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relaced ligand_distance with the variable

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Tanushree Tunstall 2022-01-30 09:47:56 +00:00
parent 8df4a85798
commit ea931b59f3
1 changed files with 23 additions and 4 deletions
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27
scripts/functions/corr_plot_df.R
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@ -1,10 +1,27 @@
#!/usr/bin/env Rscript
#########################################################
# TASK: Script to format data for Correlation plots:
# corr_data_extract()
# Input:
# corr_plot_df: data with all parameters (my_use case)
# merged_df3 or merged_df2!?
# gene: [sanity check]
# drug: relates to a column name that will need to extracted
#colnames_to_extract = c("mutationinformation" #colnames_to_extract = c("mutationinformation"
# , "duet_affinity_change") # , "duet_affinity_change")
#display_colnames_key = c(mutationinformation = "MUT" #display_colnames_key = c(mutationinformation = "MUT"
# , duet_affinity_change = "DUET") # , duet_affinity_change = "DUET")
# extract_scaled_cols = T or F, so that parameters with the _scaled suffix can be extracted.
# No formatting applied to these cols i.e display name
# TO DO: SHINY
#1) Corr type?
#2)
################################################################## ##################################################################
corr_data_extract <- function(corr_plot_df corr_data_extract <- function(corr_plot_df
, gene_name = gene #, gene_name = gene
, drug_name = drug , drug_name = drug
, colnames_to_extract , colnames_to_extract
, colnames_display_key , colnames_display_key
@ -18,7 +35,7 @@ corr_data_extract <- function(corr_plot_df
, "\n=========================================") , "\n=========================================")
cat("\nExtracting default columns for" cat("\nExtracting default columns for"
, "\nGene name:", gene #, "\nGene name:", gene
, "\nDrug name:", drug) , "\nDrug name:", drug)
colnames_to_extract = c(drug colnames_to_extract = c(drug
@ -26,7 +43,8 @@ corr_data_extract <- function(corr_plot_df
, "mutation_info_labels" , "mutation_info_labels"
, "duet_stability_change" , "duet_stability_change"
, "ligand_affinity_change" , "ligand_affinity_change"
, "ligand_distance" #, "ligand_distance"
, LigDist_colname
, "ddg_foldx" , "ddg_foldx"
, "deepddg" , "deepddg"
, "asa" , "asa"
@ -59,7 +77,8 @@ corr_data_extract <- function(corr_plot_df
# arg: colnames_display_key # arg: colnames_display_key
colnames_display_key = c(duet_stability_change = "DUET" colnames_display_key = c(duet_stability_change = "DUET"
, ligand_affinity_change = "mCSM-lig" , ligand_affinity_change = "mCSM-lig"
, ligand_distance = "ligand_distance" #, ligand_distance = "ligand_distance"
#, LigDist_colname = "ligand_distance"
, ddg_foldx = "FoldX" , ddg_foldx = "FoldX"
, deepddg = "DeepDDG" , deepddg = "DeepDDG"
, asa = "ASA" , asa = "ASA"