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added rpob plot scripts

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This commit is contained in:
Tanushree Tunstall 2022-08-29 23:26:43 +01:00
parent 8f97ab7cc8
commit 7c2e4b898e
8 changed files with 109 additions and 48 deletions
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11
scripts/functions/corr_plot_data.R
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@ -45,7 +45,7 @@ corr_data_extract <- function(df
)
display_common_colnames = c( drug, "dst_mode"
, "DUET" , "FoldX" , "DeepDDG", "Dynamut2"
, "mCSM-DUET" , "FoldX" , "DeepDDG", "Dynamut2"
, "ASA" , "RSA" , "KD" , "RD"
# previously MAF
, "Log10(MAF)" , "Log10(OR)" , "-Log10(P)"
@ -80,12 +80,13 @@ corr_data_extract <- function(df
# SPECIAL case for rpob as it exists in both ppi and na
if (tolower(gene)%in%c("rpob")){
colnames_to_extract = c(common_colnames
, "mcsm_ppi2_affinity", ppi2Dist_colname
, "mcsm_na_affinity", naDist_colname)
, "mcsm_na_affinity", naDist_colname
, "mcsm_ppi2_affinity", ppi2Dist_colname)
display_colnames = c(display_common_colnames
,"mCSM-PPI2", "PPI-Dist"
,"mCSM-NA", "NA-Dist" )
,"mCSM-NA", "NA-Dist"
,"mCSM-PPI2", "PPI-Dist")
corr_df = df[,colnames_to_extract]
colnames(corr_df) = display_colnames

16
scripts/functions/dm_om_data.R
View file

@ -83,10 +83,10 @@ dm_om_wf_lf_data <- function(df
if (tolower(gene)%in%geneL_both){
additional_dfL = list(
wf_mcsm_ppi2 = data.frame(),
wf_mcsm_ppi2 = data.frame(),
lf_mcsm_ppi2 = data.frame(),
wf_mcsm_na = data.frame(),
lf_mcsm_na = data.frame()
lf_mcsm_na = data.frame()
)
wf_lf_dataL = c(common_dfsL, additional_dfL)
}
@ -98,7 +98,7 @@ dm_om_wf_lf_data <- function(df
# display names
stability_suffix <- paste0(delta_symbol, delta_symbol, "G")
duet_dn = paste0("DUET ", stability_suffix); duet_dn
duet_dn = paste0("mCSM-DUET ", stability_suffix); duet_dn
foldx_dn = paste0("FoldX ", stability_suffix); foldx_dn
deepddg_dn = paste0("Deepddg " , stability_suffix); deepddg_dn
dynamut2_dn = paste0("Dynamut2 " , stability_suffix); dynamut2_dn
@ -119,8 +119,7 @@ dm_om_wf_lf_data <- function(df
lig_dist_dn = paste0("Lig Dist(", angstroms_symbol, ")"); lig_dist_dn
mcsm_lig_dn = paste0("mCSM-lig"); mcsm_lig_dn
mmcsm_lig_dn2 = paste0("mmCSM-lig"); mmcsm_lig_dn2
na_dist_dn = paste0("Dist to NA (", angstroms_symbol, ")"); na_dist_dn
mcsm_na_dn = paste0("mCSM-NA ", stability_suffix); mcsm_na_dn
@ -240,8 +239,8 @@ 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)
display_colnames = c(display_common_colnames, "mcsm_na_affinity" , mcsm_na_dn , "mcsm_na_outcome" , na_dist_dn)
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
@ -282,7 +281,7 @@ dm_om_wf_lf_data <- function(df
colnames(comb_df_sl) = display_colnames
comb_df_sl_ppi2 = comb_df_sl[comb_df_sl[[ppi2_dist_dn]]<DistCutOff,]
comb_df_sl_na = comb_df_sl[comb_df_sl[[na_dist_dn]]<DistCutOff,]
static_cols_end = c(na_dist_dn, static_cols_end_common)
static_cols_end = c(ppi2_dist_dn, na_dist_dn, static_cols_end_common)
}
@ -348,7 +347,6 @@ dm_om_wf_lf_data <- function(df
colnames(wf_dist_gen)
colnames(lf_dist_gen)
# Assign them to the output list
wf_lf_dataL[['wf_dist_gen']] = wf_dist_gen
wf_lf_dataL[['lf_dist_gen']] = lf_dist_gen