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agenerated corr plots with MAF and provean

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This commit is contained in:
Tanushree Tunstall 2022-08-06 13:08:42 +01:00
parent 1a513913ce
commit 569e372476
6 changed files with 115 additions and 104 deletions
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10
scripts/plotting/get_plotting_dfs.R
View file

@ -186,10 +186,16 @@ cat(s3)
# make sure the above script works because merged_df2_combined is needed
merged_df3 = as.data.frame(merged_df3)
corr_df_m3_f = corr_data_extract(merged_df3, extract_scaled_cols = F)
corr_df_m3_f = corr_data_extract(merged_df3
, gene = gene
, drug = drug
, extract_scaled_cols = F)
head(corr_df_m3_f)
corr_df_m2_f = corr_data_extract(merged_df2, extract_scaled_cols = F)
corr_df_m2_f = corr_data_extract(merged_df2
, gene = gene
, drug = drug
, extract_scaled_cols = F)
head(corr_df_m2_f)
s4 = c("\nSuccessfully sourced Corr_data.R")

51
scripts/plotting/plotting_thesis/corr_plots_thesis.R
View file

@ -1,5 +1,9 @@
merged_df3 = as.data.frame(merged_df3)
corr_plotdf = corr_data_extract(merged_df3, extract_scaled_cols = F)
corr_plotdf = corr_data_extract(merged_df3
, gene = gene
, drug = drug
, extract_scaled_cols = F)
colnames(corr_plotdf)
#================
# stability
@ -9,12 +13,13 @@ corr_ps_colnames = c("DUET"
, "DeepDDG"
, "Dynamut2"
, "MAF"
, "Log (OR)"
, "-Log (P)"
, "Log(OR)"
, "-Log(P)"
#, "ligand_distance"
, "dst_mode"
, drug)
corr_ps_colnames%in%colnames(corr_plotdf)
corr_df_ps = corr_plotdf[, corr_ps_colnames]
color_coln = which(colnames(corr_df_ps) == "dst_mode")
@ -46,10 +51,10 @@ my_corr_pairs(corr_data_all = corr_df_ps
dev.off()
#####################################################
DistCutOff = 10
LigDist_colname # = "ligand_distance" # from globals
ppi2Dist_colname = "interface_dist"
naDist_colname = "TBC"
#DistCutOff = 10
#LigDist_colname # = "ligand_distance" # from globals
#ppi2Dist_colname = "interface_dist"
#naDist_colname = "TBC"
#####################################################
#================
@ -57,14 +62,15 @@ naDist_colname = "TBC"
#================
corr_lig_colnames = c("mCSM-lig"
, "MAF"
, "Log (OR)"
, "-Log (P)"
, "ligand_distance"
, "Log(OR)"
, "-Log(P)"
, "Lig-Dist"
, "dst_mode"
, drug)
corr_lig_colnames%in%colnames(corr_plotdf)
corr_df_lig = corr_plotdf[, corr_lig_colnames]
corr_df_lig = corr_df_lig[corr_df_lig[[LigDist_colname]]<DistCutOff,]
corr_df_lig = corr_df_lig[corr_df_lig["Lig-Dist"]<DistCutOff,]
color_coln = which(colnames(corr_df_lig) == "dst_mode")
end = which(colnames(corr_df_lig) == drug)
@ -99,15 +105,15 @@ dev.off()
#================
corr_ppi2_colnames = c("mCSM-PPI2"
, "MAF"
, "Log (OR)"
, "-Log (P)"
, "interface_dist"
, "Log(OR)"
, "-Log(P)"
, "PPI-Dist" # "interface_dist"
, "dst_mode"
, drug)
corr_ppi2_colnames%in%colnames(corr_plotdf)
corr_df_ppi2 = corr_plotdf[, corr_ppi2_colnames]
corr_df_ppi2 = corr_df_ppi2[corr_df_ppi2[[ppi2Dist_colname]]<DistCutOff,]
corr_df_ppi2 = corr_df_ppi2[corr_df_ppi2["PPI-Dist"]<DistCutOff,]
color_coln = which(colnames(corr_df_ppi2) == "dst_mode")
end = which(colnames(corr_df_ppi2) == drug)
@ -146,10 +152,21 @@ dev.off()
# FIXME: ADD PROVEAN
####################################################
# CONSERVATION
corr_conservation_cols = c("ConSurf"
, "SNAP2"
, "PROVEAN"
, "MAF"
, "Log(OR)"
, "-Log(P)"
, "dst_mode"
, drug)
####################################################
colnames(corr_plotdf)
corr_conservation_cols%in%colnames(corr_plotdf)
corr_df_cons = corr_plotdf[, corr_conservation_cols]
color_coln = which(colnames(corr_df_cons) == "dst_mode")

6
scripts/plotting/plotting_thesis/preformatting.R
View file

@ -111,7 +111,9 @@ df3 = merged_df3
#df3[[consurf_colNew]] = as.factor(df3[[consurf_colNew]])
#df3[[consurf_colNew]]
# not this bit
levels(df3$consurf_outcome) = c( "nsd", 1, 2, 3, 4, 5, 6, 7, 8, 9)
#!!!!!!!!!!!!!1
#levels(df3$consurf_outcome) = c( "nsd", 1, 2, 3, 4, 5, 6, 7, 8, 9)
#levels(df3$consurf_outcome)
# SNAP2 labels
@ -242,9 +244,9 @@ corr_ppi2_colnames = c("mCSM-PPI2"
, "dst_mode"
, drug)
#FIXME: Add provean
corr_conservation_cols = c("Consurf"
, "SNAP2"
, "PROVEAN"
, "MAF"
, "Log (OR)"
, "-Log (P)"