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renamed 2 to _v2

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This commit is contained in:
Tanushree Tunstall 2022-08-22 11:41:42 +01:00
parent c9d7ea9fad
commit 802d6f8495
18 changed files with 761 additions and 976 deletions
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39
scripts/functions/corr_plot_data.R
View file

@ -16,6 +16,7 @@ corr_data_extract <- function(df
if ( missing(colnames_to_extract) || missing(colnames_display_key) ){
# log10maf
df$maf2 = log10(df$maf) # can't see otherwise
sum(is.na(df$maf2))
@ -40,7 +41,7 @@ corr_data_extract <- function(df
, "consurf_score" , "snap2_score" , "provean_score"
, "ligand_affinity_change", "mmcsm_lig"
#, "ddg_dynamut", "ddg_encom", "dds_encom", "ddg_mcsm", "ddg_sdm", "ddg_duet"
)
)
display_common_colnames = c( drug, "dst_mode"
, "DUET" , "FoldX" , "DeepDDG", "Dynamut2"
@ -51,7 +52,7 @@ corr_data_extract <- function(df
, "ConSurf" , "SNAP2" , "PROVEAN"
, "mCSM-lig", "mmCSM-lig"
# , "Dynamut" , "ENCoM-DDG" , "mCSM" , "SDM" , "DUET-d" , "ENCoM-DDS"
)
)
if (tolower(gene)%in%geneL_normal){
colnames_to_extract = c(common_colnames)
@ -59,21 +60,21 @@ corr_data_extract <- function(df
corr_df = df[,colnames_to_extract]
colnames(corr_df) = display_colnames
}
}
if (tolower(gene)%in%geneL_ppi2){
colnames_to_extract = c(common_colnames ,"mcsm_ppi2_affinity", ppi2Dist_colname)
display_colnames = c(display_common_colnames,"mCSM-PPI2" , "PPI-Dist")
corr_df = df[,colnames_to_extract]
colnames(corr_df) = display_colnames
}
}
if (tolower(gene)%in%geneL_na){
colnames_to_extract = c(common_colnames,"mcsm_na_affinity", naDist_colname)
display_colnames = c(display_common_colnames, "mCSM-NA", "NA-Dist")
display_colnames = c(display_common_colnames, "mCSM-NA", "NCA-Dist")
corr_df = df[,colnames_to_extract]
colnames(corr_df) = display_colnames
}
}
# [optional] arg: extract_scaled_cols
if (extract_scaled_cols){
@ -98,19 +99,19 @@ corr_data_extract <- function(df
# colnames(corr_df)[colnames(corr_df)%in%colnames_to_extract] <- display_colnames
# colnames(corr_df)
cat("\nExtracted ncols:", ncol(corr_df)
,"\nRenaming successful")
cat("\nSneak peak...")
print(head(corr_df))
# Move drug column to the end
last_col = colnames(corr_df[ncol(corr_df)])
#corr_df_f = corr_df %>% dplyr::relocate(all_of(drug), .after = last_col)
#return(corr_df_f)
return(corr_df)
cat("\nExtracted ncols:", ncol(corr_df)
,"\nRenaming successful")
cat("\nSneak peak...")
print(head(corr_df))
# Move drug column to the end
last_col = colnames(corr_df[ncol(corr_df)])
#corr_df_f = corr_df %>% dplyr::relocate(all_of(drug), .after = last_col)
#return(corr_df_f)
return(corr_df)
}
}

4
scripts/functions/dm_om_data.R
View file

@ -222,12 +222,12 @@ dm_om_wf_lf_data <- function(df
}
if (tolower(gene)%in%geneL_na){
colnames_to_extract = c(common_colnames,"mcsm_na_affinity" , "mcsm_na_scaled" , "mcsm_na_outcome" , naDist_colname)
colnames_to_extract = c(common_colnames ,"mcsm_na_affinity" , "mcsm_na_scaled" , "mcsm_na_outcome" , naDist_colname)
display_colnames = c(display_common_colnames, "mcsm_na_affinity" , mcsm_na_dn , "mcsm_na_outcome" , na_dist_dn)
comb_df_sl = df[, colnames_to_extract]
# Rename cols: display names
colnames(comb_df) = display_colnames
colnames(comb_df_sl) = display_colnames
# Affinity filtered data: mcsm-na --> naDist_colname
comb_df_sl_na = comb_df_sl[comb_df_sl[[na_dist_dn]]<DistCutOff,]

2
scripts/functions/plotting_globals.R
View file

@ -41,7 +41,7 @@ LigDist_cutoff <<- 10
DistCutOff <<- 10
ppi2Dist_colname <<- "interface_dist"
naDist_colname <<- "TBC"
naDist_colname <<- "nca_distance" # added it
#==================
# Angstroms symbol