
, gene_metadata
, gene = gene # ADDED
#, gene = gene # ADDED
, lig_dist_colname = LigDist_colname
, lig_dist_cutoff = LigDist_cutoff)

45
scripts/plotting/plotting_colnames.R
View file

@ -1,6 +1,4 @@
geneL_normal = c("pnca")
geneL_na = c("gid", "rpob")
geneL_ppi2 = c("alr", "embb", "katg", "rpob")
# Initialise the required dfs based on gene name
# LigDist_colname # from globals used
# ppi2Dist_colname #from globals used
@ -11,7 +9,7 @@ common_cols = c("mutationinformation"
, drug, "drug_name"
, "mutation", "mutation_info"
, "wild_type", "mutant_type", "position"
, "pos_count"
#, "pos_count", "df2_pos_count_all"
, "snp_frequency"
, "total_id_ucount"
, "drtype", "drtype_mode", "drtype_max"
@ -63,7 +61,7 @@ common_outcome_affinity_cols = c( "ligand_outcome"
#======================================================
# Plotting cols + affinity cols: conditional on gene
#======================================================
if (tolower(gene)%in%geneL_normal){
if (tolower(gene)%in%c("pnca")){
plotting_cols = common_cols
raw_affinity_cols = common_raw_affinity_cols
@ -73,35 +71,50 @@ if (tolower(gene)%in%geneL_normal){
}
# ppi2 genes
if (tolower(gene)%in%geneL_ppi2){
if (tolower(gene)%in%c("alr", "embb", "katg")){
plotting_cols = c(common_cols,
ppi2Dist_colname,
"mcsm_ppi2_affinity", "mcsm_ppi2_scaled", "mcsm_ppi2_outcome")
raw_affinity_cols = c(common_raw_affinity_cols , "mcsm_ppi2_affinity")
scaled_affinity_cols = c(common_scaled_affinity_cols , "mcsm_ppi2_scaled" )
outcome_affinity_cols = c(common_outcome_affinity_cols , "mcsm_ppi2_outcome")
affinity_dist_colnames = c(LigDist_colname, ppi2Dist_colname)
raw_affinity_cols = c(common_raw_affinity_cols , "mcsm_ppi2_affinity")
scaled_affinity_cols = c(common_scaled_affinity_cols , "mcsm_ppi2_scaled" )
outcome_affinity_cols = c(common_outcome_affinity_cols , "mcsm_ppi2_outcome")
affinity_dist_colnames = c(LigDist_colname, ppi2Dist_colname)
}
#na_genes
if (tolower(gene)%in%geneL_na){
if (tolower(gene)%in%c("gid")){
plotting_cols = c(common_cols,
naDist_colname,
"mcsm_na_affinity", "mcsm_na_scaled", "mcsm_na_outcome")
raw_affinity_cols = c(common_raw_affinity_cols , "mcsm_na_affinity")
scaled_affinity_cols = c(common_scaled_affinity_cols , "mcsm_na_scaled")
outcome_affinity_cols = c(common_outcome_affinity_cols , "mcsm_na_outcome")
affinity_dist_colnames = c(LigDist_colname, ppi2Dist_colname, naDist_colname)
raw_affinity_cols = c(common_raw_affinity_cols , "mcsm_na_affinity")
scaled_affinity_cols = c(common_scaled_affinity_cols , "mcsm_na_scaled")
outcome_affinity_cols = c(common_outcome_affinity_cols , "mcsm_na_outcome")
affinity_dist_colnames = c(LigDist_colname, naDist_colname)
}
if (tolower(gene)%in%c("rpob")){
plotting_cols = c(plotting_cols, "X5uhc_position","X5uhc_offset")
#plotting_cols = c(plotting_cols, "X5uhc_position","X5uhc_offset")
plotting_cols = c(common_cols,
ppi2Dist_colname,
"mcsm_ppi2_affinity", "mcsm_ppi2_scaled", "mcsm_ppi2_outcome",
naDist_colname,
"mcsm_na_affinity", "mcsm_na_scaled", "mcsm_na_outcome",
"X5uhc_position","X5uhc_offset")
raw_affinity_cols = c(common_raw_affinity_cols , "mcsm_ppi2_affinity", "mcsm_na_affinity")
scaled_affinity_cols = c(common_scaled_affinity_cols , "mcsm_ppi2_scaled" , "mcsm_na_scaled")
outcome_affinity_cols = c(common_outcome_affinity_cols , "mcsm_ppi2_outcome", "mcsm_na_outcome")
outcome_affinity_cols = c(common_outcome_affinity_cols , "mcsm_na_outcome")
affinity_dist_colnames = c(LigDist_colname, ppi2Dist_colname, naDist_colname)
}
#=======================================
# All: affinity cols: based on above confition
#========================================

2
scripts/plotting/plotting_thesis/basic_barplots.R
View file

@ -57,7 +57,7 @@ merged_df3 = merged_df3[, !colnames(merged_df3)%in%c("pos_count")]
head(merged_df3$pos_count)
df3 = merged_df3[, colnames(merged_df3)%in%plotting_cols]
#"nca_distance"%in%colnames(df3)
"nca_distance"%in%colnames(df3)
#=======
# output