119 lines
3.4 KiB
R
119 lines
3.4 KiB
R
#!/usr/bin/env Rscript
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#########################################################
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# TASK: producing boxplots for dr and other muts
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#########################################################
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#=======================================================================
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# working dir and loading libraries
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/plotting")
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getwd()
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#source("Header_TT.R")
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library(ggplot2)
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library(data.table)
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library(dplyr)
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#=========
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# Input
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#=========
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#source("combining_dfs_plotting.R")
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# FIXME: add a separate script to add foldx values and others
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source("output_tables.R")
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rm(df, merged_df3_short, df_output)
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#===============================================================
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df_comp = df_ordered[!is.na(df_ordered$af),]
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#%%%%%%%%%%%%%%%%%%%%%
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# REASSIGNMENT
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df = df_comp
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#%%%%%%%%%%%%%%%%%%%%%
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cols_all_muts_table = c("mutationinformation"
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, "mutation_info"
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, "af"
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, "af_percent"
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, "or_mychisq"
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, "pval_fisher"
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, "or_kin"
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, "pwald_kin"
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, "duet_stability_change"
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, "duet_outcome"
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, "ligand_distance"
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, "ligand_affinity_change"
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, "ligand_outcome"
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, "ddg"
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, "foldx_outcome"
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, "asa"
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, "rsa"
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, "kd_values"
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, "rd_values")
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df = df[,cols_all_muts_table]
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#===============================================================
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#Most Frequent mutation
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mf = df[df$af_percent == max(df$af_percent), ]
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mf
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# highest OR
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hor = df[df$or_mychisq == max(df$or_mychisq), ]
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hor
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# Most Destabilising for protein stability (DUET)
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df_d = df[df$duet_outcome == "Destabilising",]
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hd_duet = df_d[df_d$duet_stability_change == min(df_d$duet_stability_change), ]
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hd_duet
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# Most Stabilising for protein stability (DUET)
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df_s = df[df$duet_outcome == "Stabilising",]
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hs_duet = df_s[df_s$duet_stability_change == max(df_s$duet_stability_change), ]
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hs_duet
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# Closest Destabilising for protein stability
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close_d = df_d[order(df_d$ligand_distance, df_d$duet_stability_change),]
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# Closest Stabilising for protein stability
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close_s = df_s[order(df_s$ligand_distance, df_s$duet_stability_change),]
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#===============
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# ligand affinity: filtered
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#================
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df_lig = df[df$ligand_distance<10,]
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df_d_lig = df_lig[df_lig$ligand_outcome == "Destabilising",]
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hd_lig= df_d_lig[df_d_lig$ligand_affinity_change == min(df_d_lig$ligand_affinity_change), ]
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hd_lig
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df_s_lig = df[df$ligand_outcome == "Stabilising",]
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hs_lig= df_s_lig[df_s_lig$ligand_affinity_change == max(df_s_lig$ligand_affinity_change), ]
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hs_lig
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# Closest Destabilising for ligand affintiy
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close_d_lig = df_d_lig[order(df_d_lig$ligand_distance, df_d_lig$ligand_affinity_change),]
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# Closest Stabilising for ligand affinity
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close_s_lig = df_s_lig[order(df_s_lig$ligand_distance, df_s_lig$ligand_affinity_change),]
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#===============
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# foldx
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#================
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df_d_foldx = df[df$foldx_outcome == "Destabilising",]
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hd_foldx = df_d_foldx[df_d_foldx$ddg == max(df_d_foldx$ddg), ]
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hd_foldx
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# Most Stabilising for protein stability (DUET)
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df_s_foldx = df[df$foldx_outcome == "Stabilising",]
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hs_foldx = df_s_foldx[df_s_foldx$ddg == min(df_s_foldx$ddg), ]
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hs_foldx
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