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added output tables with active site

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This commit is contained in:
Tanushree Tunstall 2022-08-26 21:50:33 +01:00
parent f290d8ec9e
commit 2cbc460f87
4 changed files with 43 additions and 17 deletions
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17
scripts/plotting/plotting_thesis/gid/gid_appendix_tables.R
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@ -285,6 +285,7 @@ if (identical(colnames(mut_h_avs_dd), colnames(mut_h_avs_ss)) ){
#-------------------
# Filtered columns
# most DD/SS: ligand
# FIXME DUBIOUS as min and max can be both negative
#-------------------
df3_effects_lig = df3_effects[df3_effects[[LigDist_colname]]<DistCutOff,]
nrow(df3_effects_lig)
@ -296,7 +297,7 @@ if (identical(colnames(mut_h_lig_dd), colnames(mut_h_lig_ss)) ){
# add cols
mut_h_lig_dd$mutational_effect = "Most Destabilising for Ligand affinity"
mut_h_lig_ss$mutational_effect = "Most Stabilising for Ligand affinity"
mut_h_lig_ss$mutational_effect = "CAUTION: Most DE/Stabilising for Ligand affinity"
cat("\nPass: avg ligand affinity")
}else{
@ -415,6 +416,20 @@ if ( length(colnames(combined_table)) == length(colsNames_combined_table) ) {
stop("\nAbort: No. of cols mismatch. Cannot assign pretty colnames for output")
}
nrow(combined_table)
combined_table$drug_site = ifelse(combined_table$position%in%aa_pos_drug, "drug", "no")
table(combined_table$drug_site)
combined_table$rna_site = ifelse(combined_table$position%in%aa_pos_rna, "rna", "no")
table(combined_table$rna_site)
combined_table$sam_site = ifelse(combined_table$position%in%aa_pos_sam, "sam", "no")
table(combined_table$sam_site)
combined_table$amp_site = ifelse(combined_table$position%in%aa_pos_amp, "amp", "no")
table(combined_table$amp_site)
#--------------------
# write output file: KS test within grpup
#----------------------