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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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89
scripts/plotting/plotting_thesis/appendix_tables.R
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@ -38,18 +38,18 @@ angstroms_symbol
df3 = merged_df3
cols_to_output = c("mutationinformation"
, "position"
, affinity_dist_colnames[1]
, "ligand_affinity_change"
, "ligand_outcome"
, "mmcsm_lig"
, "mmcsm_lig_outcome"
, affinity_dist_colnames[2]
, "mcsm_ppi2_affinity"
, "mcsm_ppi2_outcome"
, "maf"
, "or_mychisq"
, "pval_fisher")
, "position"
, affinity_dist_colnames[1]
, "ligand_affinity_change"
, "ligand_outcome"
, "mmcsm_lig"
, "mmcsm_lig_outcome"
, affinity_dist_colnames[2]
, "mcsm_ppi2_affinity"
, "mcsm_ppi2_outcome"
, "maf"
, "or_mychisq"
, "pval_fisher")
cols_to_output
df3_output = df3[, cols_to_output]
@ -65,12 +65,12 @@ colnames(df3_output)
df3_output$p_adj_fdr = p.adjust(df3_output$pval_fisher, method = "fdr")
df3_output$signif_fdr = df3_output$p_adj_fdr
df3_output = dplyr::mutate(df3_output
, signif_fdr = case_when(signif_fdr == 0.05 ~ "."
, signif_fdr <=0.0001 ~ '****'
, signif_fdr <=0.001 ~ '***'
, signif_fdr <=0.01 ~ '**'
, signif_fdr <0.05 ~ '*'
, TRUE ~ 'ns'))
, signif_fdr = case_when(signif_fdr == 0.05 ~ "."
, signif_fdr <=0.0001 ~ '****'
, signif_fdr <=0.001 ~ '***'
, signif_fdr <=0.01 ~ '**'
, signif_fdr <0.05 ~ '*'
, TRUE ~ 'ns'))
# rounding
df3_output$or_mychisq = round(df3_output$or_mychisq,2)
df3_output$p_adj_fdr = round(df3_output$p_adj_fdr,2)
@ -101,17 +101,17 @@ head(df3_output)
df_lig = df3_output[df3_output[[LigDist_colname]]<DistCutOff,]
cols_to_output_lig = c("mutationinformation"
, "position"
, LigDist_colname
, "ligand_affinity_change"
, "ligand_outcome"
, "mmcsm_lig"
, "mmcsm_lig_outcome"
, "maf_percent"
, "or_mychisq"
, "pval_fisher"
, "p_adj_fdr"
, "signif_fdr")
, "position"
, LigDist_colname
, "ligand_affinity_change"
, "ligand_outcome"
, "mmcsm_lig"
, "mmcsm_lig_outcome"
, "maf_percent"
, "or_mychisq"
, "pval_fisher"
, "p_adj_fdr"
, "signif_fdr")
# select cols
Out_df_lig = df_lig[, cols_to_output_lig]
@ -123,17 +123,17 @@ Out_df_ligS = Out_df_lig[order(-Out_df_lig$or_mychisq, Out_df_lig$maf_percent),
head(Out_df_ligS); tail(Out_df_ligS)
colsNames_to_output_lig = c("Mutation"
, "position"
, paste0("Lig-Dist (", angstroms_symbol, ")")
, "mCSM-ligand affinity"
, "mCSM ligand_outcome"
, "mmCSM-ligand affinity"
, "mmCSM ligand_outcome"
, paste0("MAF ","(%)")
, "Odds Ratio"
, "P-value"
, "Adjusted P-value"
, "P-value significance")
, "position"
, paste0("Lig-Dist (", angstroms_symbol, ")")
, "mCSM-ligand affinity"
, "mCSM ligand_outcome"
, "mmCSM-ligand affinity"
, "mmCSM ligand_outcome"
, paste0("MAF ","(%)")
, "Odds Ratio"
, "P-value"
, "Adjusted P-value"
, "Adjusted P-value significance")
colnames(Out_df_ligS) = colsNames_to_output_lig
head(Out_df_ligS)
@ -142,8 +142,8 @@ head(Out_df_ligS)
# write output file: KS test within grpup
#----------------------
Out_ligT = paste0(outdir_stats
, tolower(gene)
, "_lig_muts.csv")
, tolower(gene)
, "_lig_muts.csv")
cat("Output of Ligand muts:", Out_ligT )
write.csv(Out_df_ligS, Out_ligT, row.names = FALSE)
@ -179,12 +179,13 @@ Out_df_ppi2S = Out_df_ppi2[order(-Out_df_ppi2$or_mychisq, Out_df_ppi2$maf_percen
colsNames_to_output_ppi2 = c("Mutation"
, "position"
, paste0("PPI2-Dist (", angstroms_symbol, ")")
, paste0("mCSM-PPI2 (", delta_symbol, ")")
, paste0("mCSM-PPI2 (", delta_symbol,delta_symbol,"G)")
, "mCSM-PPI2 outcome"
, paste0("MAF ","(%)")
, "Odds Ratio"
, "P-value"
, "Adjusted P-value"
, "P-value significance")
, "Adjusted P-value significance")
colnames(Out_df_ppi2S) = colsNames_to_output_ppi2
Out_df_ppi2S